8DYS | pdb_00008dys

Crystal structure of human Eukaryotic translation initiation factor 2A (eIF2A)

PDB DOI: https://doi.org/10.2210/pdb8DYS/pdb

Classification: TRANSLATION
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2022-08-05 Released: 2022-08-17
Deposition Author(s): Righetto, G.L., Zeng, H., Dong, A., Li, Y., Hutchinson, A., Seitova, A., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.228 (Depositor), 0.232 (DCC)
R-Value Work:
0.200 (Depositor), 0.207 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of human Eukaryotic translation initiation factor 2A (eIF2A)

Righetto, G.L., Zeng, H., Dong, A., Li, Y., Hutchinson, A., Seitova, A., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 67.49 kDa
Atom Count: 3,394
Modeled Residue Count: 409
Deposited Residue Count: 603
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 2A	A	603	Homo sapiens	Mutation(s): 0 Gene Names: EIF2A, CDA02, MSTP004, MSTP089
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BY44 (Homo sapiens) Explore Q9BY44 Go to UniProtKB: Q9BY44
PHAROS: Q9BY44 GTEx: ENSG00000144895
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BY44
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.228 (Depositor), 0.232 (DCC)
R-Value Work: 0.200 (Depositor), 0.207 (DCC)
R-Value Observed: 0.201 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.289	α = 90
b = 84.847	β = 90
c = 99.34	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-17

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Other private	Canada	--

Revision History (Full details and data files)

Version 1.0: 2022-08-17
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.