6caj

Electron cryo-microscopy of the eukaryotic translation initiation factor 2B from Homo sapiens

Method: ELECTRON MICROSCOPY Dmax: 163.8 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Translation initiation factor eIF-2B subunit epsilon

Homo sapiens

UniProt Q13144

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain A; UniProt 1–721 Chain B; UniProt 1–721 Not recorded Translation initiation factor eIF-2B subunit gamma × 2 (Q9NR50) Translation initiation factor eIF-2B subunit alpha × 2 (Q14232) Translation initiation factor eIF-2B subunit beta × 2 (P49770) Translation initiation factor eIF-2B subunit delta × 2 (Q9UI10) C7B 2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylamino]cyclohexyl]ethanamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.80 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

25 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EI2BE_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–721; UniProt 1–721 Author chain B; PDBConstruct 1–721; UniProt 1–721

Translation initiation factor eIF-2B subunit gamma

Homo sapiens

UniProt Q9NR50

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain I; UniProt 1–452 Chain J; UniProt 1–452 Not recorded Translation initiation factor eIF-2B subunit epsilon × 2 (Q13144) Translation initiation factor eIF-2B subunit alpha × 2 (Q14232) Translation initiation factor eIF-2B subunit beta × 2 (P49770) Translation initiation factor eIF-2B subunit delta × 2 (Q9UI10) C7B 2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylamino]cyclohexyl]ethanamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.80 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

25 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EI2BG_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain I; PDBConstruct 1–452; UniProt 1–452 Author chain J; PDBConstruct 1–452; UniProt 1–452

Translation initiation factor eIF-2B subunit alpha

Homo sapiens

UniProt Q14232

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain G; UniProt 1–305 Chain H; UniProt 1–305 Not recorded Translation initiation factor eIF-2B subunit epsilon × 2 (Q13144) Translation initiation factor eIF-2B subunit gamma × 2 (Q9NR50) Translation initiation factor eIF-2B subunit beta × 2 (P49770) Translation initiation factor eIF-2B subunit delta × 2 (Q9UI10) C7B 2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylamino]cyclohexyl]ethanamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.80 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

26 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EI2BA_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain G; PDBConstruct 1–305; UniProt 1–305 Author chain H; PDBConstruct 1–305; UniProt 1–305

Translation initiation factor eIF-2B subunit beta

Homo sapiens

UniProt P49770

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain C; UniProt 2–351 Chain D; UniProt 2–351 Not recorded Translation initiation factor eIF-2B subunit epsilon × 2 (Q13144) Translation initiation factor eIF-2B subunit gamma × 2 (Q9NR50) Translation initiation factor eIF-2B subunit alpha × 2 (Q14232) Translation initiation factor eIF-2B subunit delta × 2 (Q9UI10) C7B 2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylamino]cyclohexyl]ethanamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.80 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

26 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EI2BB_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain C; PDBConstruct 19–368; UniProt 2–351 Author chain D; PDBConstruct 19–368; UniProt 2–351

Translation initiation factor eIF-2B subunit delta

Homo sapiens

UniProt Q9UI10

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric(10) Consistent with protein copy count Chain E; UniProt 1–523 Chain F; UniProt 1–523 Not recorded Translation initiation factor eIF-2B subunit epsilon × 2 (Q13144) Translation initiation factor eIF-2B subunit gamma × 2 (Q9NR50) Translation initiation factor eIF-2B subunit alpha × 2 (Q14232) Translation initiation factor eIF-2B subunit beta × 2 (P49770) C7B 2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy)ethanoylamino]cyclohexyl]ethanamide × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.80 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

26 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EI2BD_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain E; PDBConstruct 1–523; UniProt 1–523 Author chain F; PDBConstruct 1–523; UniProt 1–523

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6caj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6caj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6caj
Deposition date deposition_date2018-01-31
Structure title titleElectron cryo-microscopy of the eukaryotic translation initiation factor 2B from Homo sapiens
Keywords keywordsguanine nucleotide exchange factor, translation initiation, ISRIB-bound, decameric complex, TRANSLATION; TRANSLATION
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier49.32
Radius of gyration Rg (electron density) rg_electron48.84
Forward intensity I(0) i01672160000.00
Molecular weight molecular_weight344760.0 kDa
Excluded volume excluded_volume433440 ų
Envelope volume envelope_volume603430 ų
Hydration-shell volume shell_volume100120 ų
Envelope diameter envelope_diameter165.8
Shell Rg shell_rg54.19
Envelope Rg envelope_rg48.95
Shape Rg shape_rg48.89
Total Rg total_rg48.87
Total atoms total_atoms24265
Residues n_residues3210
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax163.8
Rg (real space) rg_real49.23
Rg uncertainty (real space) rg_real_error1.22
I(0) (real space) i0_real1.6720e+09
I(0) uncertainty (real space) i0_real_error3.0470e+07
Rg (reciprocal space) rg_reciprocal49.32
I(0) (reciprocal space) i0_reciprocal1672000000.0000
Solution quality estimate total_estimate0.8140
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary56.3
Skewness Skewness skewness0.312
Kurtosis Kurtosis kurtosis-0.394
Angular range angular_range— – 0.1600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha241400000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id6cajG01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily1070 — Translation initiation factor eIF-2B, N-terminal domain
Domain ID domain_id6cajG02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10470 — Translation initiation factor eif-2b; domain 2
Domain ID domain_id6cajH01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily1070 — Translation initiation factor eIF-2B, N-terminal domain
Domain ID domain_id6cajH02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10470 — Translation initiation factor eif-2b; domain 2

8. Citations (1)

9. Files and Curves (10)