1D3I

CRYO-EM STRUCTURE OF HUMAN RHINOVIRUS 14 (HRV14) COMPLEXED WITH A TWO-DOMAIN FRAGMENT OF ITS CELLULAR RECEPTOR, INTERCELLULAR ADHESION MOLECULE-1 (D1D2-ICAM-1). IMPLICATIONS FOR VIRUS-RECEPTOR INTERACTIONS. ALPHA CARBONS ONLY


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
A [auth I]SCOP2B SuperfamilyImmunoglobulin (Ig) domain-like 8054755 3000071 SCOP2B (2022-06-29)
A [auth I]SCOP2B SuperfamilyImmunoglobulin (Ig) domain-like 8054735 3000071 SCOP2B (2022-06-29)
D [auth 3]SCOP2B SuperfamilyPositive stranded ssRNA viruses-like 8036766 3000918 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A [auth I]ICAM_Ne1d3iI2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: ICAM_NECOD (1.6)
A [auth I]C1-sete1d3iI1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: C1-setECOD (1.6)
B [auth 1]Rhv_5e1d3i11 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: Rhv_5ECOD (1.6)
C [auth 2]Rhv_1e1d3i21 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: Rhv_1ECOD (1.6)
D [auth 3]Rhv_3e1d3i33 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: Rhv_3ECOD (1.6)
E [auth 4]Pico_P1A_Ne1d3i41 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: Pico_P1A_NECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth I]PF03921Intercellular adhesion molecule (ICAM), N-terminal domain (ICAM_N)Intercellular adhesion molecule (ICAM), N-terminal domainICAMs normally functions to promote intercellular adhesion and signalling. However, The N-terminal domain of the receptor binds to the rhinovirus 'canyon' surrounding the icosahedral 5-fold axes, during the viral attachment process [1]. This famil ...ICAMs normally functions to promote intercellular adhesion and signalling. However, The N-terminal domain of the receptor binds to the rhinovirus 'canyon' surrounding the icosahedral 5-fold axes, during the viral attachment process [1]. This family is a family that is part of the Ig superfamily and is therefore related to the family ig (Pfam:PF00047).
Domain
B [auth 1]PF00073picornavirus capsid protein (Rhv)picornavirus capsid proteinCAUTION: This alignment is very weak. It can not be generated by clustalw. If a representative set is used for a seed, many so-called members are not recognised. The family should probably be split up into sub-families. Capsid proteins of picornavi ...CAUTION: This alignment is very weak. It can not be generated by clustalw. If a representative set is used for a seed, many so-called members are not recognised. The family should probably be split up into sub-families. Capsid proteins of picornaviruses. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids. They include rhinovirus (common cold) and poliovirus. Common structure is an 8-stranded beta sandwich. Variations (one or two extra strands) occur.
Domain
C [auth 2]PF00073picornavirus capsid protein (Rhv)picornavirus capsid proteinCAUTION: This alignment is very weak. It can not be generated by clustalw. If a representative set is used for a seed, many so-called members are not recognised. The family should probably be split up into sub-families. Capsid proteins of picornavi ...CAUTION: This alignment is very weak. It can not be generated by clustalw. If a representative set is used for a seed, many so-called members are not recognised. The family should probably be split up into sub-families. Capsid proteins of picornaviruses. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids. They include rhinovirus (common cold) and poliovirus. Common structure is an 8-stranded beta sandwich. Variations (one or two extra strands) occur.
Domain
D [auth 3]PF00073picornavirus capsid protein (Rhv)picornavirus capsid proteinCAUTION: This alignment is very weak. It can not be generated by clustalw. If a representative set is used for a seed, many so-called members are not recognised. The family should probably be split up into sub-families. Capsid proteins of picornavi ...CAUTION: This alignment is very weak. It can not be generated by clustalw. If a representative set is used for a seed, many so-called members are not recognised. The family should probably be split up into sub-families. Capsid proteins of picornaviruses. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids. They include rhinovirus (common cold) and poliovirus. Common structure is an 8-stranded beta sandwich. Variations (one or two extra strands) occur.
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth I]PROTEIN (INTERCELLULAR ADHESION MOLECULE-1)
B [auth 1]PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP1)
C [auth 2]PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP2)
D [auth 3]PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP3)
E [auth 4]PROTEIN (RHINOVIRUS 14 COAT PROTEIN VP4)

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A [auth I]IPR036179Immunoglobulin-like domain superfamilyHomologous Superfamily
A [auth I]IPR048679Intercellular adhesion molecule 1/3/5, D2 domainDomain
A [auth I]IPR003599Immunoglobulin domain subtypeDomain
A [auth I]IPR047012Intercellular adhesion molecule/vascular cell adhesion moleculeFamily
A [auth I]IPR003988Intercellular adhesion moleculeDomain
A [auth I]IPR003987Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminalDomain
A [auth I]IPR013783Immunoglobulin-like foldHomologous Superfamily
A [auth I]IPR013768Intercellular adhesion molecule, N-terminalDomain
B [auth 1]IPR001205RNA-directed RNA polymerase, C-terminal domainDomain
B [auth 1]IPR002527Picornavirus 2B proteinDomain
B [auth 1]IPR043128Reverse transcriptase/Diguanylate cyclase domainHomologous Superfamily
B [auth 1]IPR036988Picornavirus coat protein VP4 superfamilyHomologous Superfamily
B [auth 1]IPR003593AAA+ ATPase domainDomain
B [auth 1]IPR003138Picornavirus coat protein VP4Family
B [auth 1]IPR000199Peptidase C3A/C3B, picornaviralDomain
B [auth 1]IPR001676Picornavirus capsidDomain
B [auth 1]IPR014759Helicase, superfamily 3, single-stranded RNA virusDomain
B [auth 1]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
B [auth 1]IPR000081Peptidase C3, picornavirus core protein 2ADomain
B [auth 1]IPR029053Viral coat protein subunitHomologous Superfamily
B [auth 1]IPR009003Peptidase S1, PA clanHomologous Superfamily
B [auth 1]IPR043502DNA/RNA polymerase superfamilyHomologous Superfamily
B [auth 1]IPR044067Picornavirales 3C/3C-like protease domainDomain
B [auth 1]IPR033703Picornavirus/Calicivirus coat proteinDomain
B [auth 1]IPR014838Poliovirus 3A protein-likeDomain
B [auth 1]IPR036203Poliovirus core protein 3a, soluble domainHomologous Superfamily
B [auth 1]IPR043504Peptidase S1, PA clan, chymotrypsin-like foldHomologous Superfamily
B [auth 1]IPR007094RNA-directed RNA polymerase, catalytic domainDomain
B [auth 1]IPR000605Helicase, superfamily 3, single-stranded DNA/RNA virusDomain
C [auth 2]IPR001205RNA-directed RNA polymerase, C-terminal domainDomain
C [auth 2]IPR002527Picornavirus 2B proteinDomain
C [auth 2]IPR043128Reverse transcriptase/Diguanylate cyclase domainHomologous Superfamily
C [auth 2]IPR036988Picornavirus coat protein VP4 superfamilyHomologous Superfamily
C [auth 2]IPR003593AAA+ ATPase domainDomain
C [auth 2]IPR003138Picornavirus coat protein VP4Family
C [auth 2]IPR000199Peptidase C3A/C3B, picornaviralDomain
C [auth 2]IPR001676Picornavirus capsidDomain
C [auth 2]IPR014759Helicase, superfamily 3, single-stranded RNA virusDomain
C [auth 2]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
C [auth 2]IPR000081Peptidase C3, picornavirus core protein 2ADomain
C [auth 2]IPR029053Viral coat protein subunitHomologous Superfamily
C [auth 2]IPR009003Peptidase S1, PA clanHomologous Superfamily
C [auth 2]IPR043502DNA/RNA polymerase superfamilyHomologous Superfamily
C [auth 2]IPR044067Picornavirales 3C/3C-like protease domainDomain
C [auth 2]IPR033703Picornavirus/Calicivirus coat proteinDomain
C [auth 2]IPR014838Poliovirus 3A protein-likeDomain
C [auth 2]IPR036203Poliovirus core protein 3a, soluble domainHomologous Superfamily
C [auth 2]IPR043504Peptidase S1, PA clan, chymotrypsin-like foldHomologous Superfamily
C [auth 2]IPR007094RNA-directed RNA polymerase, catalytic domainDomain
C [auth 2]IPR000605Helicase, superfamily 3, single-stranded DNA/RNA virusDomain
D [auth 3]IPR001205RNA-directed RNA polymerase, C-terminal domainDomain
D [auth 3]IPR002527Picornavirus 2B proteinDomain
D [auth 3]IPR043128Reverse transcriptase/Diguanylate cyclase domainHomologous Superfamily
D [auth 3]IPR036988Picornavirus coat protein VP4 superfamilyHomologous Superfamily
D [auth 3]IPR003593AAA+ ATPase domainDomain
D [auth 3]IPR003138Picornavirus coat protein VP4Family
D [auth 3]IPR000199Peptidase C3A/C3B, picornaviralDomain
D [auth 3]IPR001676Picornavirus capsidDomain
D [auth 3]IPR014759Helicase, superfamily 3, single-stranded RNA virusDomain
D [auth 3]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
D [auth 3]IPR000081Peptidase C3, picornavirus core protein 2ADomain
D [auth 3]IPR029053Viral coat protein subunitHomologous Superfamily
D [auth 3]IPR009003Peptidase S1, PA clanHomologous Superfamily
D [auth 3]IPR043502DNA/RNA polymerase superfamilyHomologous Superfamily
D [auth 3]IPR044067Picornavirales 3C/3C-like protease domainDomain
D [auth 3]IPR033703Picornavirus/Calicivirus coat proteinDomain
D [auth 3]IPR014838Poliovirus 3A protein-likeDomain
D [auth 3]IPR036203Poliovirus core protein 3a, soluble domainHomologous Superfamily
D [auth 3]IPR043504Peptidase S1, PA clan, chymotrypsin-like foldHomologous Superfamily
D [auth 3]IPR007094RNA-directed RNA polymerase, catalytic domainDomain
D [auth 3]IPR000605Helicase, superfamily 3, single-stranded DNA/RNA virusDomain
E [auth 4]IPR001205RNA-directed RNA polymerase, C-terminal domainDomain
E [auth 4]IPR002527Picornavirus 2B proteinDomain
E [auth 4]IPR043128Reverse transcriptase/Diguanylate cyclase domainHomologous Superfamily
E [auth 4]IPR036988Picornavirus coat protein VP4 superfamilyHomologous Superfamily
E [auth 4]IPR003593AAA+ ATPase domainDomain
E [auth 4]IPR003138Picornavirus coat protein VP4Family
E [auth 4]IPR000199Peptidase C3A/C3B, picornaviralDomain
E [auth 4]IPR001676Picornavirus capsidDomain
E [auth 4]IPR014759Helicase, superfamily 3, single-stranded RNA virusDomain
E [auth 4]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
E [auth 4]IPR000081Peptidase C3, picornavirus core protein 2ADomain
E [auth 4]IPR029053Viral coat protein subunitHomologous Superfamily
E [auth 4]IPR009003Peptidase S1, PA clanHomologous Superfamily
E [auth 4]IPR043502DNA/RNA polymerase superfamilyHomologous Superfamily
E [auth 4]IPR044067Picornavirales 3C/3C-like protease domainDomain
E [auth 4]IPR033703Picornavirus/Calicivirus coat proteinDomain
E [auth 4]IPR014838Poliovirus 3A protein-likeDomain
E [auth 4]IPR036203Poliovirus core protein 3a, soluble domainHomologous Superfamily
E [auth 4]IPR043504Peptidase S1, PA clan, chymotrypsin-like foldHomologous Superfamily
E [auth 4]IPR007094RNA-directed RNA polymerase, catalytic domainDomain
E [auth 4]IPR000605Helicase, superfamily 3, single-stranded DNA/RNA virusDomain

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
A [auth I]PharosP05362