6JLZ

P-eIF2a - eIF2B complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for eIF2B inhibition in integrated stress response.

Kashiwagi, K.Yokoyama, T.Nishimoto, M.Takahashi, M.Sakamoto, A.Yonemochi, M.Shirouzu, M.Ito, T.

(2019) Science 364: 495-499

  • DOI: https://doi.org/10.1126/science.aaw4104
  • Primary Citation of Related Structures:  
    6JLY, 6JLZ, 6K71, 6K72

  • PubMed Abstract: 

    A core event in the integrated stress response, an adaptive pathway common to all eukaryotic cells in response to various stress stimuli, is the phosphorylation of eukaryotic translation initiation factor 2 (eIF2). Normally, unphosphorylated eIF2 transfers the methionylated initiator tRNA to the ribosome in a guanosine 5'-triphosphate-dependent manner. By contrast, phosphorylated eIF2 inhibits its specific guanine nucleotide exchange factor, eIF2B. To elucidate how the eIF2 phosphorylation status regulates the eIF2B activity, we determined cryo-electron microscopic and crystallographic structures of eIF2B in complex with unphosphorylated or phosphorylated eIF2. The unphosphorylated and phosphorylated forms of eIF2 bind to eIF2B in completely different manners: the nucleotide exchange-active and -inactive modes, respectively. These structures explain how phosphorylated eIF2 dominantly inhibits the nucleotide exchange activity of eIF2B.


  • Organizational Affiliation

    RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. takuhiro.ito@riken.jp.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Translation initiation factor eIF-2B subunit alpha
A, B
341Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: tif221SPCC11E10.07c
UniProt
Find proteins for Q9USP0 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupQ9USP0
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Probable translation initiation factor eIF-2B subunit beta
C, D
399Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: tif222SPAC343.14c
UniProt
Find proteins for Q9UT76 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupQ9UT76
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Probable translation initiation factor eIF-2B subunit gamma
E, F
458Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: tif223SPAC4D7.09
UniProt
Find proteins for P56288 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupP56288
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Probable translation initiation factor eIF-2B subunit delta
G, H
467Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: tif224SPAC21E11.06
UniProt
Find proteins for Q09924 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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UniProt GroupQ09924
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Probable translation initiation factor eIF-2B subunit epsilon
I, J
678Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: tif225SPAC8C9.15c
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit alphaK [auth L],
L [auth M]
304Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SUI2TIF211YJR007WJ1429
UniProt
Find proteins for P20459 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP20459
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
M [auth A]
N [auth B]
O [auth C]
P [auth D]
Q [auth E]
M [auth A],
N [auth B],
O [auth C],
P [auth D],
Q [auth E],
R [auth E],
S [auth F],
T [auth F],
U [auth G],
V [auth H],
W [auth I],
X [auth J]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
K [auth L],
L [auth M]
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.578α = 90
b = 207.712β = 96.96
c = 155.744γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan--
Japan Agency for Medical Research and Development (AMED)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-05-15
    Changes: Data collection, Database references