9RPS | pdb_00009rps

Cryo-EM structure of Shigella flexneri LptDE in complex with RTP45 superinfection exclusion protein from RTP bacteriophage and endogenous LptM

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	OstA-like beta-folder	8053502	3002196	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	LptD-like barrel	8053497	3002195	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TolB N-terminal domain-like	8053486	3000482	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03968	LptA/(LptD N-terminal domain) LPS transport protein (LptD_N)	LptA/(LptD N-terminal domain) LPS transport protein	This family of proteins are involved in lipopolysaccharide transport across the gram negative inner and outer membranes. The type examples for this family are E. coli LptA Swiss:P0ADV1 and the N-terminal domain of LptD Swiss:P31554.	Domain
A	PF04453	LPS transport system D (LptD)	LPS transport system D	-	Family
D [auth C]	PF13627	LPS-assembly lipoprotein LptM, conserved region (LptM_cons)	LPS-assembly lipoprotein LptM, conserved region	-	Motif
B	PF04390	Lipopolysaccharide-assembly (LptE)	Lipopolysaccharide-assembly	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	LPS-assembly protein LptD	-	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 localization transport lipopolysaccharide transport 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 localization transport lipopolysaccharide transport macromolecule localization lipid localization lipid transport carbohydrate derivative transport establishment of localization	protein-containing complex transporter complex cell periphery cell outer membrane cellular anatomical structure external encapsulating structure membrane cell envelope outer membrane
D [auth C]	LPS-assembly lipoprotein LptM	-	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 cell outer membrane cellular anatomical structure external encapsulating structure membrane cell envelope outer membrane
C [auth D]	Phage lipoprotein	-	-	-
B	LPS-assembly lipoprotein LptE	binding lipid binding lipopolysaccharide binding carbohydrate derivative 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 localization transport lipopolysaccharide transport 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 localization transport lipopolysaccharide transport macromolecule localization lipid localization lipid transport carbohydrate derivative transport establishment of localization	protein-containing complex transporter complex cell periphery cell outer membrane cellular anatomical structure external encapsulating structure membrane cell envelope outer membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR007543	LptD, C-terminal	Domain
A	IPR020889	LPS-assembly protein LptD	Family
A	IPR050218	Lipopolysaccharide Assembly Protein LptD	Family
A	IPR005653	Organic solvent tolerance-like, N-terminal	Domain
D [auth C]	IPR032831	LPS-assembly lipoprotein LptM, conserved region	Conserved Site
C [auth D]	IPR057115	Phage lipoprotein	Family
B	IPR007485	LPS-assembly lipoprotein LptE	Family

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.