7f66

eIF2B-SFSV NSs-1-eIF2

Method: ELECTRON MICROSCOPY Dmax: 202.5 Å Quality: GOOD

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

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 × 15 PDB declaration: pentadecameric(15) Consistent with protein copy count Chain A; UniProt 1–305 Chain B; UniProt 1–305 Not recorded Translation initiation factor eIF-2B subunit beta × 2 (P49770) Translation initiation factor eIF-2B subunit gamma × 2 (Q9NR50) Translation initiation factor eIF-2B subunit delta × 2 (Q9UI10) Translation initiation factor eIF-2B subunit epsilon × 2 (Q13144) Non-structural protein NS-S × 2 (P12792) Eukaryotic translation initiation factor 2 subunit 1 × 1 (P05198) eIF2beta × 1 Eukaryotic translation initiation factor 2 subunit 3 × 1 (P41091) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.76 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 1
Chains and sequence ranges Author chain A; PDBConstruct 3–307; UniProt 1–305 Author chain B; PDBConstruct 3–307; 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 × 15 PDB declaration: pentadecameric(15) Consistent with protein copy count Chain C; UniProt 1–351 Chain D; UniProt 1–351 Not recorded Translation initiation factor eIF-2B subunit alpha × 2 (Q14232) Translation initiation factor eIF-2B subunit gamma × 2 (Q9NR50) Translation initiation factor eIF-2B subunit delta × 2 (Q9UI10) Translation initiation factor eIF-2B subunit epsilon × 2 (Q13144) Non-structural protein NS-S × 2 (P12792) Eukaryotic translation initiation factor 2 subunit 1 × 1 (P05198) eIF2beta × 1 Eukaryotic translation initiation factor 2 subunit 3 × 1 (P41091) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.76 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 2
Chains and sequence ranges Author chain C; PDBConstruct 1–351; UniProt 1–351 Author chain D; PDBConstruct 1–351; UniProt 1–351

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 × 15 PDB declaration: pentadecameric(15) Consistent with protein copy count Chain E; UniProt 1–452 Chain F; UniProt 1–452 Not recorded 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) Translation initiation factor eIF-2B subunit epsilon × 2 (Q13144) Non-structural protein NS-S × 2 (P12792) Eukaryotic translation initiation factor 2 subunit 1 × 1 (P05198) eIF2beta × 1 Eukaryotic translation initiation factor 2 subunit 3 × 1 (P41091) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.76 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 3
Chains and sequence ranges Author chain E; PDBConstruct 1–452; UniProt 1–452 Author chain F; PDBConstruct 1–452; UniProt 1–452

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 × 15 PDB declaration: pentadecameric(15) Consistent with protein copy count Chain G; UniProt 1–523 Chain H; UniProt 1–523 Not recorded Translation initiation factor eIF-2B subunit alpha × 2 (Q14232) Translation initiation factor eIF-2B subunit beta × 2 (P49770) Translation initiation factor eIF-2B subunit gamma × 2 (Q9NR50) Translation initiation factor eIF-2B subunit epsilon × 2 (Q13144) Non-structural protein NS-S × 2 (P12792) Eukaryotic translation initiation factor 2 subunit 1 × 1 (P05198) eIF2beta × 1 Eukaryotic translation initiation factor 2 subunit 3 × 1 (P41091) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.76 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 4
Chains and sequence ranges Author chain G; PDBConstruct 1–523; UniProt 1–523 Author chain H; PDBConstruct 1–523; UniProt 1–523

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 × 15 PDB declaration: pentadecameric(15) Consistent with protein copy count Chain I; UniProt 1–721 Chain J; UniProt 1–721 Not recorded Translation initiation factor eIF-2B subunit alpha × 2 (Q14232) Translation initiation factor eIF-2B subunit beta × 2 (P49770) Translation initiation factor eIF-2B subunit gamma × 2 (Q9NR50) Translation initiation factor eIF-2B subunit delta × 2 (Q9UI10) Non-structural protein NS-S × 2 (P12792) Eukaryotic translation initiation factor 2 subunit 1 × 1 (P05198) eIF2beta × 1 Eukaryotic translation initiation factor 2 subunit 3 × 1 (P41091) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.76 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 5
Chains and sequence ranges Author chain I; PDBConstruct 1–721; UniProt 1–721 Author chain J; PDBConstruct 1–721; UniProt 1–721

Non-structural protein NS-S

Sandfly fever sicilian virus

UniProt P12792

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 × 15 PDB declaration: pentadecameric(15) Consistent with protein copy count Chain K; UniProt 7–267 Chain L; UniProt 7–267 Not recorded Translation initiation factor eIF-2B subunit alpha × 2 (Q14232) Translation initiation factor eIF-2B subunit beta × 2 (P49770) Translation initiation factor eIF-2B subunit gamma × 2 (Q9NR50) Translation initiation factor eIF-2B subunit delta × 2 (Q9UI10) Translation initiation factor eIF-2B subunit epsilon × 2 (Q13144) Eukaryotic translation initiation factor 2 subunit 1 × 1 (P05198) eIF2beta × 1 Eukaryotic translation initiation factor 2 subunit 3 × 1 (P41091) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.76 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.

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NSS_SFSV
Isoform
PDB entities 6
Chains and sequence ranges Author chain K; PDBConstruct 1–261; UniProt 7–267 Author chain L; PDBConstruct 1–261; UniProt 7–267

Eukaryotic translation initiation factor 2 subunit 1

Homo sapiens

UniProt P05198

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 × 15 PDB declaration: pentadecameric(15) Consistent with protein copy count Chain N; UniProt 1–315 Not recorded Translation initiation factor eIF-2B subunit alpha × 2 (Q14232) Translation initiation factor eIF-2B subunit beta × 2 (P49770) Translation initiation factor eIF-2B subunit gamma × 2 (Q9NR50) Translation initiation factor eIF-2B subunit delta × 2 (Q9UI10) Translation initiation factor eIF-2B subunit epsilon × 2 (Q13144) Non-structural protein NS-S × 2 (P12792) eIF2beta × 1 Eukaryotic translation initiation factor 2 subunit 3 × 1 (P41091) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.76 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.

36 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IF2A_HUMAN
Isoform
PDB entities 7
Chains and sequence ranges Author chain N; PDBConstruct 1–315; UniProt 1–315

Eukaryotic translation initiation factor 2 subunit 3

Homo sapiens

UniProt P41091

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 × 15 PDB declaration: pentadecameric(15) Consistent with protein copy count Chain S; UniProt 1–472 Not recorded Translation initiation factor eIF-2B subunit alpha × 2 (Q14232) Translation initiation factor eIF-2B subunit beta × 2 (P49770) Translation initiation factor eIF-2B subunit gamma × 2 (Q9NR50) Translation initiation factor eIF-2B subunit delta × 2 (Q9UI10) Translation initiation factor eIF-2B subunit epsilon × 2 (Q13144) Non-structural protein NS-S × 2 (P12792) Eukaryotic translation initiation factor 2 subunit 1 × 1 (P05198) eIF2beta × 1 ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.76 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.

28 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IF2G_HUMAN
Isoform
PDB entities 9
Chains and sequence ranges Author chain S; PDBConstruct 1–472; UniProt 1–472

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 7f66

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7f66
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7f66
Deposition date deposition_date2021-06-24
Structure title titleeIF2B-SFSV NSs-1-eIF2
Keywords keywordstranslation initiation factor, viral protein, TRANSLATION; TRANSLATION
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier59.37
Radius of gyration Rg (electron density) rg_electron58.45
Forward intensity I(0) i03299410000.00
Molecular weight molecular_weight479120.0 kDa
Excluded volume excluded_volume598090 ų
Envelope volume envelope_volume904620 ų
Hydration-shell volume shell_volume126560 ų
Envelope diameter envelope_diameter222.0
Shell Rg shell_rg61.01
Envelope Rg envelope_rg59.71
Shape Rg shape_rg58.59
Total Rg total_rg58.01
Total atoms total_atoms33739
Residues n_residues4561
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 dmax202.5
Rg (real space) rg_real59.51
Rg uncertainty (real space) rg_real_error2.07
I(0) (real space) i0_real3.2990e+09
I(0) uncertainty (real space) i0_real_error7.5340e+07
Rg (reciprocal space) rg_reciprocal59.23
I(0) (reciprocal space) i0_reciprocal3298000000.0000
Solution quality estimate total_estimate0.8456
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary70.1
Skewness Skewness skewness0.486
Kurtosis Kurtosis kurtosis-0.005
Angular range angular_range— – 0.1300 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha268700000.0000
Real-space data points n_real_points27
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.799; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.615

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

7. Fold Classification (SCOP + CATH) 13 domains

CATH v4.4 (13 domains)

Domain ID domain_id7f66A01
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_id7f66A02
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_id7f66B01
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_id7f66B02
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_id7f66C01
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_id7f66D01
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_id7f66E01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Domain ID domain_id7f66F01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Domain ID domain_id7f66I01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Domain ID domain_id7f66J01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Domain ID domain_id7f66N01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id7f66N02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily190 — Translation initiation factor 2; subunit 1; domain 2
Domain ID domain_id7f66N03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1130 — EIF_2_alpha

8. Citations (1)

9. Files and Curves (10)