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- PDB-6qg2: Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model A) -

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Basic information

Entry
Database: PDB / ID: 6qg2
TitleStructure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model A)
Components
  • (Eukaryotic translation initiation factor 2 subunit ...) x 3
  • (Translation initiation factor eIF-2B subunit ...) x 5
KeywordsTRANSLATION / integrated stress response / ISR / initiation factors / phosphorylation / eIF2 / eIF2B / tRNAi / GEF / heat domain / eIF2 alpha
Function / homology
Function and homology information


negative regulation of cellular response to amino acid starvation / positive regulation of cellular response to heat / Recycling of eIF2:GDP / Cellular response to mitochondrial stress / eukaryotic translation initiation factor 2B complex / ABC-family proteins mediated transport / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 2 complex / multi-eIF complex / cytoplasmic translational initiation ...negative regulation of cellular response to amino acid starvation / positive regulation of cellular response to heat / Recycling of eIF2:GDP / Cellular response to mitochondrial stress / eukaryotic translation initiation factor 2B complex / ABC-family proteins mediated transport / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 2 complex / multi-eIF complex / cytoplasmic translational initiation / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / guanyl-nucleotide exchange factor complex / formation of translation preinitiation complex / positive regulation of cellular response to amino acid starvation / eukaryotic 48S preinitiation complex / positive regulation of translational fidelity / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of translational initiation / enzyme regulator activity / translation initiation factor binding / translation initiation factor activity / guanyl-nucleotide exchange factor activity / translational initiation / cytoplasmic stress granule / ribosome binding / ribosome / GTPase activity / mRNA binding / GTP binding / mitochondrion / RNA binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Methylthioribose-1-phosphate isomerase, N-terminal / Translation initiation factor eIF-2B subunit alpha, N-terminal / : / : / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Translation initiation factor eIF-2B subunit epsilon, W2 domain / : / : / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal ...Methylthioribose-1-phosphate isomerase, N-terminal / Translation initiation factor eIF-2B subunit alpha, N-terminal / : / : / Translation initiation factor eIF-2B subunit epsilon, N-terminal / Translation initiation factor eIF-2B subunit epsilon, W2 domain / : / : / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5 / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / IF2a, S1-like domain / Eukaryotic translation initiation factor 2 alpha subunit / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C terminal / : / Nucleotidyl transferase domain / Nucleotidyl transferase / NagB/RpiA transferase-like / Bacterial transferase hexapeptide (six repeats) / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Trimeric LpxA-like superfamily / S1 domain profile. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Nucleotide-diphospho-sugar transferases / Armadillo-type fold / Translation protein, beta-barrel domain superfamily / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Translation initiation factor eIF2B subunit gamma / Eukaryotic translation initiation factor 2 subunit beta / Translation initiation factor eIF2B subunit delta / Translation initiation factor eIF2B subunit alpha / Eukaryotic translation initiation factor 2 subunit alpha / Eukaryotic translation initiation factor 2 subunit gamma / Translation initiation factor eIF2B subunit epsilon / Translation initiation factor eIF2B subunit beta
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.55 Å
AuthorsLlacer, J.L. / Gordiyenko, Y. / Ramakrishnan, V.
Funding support United Kingdom, Spain, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_U105184332 United Kingdom
Wellcome TrustWT096570 United Kingdom
Spanish Ministry of Economy and CompetitivenessBFU2017-85814-P Spain
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for the inhibition of translation through eIF2α phosphorylation.
Authors: Yuliya Gordiyenko / José Luis Llácer / V Ramakrishnan /
Abstract: One of the responses to stress by eukaryotic cells is the down-regulation of protein synthesis by phosphorylation of translation initiation factor eIF2. Phosphorylation results in low availability of ...One of the responses to stress by eukaryotic cells is the down-regulation of protein synthesis by phosphorylation of translation initiation factor eIF2. Phosphorylation results in low availability of the eIF2 ternary complex (eIF2-GTP-tRNAi) by affecting the interaction of eIF2 with its GTP-GDP exchange factor eIF2B. We have determined the cryo-EM structure of yeast eIF2B in complex with phosphorylated eIF2 at an overall resolution of 4.2 Å. Two eIF2 molecules bind opposite sides of an eIF2B hetero-decamer through eIF2α-D1, which contains the phosphorylated Ser51. eIF2α-D1 is mainly inserted between the N-terminal helix bundle domains of δ and α subunits of eIF2B. Phosphorylation of Ser51 enhances binding to eIF2B through direct interactions of phosphate groups with residues in eIF2Bα and indirectly by inducing contacts of eIF2α helix 58-63 with eIF2Bδ leading to a competition with Met-tRNA.
History
DepositionJan 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Experimental preparation / Category: em_image_scans / em_sample_support / Item: _em_sample_support.grid_type
Revision 1.2Dec 18, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Structure visualization

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Assembly

Deposited unit
A: Translation initiation factor eIF-2B subunit alpha
B: Translation initiation factor eIF-2B subunit alpha
C: Translation initiation factor eIF-2B subunit beta
D: Translation initiation factor eIF-2B subunit beta
E: Translation initiation factor eIF-2B subunit gamma
F: Translation initiation factor eIF-2B subunit gamma
G: Translation initiation factor eIF-2B subunit delta
H: Translation initiation factor eIF-2B subunit delta
I: Translation initiation factor eIF-2B subunit epsilon
J: Translation initiation factor eIF-2B subunit epsilon
K: Eukaryotic translation initiation factor 2 subunit alpha
L: Eukaryotic translation initiation factor 2 subunit alpha
M: Eukaryotic translation initiation factor 2 subunit gamma
O: Eukaryotic translation initiation factor 2 subunit beta
N: Eukaryotic translation initiation factor 2 subunit gamma
P: Eukaryotic translation initiation factor 2 subunit beta


Theoretical massNumber of molelcules
Total (without water)838,12716
Polymers838,12716
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, by pull-down too
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Translation initiation factor eIF-2B subunit ... , 5 types, 10 molecules ABCDEFGHIJ

#1: Protein Translation initiation factor eIF-2B subunit alpha / GCD complex subunit GCN3 / Guanine nucleotide exchange factor subunit GCN3 / Transcriptional ...GCD complex subunit GCN3 / Guanine nucleotide exchange factor subunit GCN3 / Transcriptional activator GCN3 / eIF-2B GDP-GTP exchange factor subunit alpha


Mass: 34062.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: GCN3, AAS2, TIF221, YKR026C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14741
#2: Protein Translation initiation factor eIF-2B subunit beta / GCD complex subunit GCD7 / Guanine nucleotide exchange factor subunit GCD7 / eIF-2B GDP-GTP ...GCD complex subunit GCD7 / Guanine nucleotide exchange factor subunit GCD7 / eIF-2B GDP-GTP exchange factor subunit beta


Mass: 42621.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: GCD7, TIF222, YLR291C, L8003.17 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32502
#3: Protein Translation initiation factor eIF-2B subunit gamma / GCD complex subunit GCD1 / Guanine nucleotide exchange factor subunit GCD1 / eIF-2B GDP-GTP ...GCD complex subunit GCD1 / Guanine nucleotide exchange factor subunit GCD1 / eIF-2B GDP-GTP exchange factor subunit gamma


Mass: 65768.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: GCD1, TIF223, TRA3, YOR260W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P09032
#4: Protein Translation initiation factor eIF-2B subunit delta / GCD complex subunit GCD2 / Guanine nucleotide exchange factor subunit GCD2 / eIF-2B GDP-GTP ...GCD complex subunit GCD2 / Guanine nucleotide exchange factor subunit GCD2 / eIF-2B GDP-GTP exchange factor subunit delta


Mass: 70945.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: GCD2, TIF224, YGR083C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P12754
#5: Protein Translation initiation factor eIF-2B subunit epsilon / GCD complex subunit GCD6 / Guanine nucleotide exchange factor subunit GCD6 / eIF-2B GDP-GTP ...GCD complex subunit GCD6 / Guanine nucleotide exchange factor subunit GCD6 / eIF-2B GDP-GTP exchange factor subunit epsilon


Mass: 81249.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: GCD6, TIF225, YDR211W, YD8142.12, YD8142B.03 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32501

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Eukaryotic translation initiation factor 2 subunit ... , 3 types, 6 molecules KLMNOP

#6: Protein Eukaryotic translation initiation factor 2 subunit alpha / eIF-2-alpha


Mass: 34843.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SUI2, TIF211, YJR007W, J1429 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20459
#7: Protein Eukaryotic translation initiation factor 2 subunit gamma / eIF-2-gamma


Mass: 57942.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: GCD11, TIF213, YER025W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32481
#8: Protein Eukaryotic translation initiation factor 2 subunit beta / eIF-2-beta


Mass: 31631.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SUI3, TIF212, YPL237W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P09064

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Structure of eIF2B-eIF2 (phosphorylated at Ser51) complex (model A)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.837 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
120 mMHepes1
25 mMMagnessium chloride1
3100 mMPotassium chloride1
45 mMbeta mercaptoethanol1
SpecimenConc.: 0.17 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil, UltrAuFoil
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 104478 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 90 K
Image recordingElectron dose: 45 e/Å2 / Detector mode: OTHER / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 4523
Details: Particles from counting (1241 images) and integrating (3282 images) mode data collections were merged. When in counting mode 60 sec images were recorded (dose 21e-/A2) and when in ...Details: Particles from counting (1241 images) and integrating (3282 images) mode data collections were merged. When in counting mode 60 sec images were recorded (dose 21e-/A2) and when in integrating mode 1.1 sec images were recorded (dose 45e-/A2)

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Processing

SoftwareName: REFMAC / Version: 5.8.0180 / Classification: refinement
EM software
IDNameVersionCategory
2EMANparticle selection
3EPUimage acquisition
5GctfCTF correction
8UCSF Chimera1.1model fitting
9Coot0.8model fitting
11REFMAC5.8model refinement
12RELION2initial Euler assignment
13RELION2final Euler assignment
14RELION2classification
15RELION23D reconstruction
Image processingDetails: FEI Falcon III
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 633220
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119037 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL / Target criteria: FSC
Atomic model building
IDPDB-ID 3D fitting-ID
15B04

5b04

1
26FYX

6fyx

1
RefinementResolution: 4.6→281.4 Å / Cor.coef. Fo:Fc: 0.914 / SU B: 327.13 / SU ML: 3.43 / ESU R: 3.458
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.51253 --
obs0.51253 131526 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.469 Å2
Baniso -1Baniso -2Baniso -3
1--7.73 Å2-1.27 Å2-5.06 Å2
2---5.23 Å216.24 Å2
3---12.96 Å2
Refinement stepCycle: 1 / Resolution: 4.6→281.4 Å / Total: 37959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01938585
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg1.2581.97152192
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.87654798
ELECTRON MICROSCOPYr_dihedral_angle_2_deg46.91424.5581652
ELECTRON MICROSCOPYr_dihedral_angle_3_deg19.521156960
ELECTRON MICROSCOPYr_dihedral_angle_4_deg10.05115223
ELECTRON MICROSCOPYr_chiral_restr0.0860.26122
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.02128323
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 4.6→4.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.595 9703 -
Rfree-0 -
obs--100 %

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