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8ZC2

SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with D1F6 Fab, head-to-head aggregate

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
A0019065biological_processreceptor-mediated endocytosis of virus by host cell
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
B0019065biological_processreceptor-mediated endocytosis of virus by host cell
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
C0019065biological_processreceptor-mediated endocytosis of virus by host cell
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
D0005515molecular_functionprotein binding
D0005886cellular_componentplasma membrane
D0007165biological_processsignal transduction
D0016020cellular_componentmembrane
D0019031cellular_componentviral envelope
D0019062biological_processvirion attachment to host cell
D0019064biological_processfusion of virus membrane with host plasma membrane
D0019065biological_processreceptor-mediated endocytosis of virus by host cell
D0019081biological_processviral translation
D0020002cellular_componenthost cell plasma membrane
D0039587biological_processsuppression by virus of host tetherin activity
D0039654biological_processfusion of virus membrane with host endosome membrane
D0039660molecular_functionstructural constituent of virion
D0042802molecular_functionidentical protein binding
D0043655cellular_componenthost extracellular space
D0044173cellular_componenthost cell endoplasmic reticulum-Golgi intermediate compartment membrane
D0044228cellular_componenthost cell surface
D0046598biological_processpositive regulation of viral entry into host cell
D0046718biological_processsymbiont entry into host cell
D0046789molecular_functionhost cell surface receptor binding
D0046813biological_processreceptor-mediated virion attachment to host cell
D0048018molecular_functionreceptor ligand activity
D0052170biological_processsymbiont-mediated suppression of host innate immune response
D0055036cellular_componentvirion membrane
D0061025biological_processmembrane fusion
D0075509biological_processendocytosis involved in viral entry into host cell
D0098670biological_processentry receptor-mediated virion attachment to host cell
E0005515molecular_functionprotein binding
E0005886cellular_componentplasma membrane
E0007165biological_processsignal transduction
E0016020cellular_componentmembrane
E0019031cellular_componentviral envelope
E0019062biological_processvirion attachment to host cell
E0019064biological_processfusion of virus membrane with host plasma membrane
E0019065biological_processreceptor-mediated endocytosis of virus by host cell
E0019081biological_processviral translation
E0020002cellular_componenthost cell plasma membrane
E0039587biological_processsuppression by virus of host tetherin activity
E0039654biological_processfusion of virus membrane with host endosome membrane
E0039660molecular_functionstructural constituent of virion
E0042802molecular_functionidentical protein binding
E0043655cellular_componenthost extracellular space
E0044173cellular_componenthost cell endoplasmic reticulum-Golgi intermediate compartment membrane
E0044228cellular_componenthost cell surface
E0046598biological_processpositive regulation of viral entry into host cell
E0046718biological_processsymbiont entry into host cell
E0046789molecular_functionhost cell surface receptor binding
E0046813biological_processreceptor-mediated virion attachment to host cell
E0048018molecular_functionreceptor ligand activity
E0052170biological_processsymbiont-mediated suppression of host innate immune response
E0055036cellular_componentvirion membrane
E0061025biological_processmembrane fusion
E0075509biological_processendocytosis involved in viral entry into host cell
E0098670biological_processentry receptor-mediated virion attachment to host cell
F0005515molecular_functionprotein binding
F0005886cellular_componentplasma membrane
F0007165biological_processsignal transduction
F0016020cellular_componentmembrane
F0019031cellular_componentviral envelope
F0019062biological_processvirion attachment to host cell
F0019064biological_processfusion of virus membrane with host plasma membrane
F0019065biological_processreceptor-mediated endocytosis of virus by host cell
F0019081biological_processviral translation
F0020002cellular_componenthost cell plasma membrane
F0039587biological_processsuppression by virus of host tetherin activity
F0039654biological_processfusion of virus membrane with host endosome membrane
F0039660molecular_functionstructural constituent of virion
F0042802molecular_functionidentical protein binding
F0043655cellular_componenthost extracellular space
F0044173cellular_componenthost cell endoplasmic reticulum-Golgi intermediate compartment membrane
F0044228cellular_componenthost cell surface
F0046598biological_processpositive regulation of viral entry into host cell
F0046718biological_processsymbiont entry into host cell
F0046789molecular_functionhost cell surface receptor binding
F0046813biological_processreceptor-mediated virion attachment to host cell
F0048018molecular_functionreceptor ligand activity
F0052170biological_processsymbiont-mediated suppression of host innate immune response
F0055036cellular_componentvirion membrane
F0061025biological_processmembrane fusion
F0075509biological_processendocytosis involved in viral entry into host cell
F0098670biological_processentry receptor-mediated virion attachment to host cell
Functional Information from PROSITE/UniProt
site_idPS00290
Number of Residues7
DetailsIG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YICNVNH
ChainResidueDetails
HTYR208-HIS214
GTYR202-HIS208

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues6
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
AILE692
BILE692
CILE692
DILE692
EILE692
FILE692

site_idSWS_FT_FI2
Number of Residues6
DetailsSITE: Cleavage; by host TMPRSS2 or CTSL => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32703818, ECO:0000269|PubMed:34159616
ChainResidueDetails
ALEU822
BLEU822
CLEU822
DLEU822
ELEU822
FLEU822

site_idSWS_FT_FI3
Number of Residues18
DetailsCARBOHYD: N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
ChainResidueDetails
AASN20
DASN20
DASP1165
DGLN1180
EASN20
EASP1165
EGLN1180
FASN20
FASP1165
FGLN1180
AASP1165
AGLN1180
BASN20
BASP1165
BGLN1180
CASN20
CASP1165
CGLN1180

site_idSWS_FT_FI4
Number of Residues30
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
ATRP64
BILE1081
CTRP64
CASN125
CTHR724
CASP808
CILE1081
DTRP64
DASN125
DTHR724
DASP808
AASN125
DILE1081
ETRP64
EASN125
ETHR724
EASP808
EILE1081
FTRP64
FASN125
FTHR724
FASP808
ATHR724
FILE1081
AASP808
AILE1081
BTRP64
BASN125
BTHR724
BASP808

site_idSWS_FT_FI5
Number of Residues18
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
ALYS77
DLYS77
DTRP152
DGLN1201
ELYS77
ETRP152
EGLN1201
FLYS77
FTRP152
FGLN1201
ATRP152
AGLN1201
BLYS77
BTRP152
BGLN1201
CLYS77
CTRP152
CGLN1201

site_idSWS_FT_FI6
Number of Residues42
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
APHE168
BASN334
BARG346
BGLU619
BTYR660
BTHR1105
CPHE168
CILE285
CASN334
CARG346
CGLU619
AILE285
CTYR660
CTHR1105
DPHE168
DILE285
DASN334
DARG346
DGLU619
DTYR660
DTHR1105
EPHE168
AASN334
EILE285
EASN334
EARG346
EGLU619
ETYR660
ETHR1105
FPHE168
FILE285
FASN334
FARG346
AARG346
FGLU619
FTYR660
FTHR1105
AGLU619
ATYR660
ATHR1105
BPHE168
BILE285

site_idSWS_FT_FI7
Number of Residues12
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
AARG237
ETHR716
FARG237
FTHR716
ATHR716
BARG237
BTHR716
CARG237
CTHR716
DARG237
DTHR716
EARG237

site_idSWS_FT_FI8
Number of Residues6
DetailsCARBOHYD: O-linked (GalNAc) threonine; by host => ECO:0000269|PubMed:32363391
ChainResidueDetails
AILE326
BILE326
CILE326
DILE326
EILE326
FILE326

site_idSWS_FT_FI9
Number of Residues6
DetailsCARBOHYD: O-linked (HexNAc...) serine; by host => ECO:0000269|PubMed:32363391
ChainResidueDetails
AARG328
BARG328
CARG328
DARG328
EARG328
FARG328

site_idSWS_FT_FI10
Number of Residues6
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
AASN606
BASN606
CASN606
DASN606
EASN606
FASN606

site_idSWS_FT_FI11
Number of Residues12
DetailsCARBOHYD: O-linked (GlcNAc...) threonine; by host GALNT1 => ECO:0000269|PubMed:34732583
ChainResidueDetails
ALYS683
EARG685
FLYS683
FARG685
AARG685
BLYS683
BARG685
CLYS683
CARG685
DLYS683
DARG685
ELYS683

site_idSWS_FT_FI12
Number of Residues6
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
ALEU1141
BLEU1141
CLEU1141
DLEU1141
ELEU1141
FLEU1141

223166

PDB entries from 2024-07-31

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