3NB3 | pdb_00003nb3

The host outer membrane proteins OmpA and OmpC are packed at specific sites in the Shigella phage Sf6 virion as structural components

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Porins	8071276	3000224	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D		e3nb3D1	A: a/b three-layered sandwiches	X: N-terminal beta-sandwich domain in anthrax protective antigen	H: L30e-like	T: L30e-like	F:	ECOD (v294.1)
C	AAA	e3nb3C1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (v294.1)
B	AAA	e3nb3B1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: AAA	ECOD (v294.1)
A		e3nb3A1	A: a/b three-layered sandwiches	X: N-terminal beta-sandwich domain in anthrax protective antigen	H: L30e-like	T: L30e-like	F:	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	PF00267	Gram-negative porin (Porin_1)	Gram-negative porin		Domain
A, B, C	PF01389	OmpA-like transmembrane domain (OmpA_membrane)	OmpA-like transmembrane domain	The structure of OmpA transmembrane domain shows that it consists of an eight stranded beta barrel [1]. This family includes some other distantly related outer membrane proteins with low scores.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	Outer membrane protein C	protein binding binding virus receptor activity exogenous protein binding wide pore channel activity passive transmembrane transporter activity channel activity porin activity transporter activity transmembrane transporter activity cation binding ion binding metal ion binding small molecule binding protein binding binding virus receptor activity exogenous protein binding wide pore channel activity passive transmembrane transporter activity channel activity porin activity transporter activity transmembrane transporter activity cation binding ion binding metal ion binding small molecule binding identical protein binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell viral process viral life cycle adhesion of symbiont to host biological process involved in interaction with host cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell viral process viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction transmembrane transport localization transport monoatomic ion transmembrane transport monoatomic ion transport establishment of localization membrane organization intermembrane lipid transfer lipid localization phospholipid transport lipid transport cellular component organization intermembrane phospholipid transfer macromolecule localization cellular component organization or biogenesis organophosphate ester transport	protein-containing complex cellular anatomical structure membrane pore complex membrane protein complex cell outer membrane external encapsulating structure extracellular region cell envelope outer membrane
A, B, C	Outer membrane protein A	wide pore channel activity passive transmembrane transporter activity channel activity porin activity transporter activity transmembrane transporter activity monoatomic ion transmembrane transporter activity identical protein binding protein binding binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process localization transport monoatomic ion transport establishment of localization biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process localization transport monoatomic ion transport establishment of localization biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction response to other organism detection of virus response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus	cellular anatomical structure membrane outer membrane protein-containing complex outer membrane protein complex membrane protein complex extracellular region outer membrane-bounded periplasmic space cell envelope periplasmic space pore complex cell outer membrane external encapsulating structure

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D	IPR050298	Gram-negative bacterial outer membrane porin	Family
D	IPR001897	Porin, gammaproteobacterial	Family
D	IPR023614	Porin domain superfamily	Homologous Superfamily
D	IPR001702	Porin, Gram-negative type	Family
D	IPR013793	Porin, Gram-negative type, conserved site	Conserved Site
A, B, C	IPR006664	Outer membrane protein, bacterial	Domain
A, B, C	IPR000498	Outer membrane protein OmpA-like, transmembrane domain	Domain
A, B, C	IPR006690	Outer membrane protein, OmpA-like, conserved site	Conserved Site
A, B, C	IPR050330	Bacterial Outer Membrane Structural/Functional	Family
A, B, C	IPR036737	OmpA-like domain superfamily	Homologous Superfamily
A, B, C	IPR011250	Outer membrane protein/outer membrane enzyme PagP, beta-barrel	Homologous Superfamily
A, B, C	IPR006665	OmpA-like domain	Domain
A, B, C	IPR002368	Outer membrane protein, OmpA	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D	PDBTM	Annotated as membrane protein by PDBTM

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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