EIF4A1

Last updated
EIF4A1
Protein EIF4A1 PDB 2g9n.png
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases EIF4A1 , DDX2A, EIF-4A, EIF4A, eIF-4A-I, eIF4A-I, eukaryotic translation initiation factor 4A1
External IDs OMIM: 602641; MGI: 95303; HomoloGene: 103998; GeneCards: EIF4A1; OMA:EIF4A1 - orthologs
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_001416
NM_001204510

NM_001159375
NM_144958

RefSeq (protein)

NP_001191439
NP_001407

NP_001152847
NP_659207

Location (UCSC) Chr 17: 7.57 – 7.58 Mb Chr 11: 69.56 – 69.56 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

Eukaryotic initiation factor 4A-I (also known as eIF4A1 or DDX2A) is a 46 kDa cytosolic protein that, in humans, is encoded by the EIF4A1 gene, which is located on chromosome 17. [5] [6] [7] It is the most prevalent member of the eIF4A family of ATP-dependant RNA helicases, and plays a critical role in the initiation of cap-dependent eukaryotic protein translation as a component of the eIF4F translation initiation complex. [8] eIF4A1 unwinds the secondary structure of RNA within the 5'-UTR of mRNA, a critical step necessary for the recruitment of the 43S preinitiation complex, and thus the translation of protein in eukaryotes. [8] It was first characterized in 1982 by Grifo, et al., who purified it from rabbit reticulocyte lysate. [9]

Contents

Background

The regulation of the translation of mRNA transcripts into protein is one of the best ways that a cell can alter its response to its environment, as changes to the transcription of genes often takes considerably more time to be enacted. Protein translation can be broken into four phases: activation, initiation, elongation, and termination. Of these steps, initiation is the one for which cells have the most control. It is the rate limiting step of protein synthesis, controlled by a myriad of proteins known as the eukaryotic initiation factors, or eIFs. Relative abundance of these factors or their relative individual activities afford eukaryotic cells broad control over the rate of initiation and thus protein synthesis. eIFs are regulated under well known intracellular signalling pathways, such as the PI3K/AKT/mTOR pathway, however other biochemical layers of regulation, such as the complexity of RNA secondary structure in the 5′-UTR, are becoming evident with further research. [8]

Examples of RNA Secondary Structure
Stem-loop.svg
An example of an RNA hairpin, consisting of complementary Watson-Crick base pairings on the same strand of RNA.
G-quadruplex.svg
G-quadruplexes are more complex RNA secondary structures made up of stacks of guanine tetrads, which are each composed of four Hoogsteen hydrogen bonding guanines arranged in a square planar fashion.

The eIF4A subfamily in mammals is made up of three paralogs, eIF4A1, eIF4A2, and eIF4A3. [10] eIF4A1 and eIF4A2 share 90% sequence similarity, and are both cytoplasmic proteins, while eIF4A3 is localized to the nucleus, and shares only 60% homology. [10] Historically, eIF4A1 and eIF4A2 were considered interchangeable, due to this being observed in in vitro experiments, but further investigation has shown that eIF4A1 is more prevalent in dividing cells while eIF4A2 is more abundant in non-dividing cells, and furthermore, more recent evidence suggests that they might have functionally distinct roles in vivo . [8] [10]

Structure

eIF4A1 is a member of the DEAD box family of RNA helicases. [11] RNA helicases are enzymes that use the energy released from the hydrolysis of ATP to manipulate the secondary structure of RNA, and the DEAD box family is the largest family of RNA helicases. [11] The name "DEAD box" refers the key D-E-A-D amino acid sequence on motif II of the helicase that participates in nucleoside triphosphate binding (in the instance of eIF4A1, ATP). Other conserved motifs, shared by all eIF4A family proteins, are the Q, I, Ia, Ib, III, IV, V and VI motifs. Motifs Ia, Ib, IV and V bind RNA, motifs I, II, and III mediate RNA-dependent ATPase activity, and motif VI, is required for both RNA binding and ATP hydrolysis. [10]

The general primary structure of eIF4A subfamily proteins. Conserved sequence motifs are represented by the colored segments with their names labeled above. Note that Motifs I and II are also known as the Walker Box A and Walker Box B motifs, respectively. Motif II, depicted in blue, is the location of the DEAD-box. EIF4A General Primary Structure, Updated.png
The general primary structure of eIF4A subfamily proteins. Conserved sequence motifs are represented by the colored segments with their names labeled above. Note that Motifs I and II are also known as the Walker Box A and Walker Box B motifs, respectively. Motif II, depicted in blue, is the location of the DEAD-box.

The DEAD box family is marked by a structurally highly conserved helicase core consisting of two RecA-like domains joined by a flexible hinge region around which the protein can open and close upon hydrolysis of ATP. [13] [10] [14] The cleft formed between these two domains forms the ATP-binding pocket. [11] The RNA molecule binds opposite to this binding pocket, stretching across each of the domains. [11] This core is flanked by variable auxiliary domains, which confer the unique function of each RNA helicase to them partly by allowing for specific binding to accessory proteins. [11]

Function

eIF4A1 is an ATP-dependent RNA helicase, [15] however the exact nature of its dependence on ATP for its function is still debated. [10] Although after ATP binding, the subsequent hydrolysis induces conformational changes in eIF4A1, other DEAD-box RNA helicases have been shown to possess helicase activity in the presence of nonhydrolyzable analogues of ATP, suggesting that binding, and not hydrolysis, is the more important element in regulating activity. [10]

eIF4A1 is a component of the eIF4F translation initiation complex, along with eIF4E, the 5'-terminal cap binding protein, and eIF4G, the scaffold protein that holds eIF4A and eIF4E together. [10] The eIF4F complex is often accompanied by the accessory proteins eIF4B and eIF4H, either of which can differentially enhance the activity of eIF4A1. After mRNA is transcribed from DNA and translocated to the cytoplasm, and the cytosolic PABP is bound to the Poly(A)-tail of the nascent mRNA, its 5'-cap will bind to eIF4E and PABP will bind to eIF4G. [8] eIF4A1 will then unwind the RNA secondary structure from 5' to 3' as the 43S PIC is recruited to the eIF4F complex. [8] The 43S PIC will scan the unwound mRNA from 5' to 3' as well, until it reaches the AUG start codon, whereupon the 60S ribosomal subunit will be recruited to begin the process of elongation. [8]

(A) Binding of mRNA to eIF4F Complex. Note that eIF4B and eIF4H could also bind to eIF4A1 to stimulate its activity.
(B) eIF4A1 unwinding of mRNA secondary structure and recruitment of the 43S PIC.
(C) 40S ribosomal subunit scanning the 5'-UTR of the mRNA transcript for a start codon.
(D) Recruitment of the 60S ribosomal subunit and the beginning of elongation. EIF4A1 Function Diagram.png
(A) Binding of mRNA to eIF4F Complex. Note that eIF4B and eIF4H could also bind to eIF4A1 to stimulate its activity.
(B) eIF4A1 unwinding of mRNA secondary structure and recruitment of the 43S PIC.
(C) 40S ribosomal subunit scanning the 5'-UTR of the mRNA transcript for a start codon.
(D) Recruitment of the 60S ribosomal subunit and the beginning of elongation.

Regulation

The transcription of eIF4A1 is driven by the transcription factor MYC. [8] On its own, the helicase activity of eIF4A1 is poor, however this feature imposes a practical restraint on eIF4A1, as nonspecific, "unintended," helicase activity in the cell would be detrimental to the function of certain endogenous, necessary RNA structures. [10] Its effectiveness considerably improves in the presence of eIF4B and eIF4H, binding partners that modulate its activity. When eIF4B binds to eIF4A1, the helicase activity of eIF4A1 is increased over 100-fold, but when eIF4H binds instead, the increase is not nearly as great, suggesting different relative concentrations of these accessory proteins may confer a further level of regulation of the efficiency of eIF4A1. [10]

Conversely, eIF4A1 activity is suppressed when it is bound to PDCD4, a tumor suppressor itself modulated by mTOR and miR-21. [8] PCDC4 is typically localized to the nucleus in healthy cells, however, under carcinogenic conditions, it translocates to the nucleus and two separate eIF4A1 molecules will bind to it, inhibiting the ability of eIF4A1 to bind to RNA by locking the molecules into their inactive conformation, thereby preventing binding to eIF4G. [16] [11]

Role in Disease

Cancer

Translational dysregulation is a hallmark of malignant transformation of cancer cells. Cancer cells in growing tumors become "addicted" to heightened levels of protein translation, and particularly dependent on up-regulated translation of pro-oncogenic mRNAs. These pro-oncogenic mRNAs have characteristically longer 5'-UTRs with more complex secondary structures, and up-regulation of eIF4A1 has been implicated in several human cancers (See Table). [8] [17] [18] Given the general trend of eIF4A1 overexpression driving cancer, there is interest in developing inhibitors for the enzyme. Several natural compounds have been identified as candidate inhibitors for development, though they inhibit both eIF4A1 and eIF4A2 non-specifically. [8] These include hippuristanol, silvestrol and pateamine A, among others. [8] Silvestrol, in particular is a rocaglate derivative, and this class of compounds could be viable eIF4A inhibitors. [19]

Putative eIF4A Inhibitors
Hippuristanol.png
Hippuristanol
Silvestrol.svg
Silvestrol
Pateamine A.png
Pateamine A
Cancer TypeeIF4A1 Dysregulation/Association
Hepatocellular carcinoma Overexpression [17]
Melanoma Overexpression [17]
Non-small cell lung carcinoma (NSCLC)Expression associated with metastasis [8]
Endometrial cancer Overexpression in atypical hyperplasia [8]
Cervical Cancer Overexpression; decreased expression after brachytherapy associated with better outcome [8]
Breast Cancer Expression associated with poor outcome in estrogen receptor negative disease [8]

Viral Infections

Viruses rely on hijacking the cellular machinery of the cells they infect to create their own viral proteins and allow them to continue infecting new cells. Their ability to manipulate eIFs like eIF4A1, therefore, considerably impacts their virulence. For instance, cytomegalovirus relies on eIF4A to drive its protein synthesis. The viral protein pUL69 stabilizes the formation of eIF4F, through binding to eIF4A, a process by which eIF4E is prevented from dissociating from the eIF4F complex. [14] eIF4E, thus, is no longer able to be sequestered by its negative regulator, 4EBP. [14] Furthermore, cytomegalovirus stimulates the synthesis of all elements of the eIF4F complex in order to drive protein synthesis. [14] Other viruses, like Cotesia plutellae bracovirus (CpBV), that favor cap-independent translation, will take advantage of eIF4A1 in the reverse context, by sequestering eIF4A1 away from the eIF4F complex with viral binding partners, in this case a protein called CpBV15β, thus inhibiting endogenous cap-dependent mRNA translation and favoring viral protein translation. [14] The compounds mentioned in the above section about cancer, hippuristanol, silvestrol, pateamine A, rocaglate derivatives, etc., could also be applied as putative viral inhibitors. [8] [19]

Related Research Articles

An internal ribosome entry site, abbreviated IRES, is an RNA element that allows for translation initiation in a cap-independent manner, as part of the greater process of protein synthesis. Initiation of eukaryotic translation nearly always occurs at and is dependent on the 5' cap of mRNA molecules, where the translation initiation complex forms and ribosomes engage the mRNA. IRES elements, however allow ribosomes to engage the mRNA and begin translation independently of the 5' cap.

Eukaryotic translation is the biological process by which messenger RNA is translated into proteins in eukaryotes. It consists of four phases: initiation, elongation, termination, and recapping.

In molecular biology, initiation factors are proteins that bind to the small subunit of the ribosome during the initiation of translation, a part of protein biosynthesis.

Eukaryotic initiation factors (eIFs) are proteins or protein complexes involved in the initiation phase of eukaryotic translation. These proteins help stabilize the formation of ribosomal preinitiation complexes around the start codon and are an important input for post-transcription gene regulation. Several initiation factors form a complex with the small 40S ribosomal subunit and Met-tRNAiMet called the 43S preinitiation complex. Additional factors of the eIF4F complex recruit the 43S PIC to the five-prime cap structure of the mRNA, from which the 43S particle scans 5'-->3' along the mRNA to reach an AUG start codon. Recognition of the start codon by the Met-tRNAiMet promotes gated phosphate and eIF1 release to form the 48S preinitiation complex, followed by large 60S ribosomal subunit recruitment to form the 80S ribosome. There exist many more eukaryotic initiation factors than prokaryotic initiation factors, reflecting the greater biological complexity of eukaryotic translation. There are at least twelve eukaryotic initiation factors, composed of many more polypeptides, and these are described below.

<span class="mw-page-title-main">4EGI-1</span> Chemical compound

4EGI-1 is a synthetic chemical compound which has been found to interfere with the growth of certain types of cancer cells in vitro. Its mechanism of action involves interruption of the binding of cellular initiation factor proteins involved in the translation of transcribed mRNA at the ribosome. The inhibition of these initiation factors prevents the initiation and translation of many proteins whose functions are essential to the rapid growth and proliferation of cancer cells.

<span class="mw-page-title-main">Hepatitis A virus internal ribosome entry site (IRES)</span>

This family represents the internal ribosome entry site (IRES) of the hepatitis A virus. HAV IRES is a 450 nucleotide long sequence located in the 735 nt long 5’ UTR of Hepatitis A viral RNA genome. IRES elements allow cap and end-independent translation of mRNA in the host cell. The IRES achieves this by mediating the internal initiation of translation by recruiting a ribosomal 40S pre-initiation complex directly to the initiation codon and eliminates the requirement for eukaryotic initiation factor, eIF4F.

<span class="mw-page-title-main">Poly(A)-binding protein</span> RNA binding protein

Poly(A)-binding protein is an RNA-binding protein which triggers the binding of eukaryotic initiation factor 4 complex (eIF4G) directly to the poly(A) tail of mRNA which is 200-250 nucleotides long. The poly(A) tail is located on the 3' end of mRNA and was discovered by Mary Edmonds, who also characterized the poly-A polymerase enzyme that generates the poly(a) tail. The binding protein is also involved in mRNA precursors by helping polyadenylate polymerase add the poly(A) nucleotide tail to the pre-mRNA before translation. The nuclear isoform selectively binds to around 50 nucleotides and stimulates the activity of polyadenylate polymerase by increasing its affinity towards RNA. Poly(A)-binding protein is also present during stages of mRNA metabolism including nonsense-mediated decay and nucleocytoplasmic trafficking. The poly(A)-binding protein may also protect the tail from degradation and regulate mRNA production. Without these two proteins in-tandem, then the poly(A) tail would not be added and the RNA would degrade quickly.

<span class="mw-page-title-main">Nuclear cap-binding protein complex</span> RNA-binding protein

Nuclear cap-binding protein complex is a RNA-binding protein which binds to the 5' cap of pre-mRNA. The cap and nuclear cap-binding protein have many functions in mRNA biogenesis including splicing, 3'-end formation by stabilizing the interaction of the 3'-end processing machinery, nuclear export and protection of the transcripts from nuclease degradation. During mRNA export, the nuclear cap-binding protein complex recruits ribosomes to begin the pioneer round of translation. When RNA is exported to the cytoplasm the nuclear cap-binding protein complex is replaced by cytoplasmic cap binding complex. The nuclear cap-binding complex is a functional heterodimer and composed of Cbc1/Cbc2 in yeast and CBP20/CBP80 in multicellular eukaryotes. Human nuclear cap-binding protein complex shows the large subunit, CBP80 consists of 757 amino acid residues. Its secondary structure contains approximately sixty percent of helical and one percent of beta sheet in the strand. The small subunit, CBP20 has 98 amino acid residues. Its secondary structure contains approximately twenty percent of helical and twenty-four percent of beta sheet in the strand. Human nuclear cap-binding protein complex plays important role in the maturation of pre-mRNA and in uracil-rich small nuclear RNA.

<span class="mw-page-title-main">Cap binding complex</span> Formation on 5 ends of mRNAs

The 5' cap of eukaryotic messenger RNA is bound at all times by various cap-binding complexes (CBCs).

<span class="mw-page-title-main">EIF4E</span> Protein-coding gene in the species Homo sapiens

Eukaryotic translation initiation factor 4E, also known as eIF4E, is a protein that in humans is encoded by the EIF4E gene.

<span class="mw-page-title-main">EIF4G2</span> Protein-coding gene in the species Homo sapiens

Eukaryotic translation initiation factor 4 gamma 2 is a protein that in humans is encoded by the EIF4G2 gene.

<span class="mw-page-title-main">Eukaryotic translation initiation factor 4 gamma 1</span> Protein-coding gene in the species Homo sapiens

Eukaryotic translation initiation factor 4 gamma 1 is a protein that in humans is encoded by the EIF4G1 gene.

<span class="mw-page-title-main">DEAD box</span> Family of proteins

DEAD box proteins are involved in an assortment of metabolic processes that typically involve RNAs, but in some cases also other nucleic acids. They are highly conserved in nine motifs and can be found in most prokaryotes and eukaryotes, but not all. Many organisms, including humans, contain DEAD-box (SF2) helicases, which are involved in RNA metabolism.

<span class="mw-page-title-main">MKNK1</span> Protein-coding gene in the species Homo sapiens

MAP kinase-interacting serine/threonine-protein kinase 1 is an enzyme that in humans is encoded by the MKNK1 gene.

<span class="mw-page-title-main">EIF4G3</span> Protein-coding gene in the species Homo sapiens

Eukaryotic translation initiation factor 4 gamma 3 is a protein that in humans is encoded by the EIF4G3 gene. The gene encodes a protein that functions in translation by aiding the assembly of the ribosome onto the messenger RNA template. Confusingly, this protein is usually referred to as eIF4GII, as although EIF4G3 is the third gene that is similar to eukaryotic translation initiation factor 4 gamma, the second isoform EIF4G2 is not an active translation initiation factor.

<span class="mw-page-title-main">EIF1</span> Protein-coding gene in the species Homo sapiens

Eukaryotic translation initiation factor 1 (eIF1) is a protein that in humans is encoded by the EIF1 gene. It is related to yeast SUI1.

Eukaryotic translation initiation factor 4 G (eIF4G) is a protein involved in eukaryotic translation initiation and is a component of the eIF4F cap-binding complex. Orthologs of eIF4G have been studied in multiple species, including humans, yeast, and wheat. However, eIF4G is exclusively found in domain Eukarya, and not in domains Bacteria or Archaea, which do not have capped mRNA. As such, eIF4G structure and function may vary between species, although the human EIF4G1 has been the focus of extensive studies.

The eukaryotic initiation factor-4A (eIF4A) family consists of 3 closely related proteins EIF4A1, EIF4A2, and EIF4A3. These factors are required for the binding of mRNA to 40S ribosomal subunits. In addition these proteins are helicases that function to unwind double-stranded RNA.

<span class="mw-page-title-main">Eukaryotic initiation factor 4F</span> Multiprotein complex used in gene expression

Eukaryotic initiation factor 4F (eIF4F) is a heterotrimeric protein complex that binds the 5' cap of messenger RNAs (mRNAs) to promote eukaryotic translation initiation. The eIF4F complex is composed of three non-identical subunits: the DEAD-box RNA helicase eIF4A, the cap-binding protein eIF4E, and the large "scaffold" protein eIF4G. The mammalian eIF4F complex was first described in 1983, and has been a major area of study into the molecular mechanisms of cap-dependent translation initiation ever since.

<span class="mw-page-title-main">BC200 lncRNA</span>

Brain cytoplasmic 200 long-noncoding RNA is a 200 nucleotide RNA transcript found predominantly in the brain with a primary function of regulating translation by inhibiting its initiation. As a long non-coding RNA, it belongs to a family of RNA transcripts that are not translated into protein (ncRNAs). Of these ncRNAs, lncRNAs are transcripts of 200 nucleotides or longer and are almost three times more prevalent than protein-coding genes. Nevertheless, only a few of the almost 60,000 lncRNAs have been characterized, and little is known about their diverse functions. BC200 is one lncRNA that has given insight into their specific role in translation regulation, and implications in various forms of cancer as well as Alzheimer's disease.

References

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Further reading

pUL69 of cytomegalovirus (UniProt)

CpBV15β of Cotesia plutellae bracovirus (UniProt)