Annotations: 9CO0

CryoEM structure of BAM in complex with the PTB2 open-state inhibitor (in SMA nanodisc)

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
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	BLIP repeat-like	8092082	3000321	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TPR-like	8058058	3001345	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	POTRA domain-like	8052274	3002100	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Porins	8052233	3000224	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	POTRA domain-like	8052273	3002100	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	POTRA domain-like	8052275	3002100	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)
E	WD40	e9co0E1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
D	WD40	e9co0D1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
C	WD40	e9co0C1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
B	WD40	e9co0B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
A	WD40	e9co0A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E	PF04355	Outer membrane protein assembly factor BamE domain (BamE)	Outer membrane protein assembly factor BamE domain	This domain is found in bacterial outer membrane lipoproteins probably involved in maintaining the structural integrity of the cell envelope [1], including Outer membrane protein assembly factor BamE from Vibrio cholerae (also known as SmpA). The lip ...	This domain is found in bacterial outer membrane lipoproteins probably involved in maintaining the structural integrity of the cell envelope [1], including Outer membrane protein assembly factor BamE from Vibrio cholerae (also known as SmpA). The lipid attachment site is a conserved N terminal cysteine residue. Sometimes found adjacent to the OmpA domain (Pfam:PF00691).	Domain
C	PF06804	Outer membrane protein assembly factor BamC-like C-terminal domain (BamC_C)	Outer membrane protein assembly factor BamC-like C-terminal domain	This entry represents the C-terminal domain of BamC and related sequences. BamC is part of the outer membrane protein assembly Bam complex (composed of the outer membrane protein BamA, and four lipoproteins BamB, BamC, BamD and BamE), which is involv ...	This entry represents the C-terminal domain of BamC and related sequences. BamC is part of the outer membrane protein assembly Bam complex (composed of the outer membrane protein BamA, and four lipoproteins BamB, BamC, BamD and BamE), which is involved in assembly and insertion of beta-barrel proteins into the outer membrane [1-5]. E. coli BamC is a nonessential member of the Bam complex that stabilises the interaction between the essential proteins BamA and BamD [6]. This entry also includes NMB0928 from Neisseria meningitidis whose function is unknown.	Domain
B	PF13360	Outer membrane protein assembly factor BamB (PQQ_2)	Outer membrane protein assembly factor BamB	-	Repeat
A	PF07244	Surface antigen variable number repeat (POTRA)	Surface antigen variable number repeat	This family is found primarily in bacterial surface antigens, normally as variable number repeats at the N-terminus. The C-terminus of these proteins is normally represented by Pfam:PF01103. The alignment centres on a -GY- or -GF- motif. Some members ...	This family is found primarily in bacterial surface antigens, normally as variable number repeats at the N-terminus. The C-terminus of these proteins is normally represented by Pfam:PF01103. The alignment centres on a -GY- or -GF- motif. Some members of this family are found in the mitochondria. It is predicted to have a mixed alpha/beta secondary structure.	Domain
A	PF01103	Omp85 superfamily domain (Omp85)	Omp85 superfamily domain	The Omp85 protein superfamily contains bacterial outer membrane proteins, which can function as protein translocases or as membrane protein assembly factors [1]. The family includes the membrane bound beta barrel of proteins such as BamA and TamA fro ...	The Omp85 protein superfamily contains bacterial outer membrane proteins, which can function as protein translocases or as membrane protein assembly factors [1]. The family includes the membrane bound beta barrel of proteins such as BamA and TamA from E. coli.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F, G, H [auth I]	PTB2 circular peptide	-	-	-
E	Outer membrane protein assembly factor BamE	protein-macromolecule adaptor activity molecular adaptor activity identical protein binding protein binding binding	membrane organization membrane biogenesis membrane assembly cellular component organization cellular component biogenesis cellular component assembly cellular process cellular component organization or biogenesis cell envelope organization Gram-negative-bacterium-type cell outer membrane assembly external encapsulating structure organization establishment of protein localization cellular localization establishment of protein localization to membrane membrane organization membrane biogenesis membrane assembly cellular component organization cellular component biogenesis cellular component assembly cellular process cellular component organization or biogenesis cell envelope organization Gram-negative-bacterium-type cell outer membrane assembly external encapsulating structure organization establishment of protein localization cellular localization establishment of protein localization to membrane localization within membrane establishment of localization localization macromolecule localization intracellular protein localization protein insertion into membrane response to stimulus response to chemical response to antibiotic	cellular anatomical structure membrane protein-containing complex extracellular region periplasmic side of cell outer membrane membrane protein complex side of membrane Bam protein complex cell outer membrane external encapsulating structure cell envelope extracellular protein-containing complex outer membrane
D	Outer membrane protein assembly factor BamD	-	membrane organization membrane biogenesis membrane assembly cellular component organization cellular component biogenesis cellular component assembly cellular process cellular component organization or biogenesis cell envelope organization Gram-negative-bacterium-type cell outer membrane assembly external encapsulating structure organization establishment of protein localization cellular localization establishment of protein localization to membrane membrane organization membrane biogenesis membrane assembly cellular component organization cellular component biogenesis cellular component assembly cellular process cellular component organization or biogenesis cell envelope organization Gram-negative-bacterium-type cell outer membrane assembly external encapsulating structure organization establishment of protein localization cellular localization establishment of protein localization to membrane localization within membrane establishment of localization localization macromolecule localization intracellular protein localization protein insertion into membrane	cellular anatomical structure membrane cell outer membrane external encapsulating structure extracellular region cell envelope outer membrane protein-containing complex periplasmic side of cell outer membrane membrane protein complex side of membrane Bam protein complex extracellular protein-containing complex
C	Outer membrane protein assembly factor BamC	identical protein binding protein binding binding	membrane organization membrane biogenesis membrane assembly cellular component organization cellular component biogenesis cellular component assembly cellular process cellular component organization or biogenesis cell envelope organization Gram-negative-bacterium-type cell outer membrane assembly external encapsulating structure organization establishment of protein localization cellular localization establishment of protein localization to membrane membrane organization membrane biogenesis membrane assembly cellular component organization cellular component biogenesis cellular component assembly cellular process cellular component organization or biogenesis cell envelope organization Gram-negative-bacterium-type cell outer membrane assembly external encapsulating structure organization establishment of protein localization cellular localization establishment of protein localization to membrane localization within membrane establishment of localization localization macromolecule localization intracellular protein localization protein insertion into membrane	cell surface cellular anatomical structure membrane protein-containing complex extracellular region periplasmic side of cell outer membrane membrane protein complex side of membrane Bam protein complex cell outer membrane external encapsulating structure cell envelope extracellular protein-containing complex outer membrane
B	Outer membrane protein assembly factor BamB	identical protein binding protein binding binding	membrane organization membrane biogenesis membrane assembly cellular component organization cellular component biogenesis cellular component assembly cellular process cellular component organization or biogenesis cell envelope organization Gram-negative-bacterium-type cell outer membrane assembly external encapsulating structure organization establishment of protein localization cellular localization establishment of protein localization to membrane membrane organization membrane biogenesis membrane assembly cellular component organization cellular component biogenesis cellular component assembly cellular process cellular component organization or biogenesis cell envelope organization Gram-negative-bacterium-type cell outer membrane assembly external encapsulating structure organization establishment of protein localization cellular localization establishment of protein localization to membrane localization within membrane establishment of localization localization macromolecule localization intracellular protein localization protein insertion into membrane	cellular anatomical structure membrane cell outer membrane external encapsulating structure extracellular region cell envelope outer membrane protein-containing complex periplasmic side of cell outer membrane membrane protein complex side of membrane Bam protein complex extracellular protein-containing complex
A	Outer membrane protein assembly factor BamA	protein binding binding protein-folding chaperone binding	membrane organization membrane biogenesis membrane assembly cellular component organization cellular component biogenesis cellular component assembly cellular process cellular component organization or biogenesis cell envelope organization Gram-negative-bacterium-type cell outer membrane assembly external encapsulating structure organization establishment of protein localization cellular localization establishment of protein localization to membrane membrane organization membrane biogenesis membrane assembly cellular component organization cellular component biogenesis cellular component assembly cellular process cellular component organization or biogenesis cell envelope organization Gram-negative-bacterium-type cell outer membrane assembly external encapsulating structure organization establishment of protein localization cellular localization establishment of protein localization to membrane localization within membrane establishment of localization localization macromolecule localization intracellular protein localization protein insertion into membrane cell adhesion	cellular anatomical structure membrane cell outer membrane external encapsulating structure extracellular region cell envelope outer membrane protein-containing complex periplasmic side of cell outer membrane membrane protein complex side of membrane Bam protein complex extracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E	IPR037873	BamE-like	Homologous Superfamily
E	IPR007450	Outer membrane protein assembly factor BamE domain	Domain
E	IPR026592	Outer membrane protein assembly factor BamE	Family
D	IPR039565	Outer membrane lipoprotein BamD-like	Domain
D	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
D	IPR017689	Outer membrane protein assembly factor BamD	Family
C	IPR010653	Outer membrane protein assembly factor BamC-like	Domain
C	IPR042268	Outer membrane protein assembly factor BamC, C-terminal	Homologous Superfamily
C	IPR014524	Outer membrane protein assembly factor BamC	Family
B	IPR018391	Pyrrolo-quinoline quinone beta-propeller repeat	Repeat
B	IPR011047	Quinoprotein alcohol dehydrogenase-like superfamily	Homologous Superfamily
B	IPR017687	Outer membrane protein assembly factor BamB	Family
B	IPR002372	Pyrrolo-quinoline quinone repeat domain	Domain
B	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A	IPR039910	Surface antigen D15-like	Family
A	IPR000184	Outer membrane protein assembly factor BamA-like	Domain
A	IPR034746	POTRA domain	Domain
A	IPR010827	POTRA domain, BamA/TamA-like	Domain
A	IPR023707	Outer membrane protein assembly factor BamA	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D, E	mpstruc	TRANSMEMBRANE PROTEINS: BETA-BARREL	Omp85-TpsB Outer Membrane Transporter Superfamily	BamABCDE complex, apo state in DDM detergent

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
F, G, H [auth I]	ACY	: AA0441 : (2-aminosuccinimidyl)acetic acid (Asp) MOD:00952 , (2-aminosuccinimidyl)acetic acid (Asn) MOD:01624
F, G, H [auth I]	NH2	: AA0441 , AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 : (2-aminosuccinimidyl)acetic acid (Asp) MOD:00952 , (2-aminosuccinimidyl)acetic acid (Asn) MOD:01624 , L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109

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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.