8A0M | pdb_00008a0m

Capsular polysaccharide synthesis multienzyme in complex with capsular polymer fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 
    0.261 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 8A0M

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

A multi-enzyme machine polymerizes the Haemophilus influenzae type b capsule.

Cifuente, J.O.Schulze, J.Bethe, A.Di Domenico, V.Litschko, C.Budde, I.Eidenberger, L.Thiesler, H.Ramon Roth, I.Berger, M.Claus, H.D'Angelo, C.Marina, A.Gerardy-Schahn, R.Schubert, M.Guerin, M.E.Fiebig, T.

(2023) Nat Chem Biol 19: 865-877

  • DOI: https://doi.org/10.1038/s41589-023-01324-3
  • Primary Citation Related Structures: 
    8A0C, 8A0M

  • PubMed Abstract: 

    Bacterial capsules have critical roles in host-pathogen interactions. They provide a protective envelope against host recognition, leading to immune evasion and bacterial survival. Here we define the capsule biosynthesis pathway of Haemophilus influenzae serotype b (Hib), a Gram-negative bacterium that causes severe infections in infants and children. Reconstitution of this pathway enabled the fermentation-free production of Hib vaccine antigens starting from widely available precursors and detailed characterization of the enzymatic machinery. The X-ray crystal structure of the capsule polymerase Bcs3 reveals a multi-enzyme machine adopting a basket-like shape that creates a protected environment for the synthesis of the complex Hib polymer. This architecture is commonly exploited for surface glycan synthesis by both Gram-negative and Gram-positive pathogens. Supported by biochemical studies and comprehensive 2D nuclear magnetic resonance, our data explain how the ribofuranosyltransferase CriT, the phosphatase CrpP, the ribitol-phosphate transferase CroT and a polymer-binding domain function as a unique multi-enzyme assembly.


  • Organizational Affiliation
    • Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Spain.

Macromolecule Content 

  • Total Structure Weight: 554.61 kDa 
  • Atom Count: 32,156 
  • Modeled Residue Count: 4,162 
  • Deposited Residue Count: 4,692 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bcs3
A, B, C, D
1,173Haemophilus influenzaeMutation(s): 0 
Gene Names: bcs3'bcs3
UniProt
Find proteins for Q2ERG0 (Haemophilus influenzae)
Explore Q2ERG0 
Go to UniProtKB:  Q2ERG0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2ERG0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KOF
(Subject of Investigation/LOI)

Query on KOF



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
J [auth B]
K [auth B]
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
P [auth C],
R [auth D],
S [auth D],
T [auth D]
beta-D-ribosyl-(1->1)-D-ribitol-5-phosphate
C10 H21 O12 P
JWGOVVCXUKJSKW-DWMNMWHPSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B],
M [auth C],
Q [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free:  0.261 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.911α = 90
b = 232.806β = 118.39
c = 129.177γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany412824531
Ministry of Economy and Competitiveness (MINECO)SpainPID2019-105649RB-I00
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI149297

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Database references
  • Version 1.2: 2023-07-05
    Changes: Structure summary
  • Version 1.3: 2023-07-12
    Changes: Database references
  • Version 1.4: 2024-05-01
    Changes: Data collection, Refinement description