[English] 日本語
Yorodumi
- PDB-6s8n: Cryo-EM structure of LptB2FGC in complex with lipopolysaccharide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s8n
TitleCryo-EM structure of LptB2FGC in complex with lipopolysaccharide
Components
  • (Lipopolysaccharide export system ...) x 2
  • Inner membrane protein yjgQ
  • Lipopolysaccharide ABC transporter, ATP-binding protein LptB
KeywordsTRANSPORT PROTEIN / lipopolysaccharide transporter / LPS / LptB2FGC / LptB / LptBFG / outer membrane / Gram-negative bacteria / ABC transporter / Inner membrane protein complex
Function / homology
Function and homology information


lipopolysaccharide transmembrane transporter activity / Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / plasma membrane => GO:0005886 / ATP-binding cassette (ABC) transporter complex / transmembrane transport / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Lipopolysaccharide assembly, LptC-related / Lipopolysaccharide export system protein LptC / Lipopolysaccharide-assembly, LptC-related / Permease LptG/LptF-related / LPS export ABC transporter permease LptF / LPS export ABC transporter permease LptG / Lipopolysaccharide export system permease LptF/LptG / Branched-chain amino acid ATP-binding cassette transporter, C-terminal / Branched-chain amino acid ATP-binding cassette transporter / LPS export ABC transporter, ATP-binding protein LptB ...Lipopolysaccharide assembly, LptC-related / Lipopolysaccharide export system protein LptC / Lipopolysaccharide-assembly, LptC-related / Permease LptG/LptF-related / LPS export ABC transporter permease LptF / LPS export ABC transporter permease LptG / Lipopolysaccharide export system permease LptF/LptG / Branched-chain amino acid ATP-binding cassette transporter, C-terminal / Branched-chain amino acid ATP-binding cassette transporter / LPS export ABC transporter, ATP-binding protein LptB / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-DCQ / lipopolysaccharide fragment / LPS export ABC transporter permease LptG / Inner membrane protein yjgQ / Lipopolysaccharide export system protein LptC / Lipopolysaccharide export system ATP-binding protein LptB / Lipopolysaccharide export system ATP-binding protein LptB / Lipopolysaccharide export system protein LptC / Lipopolysaccharide export system permease protein LptF
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsTang, X.D. / Chang, S.H. / Luo, Q.H. / Zhang, Z.Y. / Qiao, W. / Xu, C.H. / Zhang, C.B. / Niu, Y. / Yang, W.X. / Wang, T. ...Tang, X.D. / Chang, S.H. / Luo, Q.H. / Zhang, Z.Y. / Qiao, W. / Xu, C.H. / Zhang, C.B. / Niu, Y. / Yang, W.X. / Wang, T. / Zhang, Z.B. / Zhu, X.F. / Dong, C.J. / Zhang, X. / Dong, H.H.
Citation
Journal: Nat Commun / Year: 2019
Title: Cryo-EM structures of lipopolysaccharide transporter LptBFGC in lipopolysaccharide or AMP-PNP-bound states reveal its transport mechanism.
Authors: Xiaodi Tang / Shenghai Chang / Qinghua Luo / Zhengyu Zhang / Wen Qiao / Caihuang Xu / Changbin Zhang / Yang Niu / Wenxian Yang / Ting Wang / Zhibo Zhang / Xiaofeng Zhu / Xiawei Wei / ...Authors: Xiaodi Tang / Shenghai Chang / Qinghua Luo / Zhengyu Zhang / Wen Qiao / Caihuang Xu / Changbin Zhang / Yang Niu / Wenxian Yang / Ting Wang / Zhibo Zhang / Xiaofeng Zhu / Xiawei Wei / Changjiang Dong / Xing Zhang / Haohao Dong /
Abstract: Lipopolysaccharides (LPS) of Gram-negative bacteria are critical for the defence against cytotoxic substances and must be transported from the inner membrane (IM) to the outer membrane (OM) through ...Lipopolysaccharides (LPS) of Gram-negative bacteria are critical for the defence against cytotoxic substances and must be transported from the inner membrane (IM) to the outer membrane (OM) through a bridge formed by seven membrane proteins (LptBFGCADE). The IM component LptBFG powers the process through a yet unclarified mechanism. Here we report three high-resolution cryo-EM structures of LptBFG alone and complexed with LptC (LptBFGC), trapped in either the LPS- or AMP-PNP-bound state. The structures reveal conformational changes between these states and substrate binding with or without LptC. We identify two functional transmembrane arginine-containing loops interacting with the bound AMP-PNP and elucidate allosteric communications between the domains. AMP-PNP binding induces an inward rotation and shift of the transmembrane helices of LptFG and LptC to tighten the cavity, with the closure of two lateral gates, to eventually expel LPS into the bridge. Functional assays reveal the functionality of the LptF and LptG periplasmic domains. Our findings shed light on the LPS transport mechanism.
#1: Journal: Nat Commun / Year: 2019
Title: Cryo-EM structures of lipopolysaccharide transporter LptBFGC in lipopolysaccharide or AMP-PNP-bound states reveal its transport mechanism.
Authors: Xiaodi Tang / Shenghai Chang / Qinghua Luo / Zhengyu Zhang / Wen Qiao / Caihuang Xu / Changbin Zhang / Yang Niu / Wenxian Yang / Ting Wang / Zhibo Zhang / Xiaofeng Zhu / Xiawei Wei / ...Authors: Xiaodi Tang / Shenghai Chang / Qinghua Luo / Zhengyu Zhang / Wen Qiao / Caihuang Xu / Changbin Zhang / Yang Niu / Wenxian Yang / Ting Wang / Zhibo Zhang / Xiaofeng Zhu / Xiawei Wei / Changjiang Dong / Xing Zhang / Haohao Dong /
Abstract: Lipopolysaccharides (LPS) of Gram-negative bacteria are critical for the defence against cytotoxic substances and must be transported from the inner membrane (IM) to the outer membrane (OM) through ...Lipopolysaccharides (LPS) of Gram-negative bacteria are critical for the defence against cytotoxic substances and must be transported from the inner membrane (IM) to the outer membrane (OM) through a bridge formed by seven membrane proteins (LptBFGCADE). The IM component LptBFG powers the process through a yet unclarified mechanism. Here we report three high-resolution cryo-EM structures of LptBFG alone and complexed with LptC (LptBFGC), trapped in either the LPS- or AMP-PNP-bound state. The structures reveal conformational changes between these states and substrate binding with or without LptC. We identify two functional transmembrane arginine-containing loops interacting with the bound AMP-PNP and elucidate allosteric communications between the domains. AMP-PNP binding induces an inward rotation and shift of the transmembrane helices of LptFG and LptC to tighten the cavity, with the closure of two lateral gates, to eventually expel LPS into the bridge. Functional assays reveal the functionality of the LptF and LptG periplasmic domains. Our findings shed light on the LPS transport mechanism.
History
DepositionJul 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10125
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lipopolysaccharide ABC transporter, ATP-binding protein LptB
B: Lipopolysaccharide ABC transporter, ATP-binding protein LptB
C: Lipopolysaccharide export system protein LptC
F: Lipopolysaccharide export system permease protein LptF
G: Inner membrane protein yjgQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,86112
Polymers155,3705
Non-polymers5,4917
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area11100 Å2
ΔGint-62 kcal/mol
Surface area45280 Å2
MethodPISA

-
Components

-
Protein , 2 types, 3 molecules ABG

#1: Protein Lipopolysaccharide ABC transporter, ATP-binding protein LptB


Mass: 26837.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: SGF_01136 / Production host: Escherichia coli (E. coli) / References: UniProt: E7T9E6, UniProt: P0A9V4*PLUS
#4: Protein Inner membrane protein yjgQ / LPS export ABC transporter permease LptG


Mass: 39622.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria)
Gene: yjgQ, S4488, CQA91_25110, NCTC9783_00309, SAMEA3710568_03584
Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S4N3I3, UniProt: A0A0H2V3J7*PLUS

-
Lipopolysaccharide export system ... , 2 types, 2 molecules CF

#2: Protein Lipopolysaccharide export system protein LptC


Mass: 21726.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: lptC, SFxv_3552 / Production host: Escherichia coli (E. coli) / References: UniProt: D2A8C1, UniProt: P0ADW2*PLUS
#3: Protein Lipopolysaccharide export system permease protein LptF


Mass: 40345.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: lptF, SF4228, S4489 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AFA1

-
Sugars , 1 types, 2 molecules

#7: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 3 types, 5 molecules

#5: Chemical ChemComp-DCQ / 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione / decylubiquinone