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- PDB-12fh: Structure of eIF2B bound to a activator -

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Basic information

Entry
Database: PDB / ID: 12fh
TitleStructure of eIF2B bound to a activator
Components
  • Isoform 2 of Translation initiation factor eIF2B subunit delta
  • Translation initiation factor eIF2B subunit beta
  • unidentified protein fragment
KeywordsSUGAR BINDING PROTEIN / guanine nucleotide exchange factor / translation initiation / protein complex
Function / homology
Function and homology information


eukaryotic translation initiation factor 2B complex / Recycling of eIF2:GDP / oligodendrocyte development / regulation of translational initiation / cytoplasmic translational initiation / response to glucose / ovarian follicle development / myelination / translation initiation factor activity / translation initiation factor binding ...eukaryotic translation initiation factor 2B complex / Recycling of eIF2:GDP / oligodendrocyte development / regulation of translational initiation / cytoplasmic translational initiation / response to glucose / ovarian follicle development / myelination / translation initiation factor activity / translation initiation factor binding / guanyl-nucleotide exchange factor activity / central nervous system development / translational initiation / response to peptide hormone / regulation of translation / T cell receptor signaling pathway / response to heat / GTP binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
: / Initiation factor 2B-related / Initiation factor 2B-like, C-terminal / Initiation factor 2 subunit family / NagB/RpiA transferase-like
Similarity search - Domain/homology
: / Translation initiation factor eIF2B subunit beta / Translation initiation factor eIF2B subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsJain, R. / Jakob, C.G. / Qiu, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2026
Title: Discovery of Fosigotifator, a Potent eIF2B Activator with Desired Properties for Human Studies.
Authors: Frost, J.M. / Tong, Y. / Xu, X. / Shi, L. / Pliushchev, M. / Murauski, K.J. / Kohlhaas, K. / Donnelly-Roberts, D.L. / Sheehan, M.M. / Riedmaier, S. / Oberoi, H.S. / Chen, J. / Prakash, J. / ...Authors: Frost, J.M. / Tong, Y. / Xu, X. / Shi, L. / Pliushchev, M. / Murauski, K.J. / Kohlhaas, K. / Donnelly-Roberts, D.L. / Sheehan, M.M. / Riedmaier, S. / Oberoi, H.S. / Chen, J. / Prakash, J. / Hutchins, C.W. / Jakob, C.G. / Jain, R. / Qiu, W. / Henry, R.F. / Edalji, R. / Sun, C. / Carr, T. / Basso, A.M. / Brown, B.S. / Voight, E.A. / Sidrauski, C. / Dart, M.J.
History
DepositionApr 1, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of Translation initiation factor eIF2B subunit delta
B: Isoform 2 of Translation initiation factor eIF2B subunit delta
C: Translation initiation factor eIF2B subunit beta
D: Translation initiation factor eIF2B subunit beta
F: unidentified protein fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,3968
Polymers202,6755
Non-polymers7213
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.470, 230.810, 89.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Isoform 2 of Translation initiation factor eIF2B subunit delta / eIF2B GDP-GTP exchange factor subunit delta


Mass: 59649.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B4, EIF2BD / Production host: Homo sapiens (human) / References: UniProt: Q9UI10
#2: Protein Translation initiation factor eIF2B subunit beta / S20I15 / S20III15 / eIF2B GDP-GTP exchange factor subunit beta


Mass: 40998.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2B2, EIF2BB / Production host: Homo sapiens (human) / References: UniProt: P49770

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Protein/peptide , 1 types, 1 molecules F

#3: Protein/peptide unidentified protein fragment


Mass: 1379.692 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 5 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: SO4 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Chemical ChemComp-A1DBY / N,N'-[(1S,2S,4R)-2-hydroxybicyclo[2.2.2]octane-1,4-diyl]bis[2-(4-chloro-3-fluorophenoxy)acetamide]


Mass: 529.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H24Cl2F2N2O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.22 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 0.9 M (NH4)2SO4, 0.45 % PEG8K, and 0.09 M HEPES pH 7.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→115 Å / Num. obs: 38403 / % possible obs: 94.1 % / Redundancy: 6.6 % / CC1/2: 0.998 / Net I/σ(I): 10.9
Reflection shellResolution: 3.1→3.3 Å / Rmerge(I) obs: 1.18 / Num. unique obs: 1920 / CC1/2: 0.601

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→49.98 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2706 1600 4.74 %
Rwork0.2151 --
obs0.2177 33757 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→49.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10493 0 45 2 10540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410737
X-RAY DIFFRACTIONf_angle_d0.92914570
X-RAY DIFFRACTIONf_dihedral_angle_d15.6993998
X-RAY DIFFRACTIONf_chiral_restr0.0531694
X-RAY DIFFRACTIONf_plane_restr0.0061880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.610.4391930.36811984X-RAY DIFFRACTION66
3.61-3.740.50681370.38372734X-RAY DIFFRACTION91
3.74-3.890.34711530.27063004X-RAY DIFFRACTION100
3.89-4.070.26461430.23082994X-RAY DIFFRACTION100
4.07-4.280.25671400.19483024X-RAY DIFFRACTION100
4.28-4.550.2241440.17073008X-RAY DIFFRACTION100
4.55-4.90.22391500.15833017X-RAY DIFFRACTION100
4.9-5.40.23831610.18173027X-RAY DIFFRACTION100
5.4-6.170.261460.21573073X-RAY DIFFRACTION100
6.18-7.770.25891630.20893083X-RAY DIFFRACTION100
7.78-49.980.21481700.18323209X-RAY DIFFRACTION99

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