Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help

8XM5

Cryo-EM structure of SARS-CoV-2 Omicron EG.5 spike protein(6P), RBD-closed state

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
A0039587biological_processsuppression by virus of host tetherin activity
A0039654biological_processfusion of virus membrane with host endosome membrane
A0039660molecular_functionstructural constituent of virion
A0042802molecular_functionidentical protein binding
A0043655cellular_componenthost extracellular space
A0044173cellular_componenthost cell endoplasmic reticulum-Golgi intermediate compartment membrane
A0044228cellular_componenthost cell surface
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
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
B0039587biological_processsuppression by virus of host tetherin activity
B0039654biological_processfusion of virus membrane with host endosome membrane
B0039660molecular_functionstructural constituent of virion
B0042802molecular_functionidentical protein binding
B0043655cellular_componenthost extracellular space
B0044173cellular_componenthost cell endoplasmic reticulum-Golgi intermediate compartment membrane
B0044228cellular_componenthost cell surface
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
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
C0039587biological_processsuppression by virus of host tetherin activity
C0039654biological_processfusion of virus membrane with host endosome membrane
C0039660molecular_functionstructural constituent of virion
C0042802molecular_functionidentical protein binding
C0043655cellular_componenthost extracellular space
C0044173cellular_componenthost cell endoplasmic reticulum-Golgi intermediate compartment membrane
C0044228cellular_componenthost cell surface
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
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues3
DetailsSITE: Cleavage; by host furin => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32142651, ECO:0000269|PubMed:32362314, ECO:0000269|PubMed:32703818, ECO:0000269|PubMed:34159616
ChainResidueDetails
ASER686
BSER686
CSER686

site_idSWS_FT_FI2
Number of Residues3
DetailsSITE: Cleavage; by host TMPRSS2 or CTSL => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32703818, ECO:0000269|PubMed:34159616
ChainResidueDetails
ASER816
BSER816
CSER816

site_idSWS_FT_FI3
Number of Residues15
DetailsCARBOHYD: N-linked (GlcNAc...) (hybrid) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
ChainResidueDetails
AASN61
BPHE1075
CASN61
CASN122
CPHE718
CPHE802
CPHE1075
AASN122
APHE718
APHE802
APHE1075
BASN61
BASN122
BPHE718
BPHE802

site_idSWS_FT_FI4
Number of Residues9
DetailsCARBOHYD: N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
ChainResidueDetails
AASN74
ALYS150
AGLU1195
BASN74
BLYS150
BGLU1195
CASN74
CLYS150
CGLU1195

site_idSWS_FT_FI5
Number of Residues21
DetailsCARBOHYD: N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
ChainResidueDetails
ACYS166
BILE332
BALA344
BCYS617
BASN658
BGLY1099
CCYS166
CGLY283
CILE332
CALA344
CCYS617
AGLY283
CASN658
CGLY1099
AILE332
AALA344
ACYS617
AASN658
AGLY1099
BCYS166
BGLY283

site_idSWS_FT_FI6
Number of Residues6
DetailsCARBOHYD: N-linked (GlcNAc...) (high mannose) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
ChainResidueDetails
AILE235
AASN710
BILE235
BASN710
CILE235
CASN710

site_idSWS_FT_FI7
Number of Residues3
DetailsCARBOHYD: O-linked (GalNAc) threonine; by host => ECO:0000269|PubMed:32363391
ChainResidueDetails
AGLU324
BGLU324
CGLU324

site_idSWS_FT_FI8
Number of Residues3
DetailsCARBOHYD: O-linked (HexNAc...) serine; by host => ECO:0000269|PubMed:32363391
ChainResidueDetails
AILE326
BILE326
CILE326

site_idSWS_FT_FI9
Number of Residues3
DetailsCARBOHYD: N-linked (GlcNAc...) (hybrid) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
ChainResidueDetails
ATHR604
BTHR604
CTHR604

site_idSWS_FT_FI10
Number of Residues6
DetailsCARBOHYD: O-linked (GlcNAc...) threonine; by host GALNT1 => ECO:0000269|PubMed:34732583
ChainResidueDetails
AGLN677
ALYS679
BGLN677
BLYS679
CGLN677
CLYS679

site_idSWS_FT_FI11
Number of Residues3
DetailsCARBOHYD: N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
ChainResidueDetails
AASN1135
BASN1135
CASN1135

site_idSWS_FT_FI12
Number of Residues6
DetailsCARBOHYD: N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
ChainResidueDetails
AHIS1159
AALA1174
BHIS1159
BALA1174
CHIS1159
CALA1174

225946

PDB entries from 2024-10-09

PDB statisticsPDBj update infoContact PDBjnumon