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- PDB-9y5u: eIF2B lacking the latch helix bound to ISRACT-02 (Inactive state) -

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Basic information

Entry
Database: PDB / ID: 9y5u
TitleeIF2B lacking the latch helix bound to ISRACT-02 (Inactive state)
Components
  • (Translation initiation factor eIF-2B subunit ...) x 4
  • Translation initiation factor eIF2B subunit beta
KeywordsTRANSLATION / Guanine nucleotide exchange factor / GEF / initiation
Function / homology
Function and homology information


eukaryotic translation initiation factor 2B complex / Recycling of eIF2:GDP / astrocyte development / astrocyte differentiation / oligodendrocyte development / regulation of translational initiation / cytoplasmic translational initiation / positive regulation of translational initiation / response to glucose / ovarian follicle development ...eukaryotic translation initiation factor 2B complex / Recycling of eIF2:GDP / astrocyte development / astrocyte differentiation / oligodendrocyte development / regulation of translational initiation / cytoplasmic translational initiation / positive regulation of translational initiation / response to glucose / ovarian follicle development / myelination / translation initiation factor activity / translation initiation factor binding / guanyl-nucleotide exchange factor activity / response to endoplasmic reticulum stress / central nervous system development / hippocampus development / translational initiation / response to peptide hormone / regulation of translation / T cell receptor signaling pathway / response to heat / positive regulation of apoptotic process / GTP binding / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 / : / : / : / : / : / EIF2B subunit epsilon LbH domain / Initiation factor 2B-related ...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 / : / : / : / : / : / EIF2B subunit epsilon LbH domain / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / 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. / Nucleotidyl transferase domain / Nucleotidyl transferase / NagB/RpiA transferase-like / Trimeric LpxA-like superfamily / Nucleotide-diphospho-sugar transferases / Armadillo-type fold
Similarity search - Domain/homology
: / Translation initiation factor eIF2B subunit beta / Translation initiation factor eIF2B subunit epsilon / Translation initiation factor eIF2B subunit alpha / Translation initiation factor eIF2B subunit gamma / Translation initiation factor eIF2B subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsDalwadi, U. / Croll, T. / Subramanian, A. / Lee, D.J. / Arthur, C. / Walter, P. / Frost, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat.Chem.Biol. / Year: 2026
Title: Allosteric disordering of eIF2B regulates the integrated stress response
Authors: Dalwadi, U. / Subramanian, A. / Deal, A. / Conrad, J.E. / Nadjsombati, T. / Venkatesh, M. / Boone, M. / Egea, P.F. / He, L. / Jain, N. / Lee, D.J. / Liu, Y. / Reineke, L.C. / Saito, K. / ...Authors: Dalwadi, U. / Subramanian, A. / Deal, A. / Conrad, J.E. / Nadjsombati, T. / Venkatesh, M. / Boone, M. / Egea, P.F. / He, L. / Jain, N. / Lee, D.J. / Liu, Y. / Reineke, L.C. / Saito, K. / Talledge, N. / Toutkoushian, H. / Le Vasseur, M. / Zappa, F. / de Groot, R.J. / Acosta-Alvear, D. / Arthur, C.P. / Nunnari, J. / Marqusee, S. / Lawrence, R.E. / Costa-Mattioli, M. / Crawford, J.J. / van Kuppeveld, F.J.M. / Croll, T.I. / Walter, P. / Frost, A.
History
DepositionSep 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Translation initiation factor eIF-2B subunit epsilon
B: Translation initiation factor eIF-2B subunit epsilon
C: Translation initiation factor eIF2B subunit beta
D: Translation initiation factor eIF2B subunit beta
E: Translation initiation factor eIF-2B subunit delta
F: Translation initiation factor eIF-2B subunit delta
G: Translation initiation factor eIF-2B subunit alpha
H: Translation initiation factor eIF-2B subunit alpha
I: Translation initiation factor eIF-2B subunit gamma
J: Translation initiation factor eIF-2B subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)523,93815
Polymers523,18010
Non-polymers7585
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Translation initiation factor eIF-2B subunit ... , 4 types, 8 molecules ABEFGHIJ

#1: Protein Translation initiation factor eIF-2B subunit epsilon / eIF-2B GDP-GTP exchange factor subunit epsilon


Mass: 80452.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B5, EIF2BE / Production host: Escherichia coli (E. coli) / References: UniProt: Q13144
#3: Protein Translation initiation factor eIF-2B subunit delta / eIF-2B GDP-GTP exchange factor subunit delta


Mass: 57640.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B4, EIF2BD / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UI10
#4: Protein Translation initiation factor eIF-2B subunit alpha / eIF-2B GDP-GTP exchange factor subunit alpha


Mass: 33754.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B1, EIF2BA / Production host: Escherichia coli (E. coli) / References: UniProt: Q14232
#5: Protein Translation initiation factor eIF-2B subunit gamma / eIF-2B GDP-GTP exchange factor subunit gamma


Mass: 50304.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NR50

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Protein , 1 types, 2 molecules CD

#2: Protein Translation initiation factor eIF2B subunit beta / S20I15 / S20III15 / eIF2B GDP-GTP exchange factor subunit beta


Mass: 39438.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B2, EIF2BB / Production host: Escherichia coli (E. coli) / References: UniProt: P49770

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Non-polymers , 3 types, 5 molecules

#6: Chemical ChemComp-A1CSR / 3-(4-chlorophenoxy)-N-{(1r,4r)-4-[2-(4-chlorophenoxy)acetamido]cyclohexyl}-N-[(pyridin-4-yl)methyl]propanamide


Mass: 556.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H31Cl2N3O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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Details

Has ligand of interestY
Has protein modificationN

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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: Eukaryotic translation initiation factor 2B (latch helix deletion)
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightValue: 0.521758 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
Details: 20 mM HEPES KOH pH 7.4, 200 mM KCl, 5 mM MgCl2, 1 mM TCEP
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid or 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acidHEPES1
2200 mMPotassium ChlorideKCl1
35 mMMagnesium ChlorideMgCl21
41 mMtris(2-carboxyethyl)phosphineTCEP1
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4897
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
2EPUimage acquisition
4cryoSPARC4.4.1CTF correction
7ISOLDEmodel fitting
9Servalcatmodel refinement
10cryoSPARC4.4.1initial Euler assignment
11cryoSPARC4.4.1final Euler assignment
12cryoSPARC4.4.1classification
13cryoSPARC4.4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2376924
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 325317 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingPDB-ID: 7L7G

7l7g


Accession code: 7L7G / Source name: PDB / Type: experimental model
RefinementResolution: 2.9→2.9 Å / Num. reflection obs: 4356841 / Average fsc work: 0.7579
Displacement parametersBiso mean: 94.13 Å2
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.008291810.0119
ELECTRON MICROSCOPYs_angle_nonh_deg1.7096395361.8249
ELECTRON MICROSCOPYs_dihedral_angle_1_deg7.604236525
ELECTRON MICROSCOPYs_dihedral_angle_2_deg4.68088945
ELECTRON MICROSCOPYs_dihedral_angle_3_deg11.4345785210
ELECTRON MICROSCOPYs_dihedral_angle_6_deg14.4431144210
ELECTRON MICROSCOPYs_chiral_restr0.068346130.1309
ELECTRON MICROSCOPYs_planes0.0053404830.02
ELECTRON MICROSCOPYs_nbd0.2114413070.2
ELECTRON MICROSCOPYs_nbtor0.2265522480.2
ELECTRON MICROSCOPYs_hbond_nbd0.11827220.2
ELECTRON MICROSCOPYs_metal_ion0.249230.2
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsFsc work
2.8-2.826ELECTRON MICROSCOPY1167210.3502
2.826-2.848ELECTRON MICROSCOPY990370.3815
2.848-2.871ELECTRON MICROSCOPY991270.4056
2.871-2.894ELECTRON MICROSCOPY962850.4261
2.894-2.918ELECTRON MICROSCOPY951250.4475
2.918-2.942ELECTRON MICROSCOPY936210.4727
2.942-2.966ELECTRON MICROSCOPY922150.5056
2.966-2.991ELECTRON MICROSCOPY909010.5381
2.991-3.016ELECTRON MICROSCOPY883890.5634
3.016-3.042ELECTRON MICROSCOPY869470.5803
3.042-3.068ELECTRON MICROSCOPY864930.5977
3.068-3.095ELECTRON MICROSCOPY849250.6183
3.095-3.122ELECTRON MICROSCOPY824970.6392
3.122-3.149ELECTRON MICROSCOPY820510.6592
3.149-3.177ELECTRON MICROSCOPY803290.68
3.178-3.206ELECTRON MICROSCOPY789330.7017
3.206-3.235ELECTRON MICROSCOPY766990.7275
3.235-3.264ELECTRON MICROSCOPY759570.7488
3.264-3.294ELECTRON MICROSCOPY753250.767
3.295-3.325ELECTRON MICROSCOPY731550.7846
3.325-3.356ELECTRON MICROSCOPY717970.797
3.356-3.388ELECTRON MICROSCOPY702970.809
3.388-3.42ELECTRON MICROSCOPY702690.8187
3.421-3.453ELECTRON MICROSCOPY669430.8284
3.454-3.487ELECTRON MICROSCOPY668610.8416
3.487-3.521ELECTRON MICROSCOPY654970.8538
3.522-3.556ELECTRON MICROSCOPY640950.8631
3.557-3.592ELECTRON MICROSCOPY629050.8702
3.592-3.629ELECTRON MICROSCOPY610450.8789
3.629-3.666ELECTRON MICROSCOPY611490.8884
3.666-3.704ELECTRON MICROSCOPY593830.8952
3.704-3.743ELECTRON MICROSCOPY579450.9005
3.743-3.782ELECTRON MICROSCOPY561610.9055
3.782-3.823ELECTRON MICROSCOPY553630.9087
3.823-3.864ELECTRON MICROSCOPY542730.9112
3.864-3.906ELECTRON MICROSCOPY531730.9119
3.907-3.949ELECTRON MICROSCOPY518850.9123
3.95-3.994ELECTRON MICROSCOPY512950.9148
3.994-4.039ELECTRON MICROSCOPY498450.9186
4.039-4.085ELECTRON MICROSCOPY486370.9225
4.085-4.132ELECTRON MICROSCOPY472390.9242
4.132-4.18ELECTRON MICROSCOPY465690.9261
4.181-4.23ELECTRON MICROSCOPY457690.9293
4.23-4.28ELECTRON MICROSCOPY440670.9326
4.281-4.332ELECTRON MICROSCOPY432730.9358
4.333-4.386ELECTRON MICROSCOPY423330.9367
4.386-4.44ELECTRON MICROSCOPY415930.9352
4.44-4.496ELECTRON MICROSCOPY400150.9339
4.496-4.553ELECTRON MICROSCOPY391890.9356
4.553-4.611ELECTRON MICROSCOPY378610.9386
4.612-4.672ELECTRON MICROSCOPY374550.9403
4.673-4.734ELECTRON MICROSCOPY363730.9409
4.734-4.797ELECTRON MICROSCOPY350130.9406
4.798-4.863ELECTRON MICROSCOPY348490.9386
4.863-4.93ELECTRON MICROSCOPY333430.9354
4.93-4.999ELECTRON MICROSCOPY328650.9324
4.999-5.07ELECTRON MICROSCOPY312850.928
5.07-5.142ELECTRON MICROSCOPY306030.9222
5.143-5.218ELECTRON MICROSCOPY303130.9173
5.218-5.295ELECTRON MICROSCOPY287410.9111
5.296-5.374ELECTRON MICROSCOPY284550.903
5.375-5.457ELECTRON MICROSCOPY271570.8985
5.457-5.541ELECTRON MICROSCOPY270450.8965
5.542-5.628ELECTRON MICROSCOPY257770.8913
5.631-5.718ELECTRON MICROSCOPY244350.8831
5.719-5.811ELECTRON MICROSCOPY242770.8749
5.812-5.907ELECTRON MICROSCOPY233170.866
5.908-6.007ELECTRON MICROSCOPY228510.8596
6.008-6.109ELECTRON MICROSCOPY217450.8589
6.11-6.216ELECTRON MICROSCOPY210330.8575
6.217-6.326ELECTRON MICROSCOPY207130.8506
6.327-6.44ELECTRON MICROSCOPY196470.8396
6.441-6.558ELECTRON MICROSCOPY188410.8298
6.559-6.679ELECTRON MICROSCOPY182170.8256
6.681-6.807ELECTRON MICROSCOPY177270.8249
6.809-6.94ELECTRON MICROSCOPY171250.8261
6.942-7.076ELECTRON MICROSCOPY161250.8249
7.078-7.22ELECTRON MICROSCOPY158710.8199
7.221-7.369ELECTRON MICROSCOPY152250.8204
7.37-7.524ELECTRON MICROSCOPY145330.829
7.525-7.686ELECTRON MICROSCOPY137530.8408
7.687-7.853ELECTRON MICROSCOPY130590.8414
7.856-8.031ELECTRON MICROSCOPY129730.832
8.035-8.215ELECTRON MICROSCOPY120210.8275
8.218-8.406ELECTRON MICROSCOPY117310.8373
8.411-8.611ELECTRON MICROSCOPY109810.8426
8.614-8.824ELECTRON MICROSCOPY107250.8501
8.826-9.047ELECTRON MICROSCOPY101170.863
9.05-9.282ELECTRON MICROSCOPY93750.8676
9.285-9.526ELECTRON MICROSCOPY91330.8641
9.533-9.79ELECTRON MICROSCOPY85770.8665
9.794-10.066ELECTRON MICROSCOPY82270.8788
10.07-10.353ELECTRON MICROSCOPY75970.8891
10.362-10.666ELECTRON MICROSCOPY73770.9007
10.671-10.994ELECTRON MICROSCOPY69010.9068
10.999-11.343ELECTRON MICROSCOPY63030.9041
11.349-11.715ELECTRON MICROSCOPY60730.9036
11.721-12.104ELECTRON MICROSCOPY56130.8978
12.118-12.536ELECTRON MICROSCOPY52750.8976
12.544-12.991ELECTRON MICROSCOPY49810.9021
13-13.472ELECTRON MICROSCOPY45330.9011
13.491-14.009ELECTRON MICROSCOPY43030.8942
14.02-14.58ELECTRON MICROSCOPY40170.8901
14.592-15.2ELECTRON MICROSCOPY35650.8956
15.214-15.874ELECTRON MICROSCOPY33010.9031
15.89-16.594ELECTRON MICROSCOPY29910.9033
16.63-17.421ELECTRON MICROSCOPY28570.8913
17.441-18.312ELECTRON MICROSCOPY25170.8861
18.36-19.272ELECTRON MICROSCOPY21790.8896
19.328-20.4ELECTRON MICROSCOPY20850.8908
20.433-21.633ELECTRON MICROSCOPY18610.887
21.673-23.025ELECTRON MICROSCOPY16690.9052
23.169-24.607ELECTRON MICROSCOPY13110.9235
24.666-26.351ELECTRON MICROSCOPY12490.9275
26.495-28.527ELECTRON MICROSCOPY10890.9361
28.71-30.994ELECTRON MICROSCOPY9070.9546
31.111-33.625ELECTRON MICROSCOPY7290.9706
34.081-37.47ELECTRON MICROSCOPY6250.9851
37.677-41.835ELECTRON MICROSCOPY5710.9871
42.125-47.344ELECTRON MICROSCOPY3810.9816
47.765-54.509ELECTRON MICROSCOPY3010.9803
55.154-63.187ELECTRON MICROSCOPY2250.9817
65.259-78ELECTRON MICROSCOPY1750.982
79.926-99.136ELECTRON MICROSCOPY1050.9815
103.184-126.374ELECTRON MICROSCOPY490.9837
145.924-357.44ELECTRON MICROSCOPY400.8947

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