7SFW | pdb_00007sfw

CryoEM structure of Venezuelan Equine Encephalitis virus (VEEV) TC-83 strain VLP in complex with Fab hVEEV-63 (focus refine of the asymmetric unit)


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
CSCOP2B SuperfamilyTrypsin-like serine proteases 8044424 3000114 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyTrypsin-like serine proteases 8044424 3000114 SCOP2B (2022-06-29)
ISCOP2B SuperfamilyTrypsin-like serine proteases 8044424 3000114 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyTrypsin-like serine proteases 8044424 3000114 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
OV-set_8e7sfwO1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
QV-set_8e7sfwQ1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
SV-set_8e7sfwS1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
MV-set_8e7sfwM1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
NV-set_3e7sfwN1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_3ECOD (1.6)
TV-set_3e7sfwT1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_3ECOD (1.6)
RV-set_3e7sfwR1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_3ECOD (1.6)
PV-set_3e7sfwP1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_3ECOD (1.6)
CPeptidase_S3e7sfwC1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: FMN-binding split barrelF: Peptidase_S3ECOD (1.6)
FPeptidase_S3e7sfwF1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: FMN-binding split barrelF: Peptidase_S3ECOD (1.6)
IPeptidase_S3e7sfwI1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: FMN-binding split barrelF: Peptidase_S3ECOD (1.6)
LPeptidase_S3e7sfwL1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: FMN-binding split barrelF: Peptidase_S3ECOD (1.6)
DAlpha_E1_glycop_2nde7sfwD3 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: Alpha_E1_glycop_2ndECOD (1.6)
DAlpha_E1_glycop_1ste7sfwD2 A: beta complex topologyX: Viral glycoprotein, central and dimerisation domains-likeH: Viral glycoprotein, central and dimerisation domains (From Topology)T: Viral glycoprotein, central and dimerisation domainsF: Alpha_E1_glycop_1stECOD (1.6)
DAlpha_E1_glycop_likee7sfwD1 A: extended segmentsX: Transmembrane helix of E1 envelope glycoprotein (From Topology)H: Transmembrane helix of E1 envelope glycoprotein (From Topology)T: Transmembrane helix of E1 envelope glycoproteinF: Alpha_E1_glycop_likeECOD (1.6)
JAlpha_E1_glycop_2nde7sfwJ2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: Alpha_E1_glycop_2ndECOD (1.6)
JAlpha_E1_glycop_1ste7sfwJ1 A: beta complex topologyX: Viral glycoprotein, central and dimerisation domains-likeH: Viral glycoprotein, central and dimerisation domains (From Topology)T: Viral glycoprotein, central and dimerisation domainsF: Alpha_E1_glycop_1stECOD (1.6)
JAlpha_E1_glycop_likee7sfwJ3 A: extended segmentsX: Transmembrane helix of E1 envelope glycoprotein (From Topology)H: Transmembrane helix of E1 envelope glycoprotein (From Topology)T: Transmembrane helix of E1 envelope glycoproteinF: Alpha_E1_glycop_likeECOD (1.6)
GAlpha_E1_glycop_2nde7sfwG3 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: Alpha_E1_glycop_2ndECOD (1.6)
GAlpha_E1_glycop_1ste7sfwG2 A: beta complex topologyX: Viral glycoprotein, central and dimerisation domains-likeH: Viral glycoprotein, central and dimerisation domains (From Topology)T: Viral glycoprotein, central and dimerisation domainsF: Alpha_E1_glycop_1stECOD (1.6)
GAlpha_E1_glycop_likee7sfwG1 A: extended segmentsX: Transmembrane helix of E1 envelope glycoprotein (From Topology)H: Transmembrane helix of E1 envelope glycoprotein (From Topology)T: Transmembrane helix of E1 envelope glycoproteinF: Alpha_E1_glycop_likeECOD (1.6)
AAlpha_E1_glycop_2nde7sfwA3 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: Alpha_E1_glycop_2ndECOD (1.6)
AAlpha_E1_glycop_1ste7sfwA2 A: beta complex topologyX: Viral glycoprotein, central and dimerisation domains-likeH: Viral glycoprotein, central and dimerisation domains (From Topology)T: Viral glycoprotein, central and dimerisation domainsF: Alpha_E1_glycop_1stECOD (1.6)
AAlpha_E1_glycop_likee7sfwA1 A: extended segmentsX: Transmembrane helix of E1 envelope glycoprotein (From Topology)H: Transmembrane helix of E1 envelope glycoprotein (From Topology)T: Transmembrane helix of E1 envelope glycoproteinF: Alpha_E1_glycop_likeECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
M, O, Q, S
Heavy ChainIGHV1 -spike glycoprotein e2SAbDab (2025-12-19)
N, P, R, T
Light ChainIGLV3 Lambdaspike glycoprotein e2SAbDab (2025-12-19)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
B, E, H, K
PF00943Alphavirus E2 glycoprotein (Alpha_E2_glycop)Alphavirus E2 glycoprotein- Family
C, F, I, L
PF00944Alphavirus core protein (Peptidase_S3)Alphavirus core proteinAlso known as coat protein C and capsid protein C. This makes the literature very confusing. Alphaviruses consist of a nucleoprotein core, a lipid membrane which envelopes the core, and glycoprotein spikes protruding from the lipid membrane. Domain
A, D, G, J
PF01589Alphavirus E1 glycoprotein (Alpha_E1_glycop)Alphavirus E1 glycoprotein- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
B, E, H, K
Spike glycoprotein E2
M, O, Q, S
hVEEV-63 Fab heavy chain---
N, P, R, T
hVEEV-63 Fab light chain---
C, F, I, L
Capsid protein
A, D, G, J
Spike glycoprotein E1

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
B, E, H, K
IPR002533Alphavirus E3 spike glycoproteinDomain
B, E, H, K
IPR038055Flaviviral glycoprotein E, dimerisation domainHomologous Superfamily
B, E, H, K
IPR014756Immunoglobulin E-setHomologous Superfamily
B, E, H, K
IPR042304Alphavirus E2 glycoprotein, domain AHomologous Superfamily
B, E, H, K
IPR036253Flavivirus glycoprotein, central and dimerisation domain superfamilyHomologous Superfamily
B, E, H, K
IPR009003Peptidase S1, PA clanHomologous Superfamily
B, E, H, K
IPR042305Alphavirus E2 glycoprotein, domain BHomologous Superfamily
B, E, H, K
IPR042306Alphavirus E2 glycoprotein, domain CHomologous Superfamily
B, E, H, K
IPR000936Alphavirus E2 glycoproteinFamily
B, E, H, K
IPR000930Peptidase S3, togavirinDomain
B, E, H, K
IPR002548Alphavirus E1 glycoproteinDomain
B, E, H, K
IPR000336Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamilyHomologous Superfamily
B, E, H, K
IPR043504Peptidase S1, PA clan, chymotrypsin-like foldHomologous Superfamily
C, F, I, L
IPR002533Alphavirus E3 spike glycoproteinDomain
C, F, I, L
IPR038055Flaviviral glycoprotein E, dimerisation domainHomologous Superfamily
C, F, I, L
IPR014756Immunoglobulin E-setHomologous Superfamily
C, F, I, L
IPR042304Alphavirus E2 glycoprotein, domain AHomologous Superfamily
C, F, I, L
IPR036253Flavivirus glycoprotein, central and dimerisation domain superfamilyHomologous Superfamily
C, F, I, L
IPR009003Peptidase S1, PA clanHomologous Superfamily
C, F, I, L
IPR042305Alphavirus E2 glycoprotein, domain BHomologous Superfamily
C, F, I, L
IPR042306Alphavirus E2 glycoprotein, domain CHomologous Superfamily
C, F, I, L
IPR000936Alphavirus E2 glycoproteinFamily
C, F, I, L
IPR000930Peptidase S3, togavirinDomain
C, F, I, L
IPR002548Alphavirus E1 glycoproteinDomain
C, F, I, L
IPR000336Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamilyHomologous Superfamily
C, F, I, L
IPR043504Peptidase S1, PA clan, chymotrypsin-like foldHomologous Superfamily
A, D, G, J
IPR002533Alphavirus E3 spike glycoproteinDomain
A, D, G, J
IPR038055Flaviviral glycoprotein E, dimerisation domainHomologous Superfamily
A, D, G, J
IPR014756Immunoglobulin E-setHomologous Superfamily
A, D, G, J
IPR042304Alphavirus E2 glycoprotein, domain AHomologous Superfamily
A, D, G, J
IPR036253Flavivirus glycoprotein, central and dimerisation domain superfamilyHomologous Superfamily
A, D, G, J
IPR009003Peptidase S1, PA clanHomologous Superfamily
A, D, G, J
IPR042305Alphavirus E2 glycoprotein, domain BHomologous Superfamily
A, D, G, J
IPR042306Alphavirus E2 glycoprotein, domain CHomologous Superfamily
A, D, G, J
IPR000936Alphavirus E2 glycoproteinFamily
A, D, G, J
IPR000930Peptidase S3, togavirinDomain
A, D, G, J
IPR002548Alphavirus E1 glycoproteinDomain
A, D, G, J
IPR000336Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamilyHomologous Superfamily
A, D, G, J
IPR043504Peptidase S1, PA clan, chymotrypsin-like foldHomologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

ChainsExternal LinkTypeClassSuperfamilyFamily
A, B, C, D, E
OPMTransmembraneBitopic proteinsViral membrane fusion glycoproteinAlphavirus E1 glycoprotein

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

ChainsExternal LinkComment
A, B, C, D, E
PDBTMAnnotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

ChainsExternal LinkComment
A, B, C, D, E
MemProtMDAnnotated as membrane protein by MemProtMD