6S8N

Cryo-EM structure of LptB2FGC in complex with lipopolysaccharide

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6s8na_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Shigella flexneri ) [TaxId: 623 ],	SCOPe (2.08)
B	d6s8nb_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Shigella flexneri ) [TaxId: 623 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	ABC transporter-like P-loop ATPases	8098386	3002020	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ABC transporter-like P-loop ATPases	8098386	3002020	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)
A	ABC_tran	e6s8nA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ABC_tran	ECOD (1.6)
B	ABC_tran	e6s8nB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ABC_tran	ECOD (1.6)
D [auth F]	YjgP_YjgQ_1st	e6s8nF1	A: alpha bundles	X: Type II ABC exporter transmembrane domain fold	H: Type II ABC exporter transmembrane domain-related	T: ABCG5/ABCG8 transmembrane domain	F: YjgP_YjgQ_1st	ECOD (1.6)
E [auth G]	YjgP_YjgQ_1st	e6s8nG1	A: alpha bundles	X: Type II ABC exporter transmembrane domain fold	H: Type II ABC exporter transmembrane domain-related	T: ABCG5/ABCG8 transmembrane domain	F: YjgP_YjgQ_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF12399	Branched-chain amino acid ATP-binding cassette transporter (BCA_ABC_TP_C)	Branched-chain amino acid ATP-binding cassette transporter	This domain family is found in bacteria, archaea and eukaryotes, and is approximately 30 amino acids in length. The family is found in association with Pfam:PF00005. There is a conserved AYLG sequence motif. This family is the C terminal of an ATP de ...	This domain family is found in bacteria, archaea and eukaryotes, and is approximately 30 amino acids in length. The family is found in association with Pfam:PF00005. There is a conserved AYLG sequence motif. This family is the C terminal of an ATP dependent branched-chain amino acid transporter [1]. This domain is essential for LPS transport, through critical interactions with Walker A and switch helix domains [2].	Domain
A, B	PF00005	ABC transporter (ABC_tran)	ABC transporter	ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are comp ...	ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain Pfam:PF00664. These four domains may belong to a single polypeptide as in Swiss:P13569, or belong in different polypeptide chains.	Domain
C	PF06835	Lipopolysaccharide-assembly, LptC-related (LptC)	Lipopolysaccharide-assembly, LptC-related	-	Family
D [auth F]	PF03739	Lipopolysaccharide export system permease LptF/LptG (LptF_LptG)	Lipopolysaccharide export system permease LptF/LptG	-	Family
E [auth G]	PF03739	Lipopolysaccharide export system permease LptF/LptG (LptF_LptG)	Lipopolysaccharide export system permease LptF/LptG	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Lipopolysaccharide ABC transporter, ATP-binding protein LptB	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity	transmembrane transport localization transport cellular process establishment of localization	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex cellular anatomical entity transporter complex ATP-binding cassette (ABC) transporter complex cell periphery transmembrane transporter complex intracellular anatomical structure cytoplasm
C	Lipopolysaccharide export system protein LptC	carbohydrate derivative transmembrane transporter activity macromolecule transmembrane transporter activity lipid transporter activity lipopolysaccharide transmembrane transporter activity lipid transmembrane transporter activity transporter activity transmembrane transporter activity	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	cell periphery plasma membrane membrane cellular anatomical entity
D [auth F]	Lipopolysaccharide export system permease protein LptF	-	transmembrane transport localization transport cellular process establishment of localization lipopolysaccharide transport macromolecule localization lipid localization lipid transport carbohydrate derivative transport	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex cellular anatomical entity transporter complex ATP-binding cassette (ABC) transporter complex cell periphery transmembrane transporter complex
E [auth G]	Inner membrane protein yjgQ	-	transmembrane transport localization transport cellular process establishment of localization lipopolysaccharide transport macromolecule localization lipid localization lipid transport carbohydrate derivative transport	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex cellular anatomical entity transporter complex ATP-binding cassette (ABC) transporter complex cell periphery transmembrane transporter complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR051120	ABC Transporter, Amino Acid and LPS Transport	Family
A, B	IPR032823	Branched-chain amino acid ATP-binding cassette transporter, C-terminal	Domain
A, B	IPR003593	AAA+ ATPase domain	Domain
A, B	IPR017871	ABC transporter-like, conserved site	Conserved Site
A, B	IPR030921	LPS export ABC transporter, ATP-binding protein LptB	Family
A, B	IPR003439	ABC transporter-like, ATP-binding domain	Domain
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C	IPR010664	Lipopolysaccharide assembly, LptC-related	Family
C	IPR026265	Lipopolysaccharide export system protein LptC	Family
C	IPR052363	Lipopolysaccharide export system LptC	Family
D [auth F]	IPR005495	Permease LptG/LptF-related	Family
D [auth F]	IPR030922	LPS export ABC transporter permease LptF	Family
E [auth G]	IPR030923	LPS export ABC transporter permease LptG	Family
E [auth G]	IPR005495	Permease LptG/LptF-related	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D [auth F], E [auth G]	OPM	Transmembrane	Alpha-helical polytopic	ABC transporters	Branched-chain amino acid ABC transporter

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D [auth F], E [auth G]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D [auth F], E [auth G]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D [auth F], E [auth G]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	ATP Binding Cassette (ABC) Transporters	Lipopolysaccharide transporter complex LptB₂FGC in complex with lipopolysaccharide:

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.