9AVR

Human eIF4A-1 in complex with AMP-PNP, RNA, and the inhibitor silvestrol

• PDB DOI: https://doi.org/10.2210/pdb9AVR/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-04 Released: 2024-10-23 
• Deposition Author(s): Bhatt, G.B., Naineni, S.K., Cencic, R.C., Jiramongkolsiri, E.J., Huang, S.H., Pelletier, J.P., Nagar, B.N.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.197 
• R-Value Work: 0.147 
• R-Value Observed: 0.152 

Starting Model: in silico

Literature

Human eIF4A-1 in complex with AMP-PNP, RNA, and the inhibitor silvestrol

Bhatt, G.B., Naineni, S.K., Nagar, B.N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.97 kDa 
• Atom Count: 3,561 
• Modelled Residue Count: 381 
• Deposited Residue Count: 416 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic initiation factor 4A-I	A	406	Homo sapiens	Mutation(s): 0  Gene Names: EIF4A1, DDX2A, EIF4A EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for P60842 (Homo sapiens) Explore P60842  Go to UniProtKB:  P60842
PHAROS:  P60842 GTEx:  ENSG00000161960

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA oligonucleotide (AG)5	B	10	Homo sapiens

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AG8 (Subject of Investigation/LOI)	G [auth B]	silvestrol C34 H38 O13 GVKXFVCXBFGBCD-QKDMMWSPSA-N
ANP (Subject of Investigation/LOI)	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
IOD	E [auth A], F [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.197 
• R-Value Work: 0.147 
• R-Value Observed: 0.152 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.48	α = 90
b = 84.295	β = 90
c = 88.412	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-23 
Deposition Author(s): Bhatt, G.B., Naineni, S.K., Cencic, R.C., Jiramongkolsiri, E.J., Huang, S.H., Pelletier, J.P., Nagar, B.N.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History  

• Version 1.0: 2024-10-23
  Type: Initial release