5M2O | pdb_00005m2o

R. flavefaciens' third ScaB cohesin in complex with a group 1 dockerin

• PDB DOI: https://doi.org/10.2210/pdb5M2O/pdb

• Classification: PROTEIN BINDING
• Organism(s): Ruminococcus flavefaciens FD-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-10-13 Released: 2017-07-05 
• Deposition Author(s): Bule, P., Najmudin, S., Carvalho, A.L., Fontes, C.M.G.A.
• Funding Organization(s): Fundacao para a Ciencia e Tecnologia

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 
  0.153 (Depositor), 0.130 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.135 (DCC) 
• R-Value Observed: 
  0.136 (Depositor) 

Starting Model: experimental

Literature

Assembly of Ruminococcus flavefaciens cellulosome revealed by structures of two cohesin-dockerin complexes.

Bule, P., Alves, V.D., Israeli-Ruimy, V., Carvalho, A.L., Ferreira, L.M., Smith, S.P., Gilbert, H.J., Najmudin, S., Bayer, E.A., Fontes, C.M.

(2017) Sci Rep 7: 759-759

• PubMed: 28389644 
• DOI: https://doi.org/10.1038/s41598-017-00919-w
• Primary Citation Related Structures: 
  5M2O, 5M2S


• PubMed Abstract: 
  

  Cellulosomes are sophisticated multi-enzymatic nanomachines produced by anaerobes to effectively deconstruct plant structural carbohydrates. Cellulosome assembly involves the binding of enzyme-borne dockerins (Doc) to repeated cohesin (Coh) modules located in a non-catalytic scaffoldin. Docs appended to cellulosomal enzymes generally present two similar Coh-binding interfaces supporting a dual-binding mode, which may confer increased positional adjustment of the different complex components. Ruminococcus flavefaciens' cellulosome is assembled from a repertoire of 223 Doc-containing proteins classified into 6 groups. Recent studies revealed that Docs of groups 3 and 6 are recruited to the cellulosome via a single-binding mode mechanism with an adaptor scaffoldin. To investigate the extent to which the single-binding mode contributes to the assembly of R. flavefaciens cellulosome, the structures of two group 1 Docs bound to Cohs of primary (ScaA) and adaptor (ScaB) scaffoldins were solved. The data revealed that group 1 Docs display a conserved mechanism of Coh recognition involving a single-binding mode. Therefore, in contrast to all cellulosomes described to date, the assembly of R. flavefaciens cellulosome involves single but not dual-binding mode Docs. Thus, this work reveals a novel mechanism of cellulosome assembly and challenges the ubiquitous implication of the dual-binding mode in the acquisition of cellulosome flexibility.

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Organizational Affiliation: 
• CIISA - Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477, Lisboa, Portugal.
Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 76100, Israel.
UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada.
Institute for Cell and Molecular Biosciences, Newcastle University, The Medical School, Newcastle upon Tyne, NE2 4HH, United Kingdom.
CIISA - Faculdade de Medicina Veterinária, ULisboa, Pólo Universitário do Alto da Ajuda, Avenida da Universidade Técnica, 1300-477, Lisboa, Portugal. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.32 kDa 
• Atom Count: 1,947 
• Modeled Residue Count: 211 
• Deposited Residue Count: 245 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative cellulosomal scaffoldin protein	A	149	Ruminococcus flavefaciens FD-1	Mutation(s): 0  Gene Names: scaB
UniProt
Find proteins for A0AEF4 (Ruminococcus flavefaciens) Explore A0AEF4  Go to UniProtKB:  A0AEF4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Group I Dockerin	B	96	Ruminococcus flavefaciens FD-1	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth B], D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free:  0.153 (Depositor), 0.130 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.135 (DCC) 
• R-Value Observed: 0.136 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.767	α = 90
b = 63.51	β = 90
c = 84.482	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-07-05 
Deposition Author(s): Bule, P., Najmudin, S., Carvalho, A.L., Fontes, C.M.G.A.

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Funding Organization	Location	Grant Number
Fundacao para a Ciencia e Tecnologia	Portugal	PTDC/BIA-MIC/5947/2014
Fundacao para a Ciencia e Tecnologia	Portugal	SFRH/BD/86821/2012

Revision History  

• Version 1.0: 2017-07-05
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description