6T72 | pdb_00006t72

Structure of the RsaA N-terminal domain bound to LPS


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6T72

This is version 2.1 of the entry. See complete history

Literature

In Situ Structure of an Intact Lipopolysaccharide-Bound Bacterial Surface Layer.

von Kugelgen, A.Tang, H.Hardy, G.G.Kureisaite-Ciziene, D.Brun, Y.V.Stansfeld, P.J.Robinson, C.V.Bharat, T.A.M.

(2020) Cell 180: 348-358.e15

  • DOI: https://doi.org/10.1016/j.cell.2019.12.006
  • Primary Citation Related Structures: 
    6T72, 6Z7P

  • PubMed Abstract: 

    Most bacterial and all archaeal cells are encapsulated by a paracrystalline, protective, and cell-shape-determining proteinaceous surface layer (S-layer). On Gram-negative bacteria, S-layers are anchored to cells via lipopolysaccharide. Here, we report an electron cryomicroscopy structure of the Caulobacter crescentus S-layer bound to the O-antigen of lipopolysaccharide. Using native mass spectrometry and molecular dynamics simulations, we deduce the length of the O-antigen on cells and show how lipopolysaccharide binding and S-layer assembly is regulated by calcium. Finally, we present a near-atomic resolution in situ structure of the complete S-layer using cellular electron cryotomography, showing S-layer arrangement at the tip of the O-antigen. A complete atomic structure of the S-layer shows the power of cellular tomography for in situ structural biology and sheds light on a very abundant class of self-assembling molecules with important roles in prokaryotic physiology with marked potential for synthetic biology and surface-display applications.


  • Organizational Affiliation
    • Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom; Central Oxford Structural Microscopy and Imaging Centre, South Parks Road, Oxford OX1 3RE, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 28.1 kDa 
  • Atom Count: 1,877 
  • Modeled Residue Count: 242 
  • Deposited Residue Count: 255 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
S-layer protein255Caulobacter vibrioides CB15Mutation(s): 0 
Gene Names: rsaACC_1007
UniProt
Find proteins for P35828 (Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15))
Explore P35828 
Go to UniProtKB:  P35828
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35828
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
4-acetamido-4,6-dideoxy-alpha-D-mannopyranose-(1-3)-4-acetamido-4,6-dideoxy-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-4-acetamido-4,6-dideoxy-alpha-D-mannopyranose-(1-3)-4-acetamido-4,6-dideoxy-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-4-acetamido-4,6-dideoxy-alpha-D-mannopyranose-(1-3)-4-acetamido-4,6-dideoxy-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-4-acetamido-4,6-dideoxy-alpha-D-mannopyranose-(1-3)-4-acetamido-4,6-dideoxy-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose
B
12N/A
Glycosylation Resources
GlyTouCan: G50564AO
GlyCosmos: G50564AO

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTREFMAC5

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom202231/Z/16/Z

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Data collection, Database references, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-05-22
    Changes: Data collection, Database references, Derived calculations, Structure summary