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 9RQI | pdb_00009rqi

Cryo-EM structure of Shigella flexneri LptDE bound by phage RBP reveals N-terminal strand insertion into lateral gate


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
BSCOP2B SuperfamilyTolB N-terminal domain-like 8053486 3000482 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyLptD-like barrel 8053497 3002195 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
BRVT_1e9rqiB1 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF: RVT_1ECOD (v295.2)
ARNA_pol_Rpb1_5e9rqiA1 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF: RNA_pol_Rpb1_5ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF04390Lipopolysaccharide-assembly (LptE)Lipopolysaccharide-assembly- Family
PF04453LPS transport system D, C-terminal domain (LptD)LPS transport system D, C-terminal domainLipopolysaccharide (LPS) is essential for most Gram-negative bacteria and has crucial roles in protection of the bacteria from harsh environments and toxic compounds, including antibiotics. This entry includes members such as LPTD found in Shigella f ...Lipopolysaccharide (LPS) is essential for most Gram-negative bacteria and has crucial roles in protection of the bacteria from harsh environments and toxic compounds, including antibiotics. This entry includes members such as LPTD found in Shigella flexneri and Yersinia pestis. Structural analysis indicates that LptD forms a novel 26-stranded beta-barrel. It interacts with LPTE where LptE adopts a roll-like structure located inside the barrel of LptD. The LPS translocon LptD is unable to fold properly in the absence of LptE and the two proteins form a unique barrel and plug architecture for LPS transport and insertion [1,2]. LptD is an essential outer membrane protein that mediates the final transport of lipopolysaccharide (LPS) to outer leaflet. It has been suggested that LptD is a promising target for the development of effective vaccines and antibody-based therapies to control Vibrio infection [3]. This entry represents the C-terminal beta-barrel domain embedded in the outer membrane [4].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Tail fiber protein- - -
LPS-assembly lipoprotein LptE
LPS-assembly protein LptD-