Loading
PDBj
English日本語简体中文繁體中文한국어
✖
MenuPDBj@FacebookPDBj@X(formerly Twitter)PDBj@BlueSkyPDBj@YouTubewwPDB FoundationwwPDBDonate
RCSB PDBPDBeBMRBAdv. SearchSearch help
SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

8ZC0

SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with 3 D1F6 Fabs (2 RBD up)

Functional Information from GO Data
ChainGOidnamespacecontents
A0005515molecular_functionprotein binding
A0005886cellular_componentplasma membrane
A0007165biological_processsignal transduction
A0016020cellular_componentmembrane
A0019031cellular_componentviral envelope
A0019062biological_processvirion attachment to host cell
A0019064biological_processfusion of virus membrane with host plasma membrane
A0019081biological_processviral translation
A0020002cellular_componenthost cell plasma membrane
A0033644cellular_componenthost cell membrane
A0039587biological_processsymbiont-mediated-mediated suppression of host tetherin activity
A0039654biological_processfusion of virus membrane with host endosome membrane
A0039660molecular_functionstructural constituent of virion
A0039663biological_processmembrane fusion involved in viral entry into host cell
A0042802molecular_functionidentical protein binding
A0043655cellular_componenthost extracellular space
A0044173cellular_componenthost cell endoplasmic reticulum-Golgi intermediate compartment membrane
A0044228cellular_componenthost cell surface
A0044423cellular_componentvirion component
A0046598biological_processpositive regulation of viral entry into host cell
A0046718biological_processsymbiont entry into host cell
A0046789molecular_functionhost cell surface receptor binding
A0046813biological_processreceptor-mediated virion attachment to host cell
A0048018molecular_functionreceptor ligand activity
A0052170biological_processsymbiont-mediated suppression of host innate immune response
A0055036cellular_componentvirion membrane
A0061025biological_processmembrane fusion
A0075509biological_processendocytosis involved in viral entry into host cell
A0098670biological_processentry receptor-mediated virion attachment to host cell
A0141146biological_processsymbiont-mediated disruption of host tissue
B0005515molecular_functionprotein binding
B0005886cellular_componentplasma membrane
B0007165biological_processsignal transduction
B0016020cellular_componentmembrane
B0019031cellular_componentviral envelope
B0019062biological_processvirion attachment to host cell
B0019064biological_processfusion of virus membrane with host plasma membrane
B0019081biological_processviral translation
B0020002cellular_componenthost cell plasma membrane
B0033644cellular_componenthost cell membrane
B0039587biological_processsymbiont-mediated-mediated suppression of host tetherin activity
B0039654biological_processfusion of virus membrane with host endosome membrane
B0039660molecular_functionstructural constituent of virion
B0039663biological_processmembrane fusion involved in viral entry into host cell
B0042802molecular_functionidentical protein binding
B0043655cellular_componenthost extracellular space
B0044173cellular_componenthost cell endoplasmic reticulum-Golgi intermediate compartment membrane
B0044228cellular_componenthost cell surface
B0044423cellular_componentvirion component
B0046598biological_processpositive regulation of viral entry into host cell
B0046718biological_processsymbiont entry into host cell
B0046789molecular_functionhost cell surface receptor binding
B0046813biological_processreceptor-mediated virion attachment to host cell
B0048018molecular_functionreceptor ligand activity
B0052170biological_processsymbiont-mediated suppression of host innate immune response
B0055036cellular_componentvirion membrane
B0061025biological_processmembrane fusion
B0075509biological_processendocytosis involved in viral entry into host cell
B0098670biological_processentry receptor-mediated virion attachment to host cell
B0141146biological_processsymbiont-mediated disruption of host tissue
C0005515molecular_functionprotein binding
C0005886cellular_componentplasma membrane
C0007165biological_processsignal transduction
C0016020cellular_componentmembrane
C0019031cellular_componentviral envelope
C0019062biological_processvirion attachment to host cell
C0019064biological_processfusion of virus membrane with host plasma membrane
C0019081biological_processviral translation
C0020002cellular_componenthost cell plasma membrane
C0033644cellular_componenthost cell membrane
C0039587biological_processsymbiont-mediated-mediated suppression of host tetherin activity
C0039654biological_processfusion of virus membrane with host endosome membrane
C0039660molecular_functionstructural constituent of virion
C0039663biological_processmembrane fusion involved in viral entry into host cell
C0042802molecular_functionidentical protein binding
C0043655cellular_componenthost extracellular space
C0044173cellular_componenthost cell endoplasmic reticulum-Golgi intermediate compartment membrane
C0044228cellular_componenthost cell surface
C0044423cellular_componentvirion component
C0046598biological_processpositive regulation of viral entry into host cell
C0046718biological_processsymbiont entry into host cell
C0046789molecular_functionhost cell surface receptor binding
C0046813biological_processreceptor-mediated virion attachment to host cell
C0048018molecular_functionreceptor ligand activity
C0052170biological_processsymbiont-mediated suppression of host innate immune response
C0055036cellular_componentvirion membrane
C0061025biological_processmembrane fusion
C0075509biological_processendocytosis involved in viral entry into host cell
C0098670biological_processentry receptor-mediated virion attachment to host cell
C0141146biological_processsymbiont-mediated disruption of host tissue
Functional Information from PROSITE/UniProt
site_idPS00290
Number of Residues7
DetailsIG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YSCQVTH
ChainResidueDetails
GTYR202-HIS208
HTYR208-HIS214
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues579
DetailsDomain: {"description":"BetaCoV S1-CTD","evidences":[{"source":"PROSITE-ProRule","id":"PRU01269","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"32132184","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues63
DetailsRegion: {"description":"Putative superantigen; may bind T-cell receptor alpha/TRAC","evidences":[{"source":"PubMed","id":"32989130","evidenceCode":"ECO:0000303"}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues666
DetailsRegion: {"description":"Receptor-binding domain (RBD)","evidences":[{"source":"PubMed","id":"32132184","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues219
DetailsRegion: {"description":"Disordered","evidences":[{"source":"PubMed","id":"35108439","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues6
DetailsRegion: {"description":"Integrin-binding motif;","evidences":[{"source":"PubMed","id":"33102950","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues213
DetailsRegion: {"description":"Receptor-binding motif; binding to human ACE2","evidences":[{"source":"UniProtKB","id":"P59594","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues24
DetailsRegion: {"description":"Immunodominant HLA epitope recognized by the CD8+; called NF9 peptide","evidences":[{"source":"PubMed","id":"34171266","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues150
DetailsRegion: {"description":"Heptad repeat 1","evidences":[{"source":"HAMAP-Rule","id":"MF_04099","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues132
DetailsCoiled coil: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04099","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues3
DetailsSite: {"description":"Cleavage; by host TMPRSS2 or CTSL","evidences":[{"source":"HAMAP-Rule","id":"MF_04099","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"32703818","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34159616","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues15
DetailsGlycosylation: {"description":"N-linked (GlcNAc...) (hybrid) asparagine; by host","evidences":[{"source":"HAMAP-Rule","id":"MF_04099","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"32155444","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32363391","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32366695","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32979942","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues6
DetailsGlycosylation: {"description":"N-linked (GlcNAc...) (high mannose) asparagine; by host","evidences":[{"source":"HAMAP-Rule","id":"MF_04099","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"32155444","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32363391","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32366695","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32979942","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues18
DetailsGlycosylation: {"description":"N-linked (GlcNAc...) (complex) asparagine; by host","evidences":[{"source":"HAMAP-Rule","id":"MF_04099","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"32155444","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32363391","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32366695","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32979942","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues3
DetailsGlycosylation: {"description":"O-linked (GalNAc) threonine; by host","evidences":[{"source":"PubMed","id":"32363391","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI15
Number of Residues3
DetailsGlycosylation: {"description":"O-linked (HexNAc...) serine; by host","evidences":[{"source":"PubMed","id":"32363391","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI16
Number of Residues3
DetailsGlycosylation: {"description":"N-linked (GlcNAc...) (hybrid) asparagine; by host","evidences":[{"source":"HAMAP-Rule","id":"MF_04099","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"32155444","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32366695","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32979942","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI17
Number of Residues3
DetailsGlycosylation: {"description":"N-linked (GlcNAc...) (complex) asparagine; by host","evidences":[{"source":"HAMAP-Rule","id":"MF_04099","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"32155444","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32366695","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32979942","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

238582

PDB entries from 2025-07-09

PDB statisticsPDBj update infoContact PDBjnumon