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8ZC6

SARS-CoV-2 Omicron BA.4 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
AALA694
BALA694
CALA694
DALA694
EALA694
FALA694

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
AASN824
BASN824
CASN824
DASN824
EASN824
FASN824

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
DGLY1167
DGLU1182
EASN20
EGLY1167
EGLU1182
FASN20
FGLY1167
FGLU1182
AGLY1167
AGLU1182
BASN20
BGLY1167
BGLU1182
CASN20
CGLY1167
CGLU1182

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
BHIS1083
CTRP64
CVAL127
CILE726
CSER810
CHIS1083
DTRP64
DVAL127
DILE726
DSER810
AVAL127
DHIS1083
ETRP64
EVAL127
EILE726
ESER810
EHIS1083
FTRP64
FVAL127
FILE726
FSER810
AILE726
FHIS1083
ASER810
AHIS1083
BTRP64
BVAL127
BILE726
BSER810

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
APHE79
DPHE79
DGLU154
DLEU1203
EPHE79
EGLU154
ELEU1203
FPHE79
FGLU154
FLEU1203
AGLU154
ALEU1203
BPHE79
BGLU154
BLEU1203
CPHE79
CGLU154
CLEU1203

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
ATYR170
BCYS336
BALA348
BPRO621
BCYS662
BARG1107
CTYR170
CASP287
CCYS336
CALA348
CPRO621
AASP287
CCYS662
CARG1107
DTYR170
DASP287
DCYS336
DALA348
DPRO621
DCYS662
DARG1107
ETYR170
ACYS336
EASP287
ECYS336
EALA348
EPRO621
ECYS662
EARG1107
FTYR170
FASP287
FCYS336
FALA348
AALA348
FPRO621
FCYS662
FARG1107
APRO621
ACYS662
AARG1107
BTYR170
BASP287

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
AGLN239
EPHE718
FGLN239
FPHE718
APHE718
BGLN239
BPHE718
CGLN239
CPHE718
DGLN239
DPHE718
EGLN239

site_idSWS_FT_FI8
Number of Residues6
DetailsCARBOHYD: O-linked (GalNAc) threonine; by host => ECO:0000269|PubMed:32363391
ChainResidueDetails
AARG328
BARG328
CARG328
DARG328
EARG328
FARG328

site_idSWS_FT_FI9
Number of Residues6
DetailsCARBOHYD: O-linked (HexNAc...) serine; by host => ECO:0000269|PubMed:32363391
ChainResidueDetails
APRO330
BPRO330
CPRO330
DPRO330
EPRO330
FPRO330

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
AVAL608
BVAL608
CVAL608
DVAL608
EVAL608
FVAL608

site_idSWS_FT_FI11
Number of Residues12
DetailsCARBOHYD: O-linked (GlcNAc...) threonine; by host GALNT1 => ECO:0000269|PubMed:34732583
ChainResidueDetails
AARG685
EVAL687
FARG685
FVAL687
AVAL687
BARG685
BVAL687
CARG685
CVAL687
DARG685
DVAL687
EARG685

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
APRO1143
BPRO1143
CPRO1143
DPRO1143
EPRO1143
FPRO1143

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PDB entries from 2024-07-24

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