5M0Y | pdb_00005m0y

Crystal Structure of the CohScaA-XDocCipB type II complex from Clostridium thermocellum at 1.5Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.203 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5M0Y

This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 5g5b

Literature

Diverse specificity of cellulosome attachment to the bacterial cell surface.

Bras, J.L.Pinheiro, B.A.Cameron, K.Cuskin, F.Viegas, A.Najmudin, S.Bule, P.Pires, V.M.Romao, M.J.Bayer, E.A.Spencer, H.L.Smith, S.Gilbert, H.J.Alves, V.D.Carvalho, A.L.Fontes, C.M.

(2016) Sci Rep 6: 38292-38292

  • DOI: https://doi.org/10.1038/srep38292
  • Primary Citation Related Structures: 
    5G5D, 5K39, 5M0Y

  • PubMed Abstract: 

    During the course of evolution, the cellulosome, one of Nature's most intricate multi-enzyme complexes, has been continuously fine-tuned to efficiently deconstruct recalcitrant carbohydrates. To facilitate the uptake of released sugars, anaerobic bacteria use highly ordered protein-protein interactions to recruit these nanomachines to the cell surface. Dockerin modules located within a non-catalytic macromolecular scaffold, whose primary role is to assemble cellulosomal enzymatic subunits, bind cohesin modules of cell envelope proteins, thereby anchoring the cellulosome onto the bacterial cell. Here we have elucidated the unique molecular mechanisms used by anaerobic bacteria for cellulosome cellular attachment. The structure and biochemical analysis of five cohesin-dockerin complexes revealed that cell surface dockerins contain two cohesin-binding interfaces, which can present different or identical specificities. In contrast to the current static model, we propose that dockerins utilize multivalent modes of cohesin recognition to recruit cellulosomes to the cell surface, a mechanism that maximises substrate access while facilitating complex assembly.


  • Organizational Affiliation
    • Centro Interdisciplinar de Investigação em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, 1300-477 Lisboa, Portugal.

Macromolecule Content 

  • Total Structure Weight: 39.83 kDa 
  • Atom Count: 2,854 
  • Modeled Residue Count: 331 
  • Deposited Residue Count: 350 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ig domain protein group 2 domain proteinA [auth B]164Acetivibrio thermocellus ATCC 27405Mutation(s): 0 
Gene Names: Cthe_1806
UniProt
Find proteins for A3DGE8 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Explore A3DGE8 
Go to UniProtKB:  A3DGE8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3DGE8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cellulosome anchoring protein cohesin regionB [auth A]186Acetivibrio thermocellus ATCC 27405Mutation(s): 0 
Gene Names: Cthe_1307
UniProt
Find proteins for A3DF10 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Explore A3DF10 
Go to UniProtKB:  A3DF10
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3DF10
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P6G

Query on P6G



Download:Ideal Coordinates CCD File
N [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
J [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
G [auth B]
H [auth B]
I [auth B]
K [auth A]
L [auth A]
G [auth B],
H [auth B],
I [auth B],
K [auth A],
L [auth A],
M [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
C [auth B],
D [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.203 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.408α = 90
b = 63.741β = 90
c = 141.196γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description