Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.55 kDa 
• Atom Count: 3255 
• Residue Count: 285 
• Unique protein chains: 1

3GO5

Crystal structure of a multidomain protein with nucleic acid binding domains (sp_0946) from streptococcus pneumoniae tigr4 at 1.40 A resolution

• DOI: 10.2210/pdb3GO5/pdb

• Classification: GENE REGULATION
• Organism(s): Streptococcus pneumoniae TIGR4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-18 Released: 2009-04-07 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.175 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 

Literature

Structure of a virulence regulatory factor CvfB reveals a novel winged helix RNA binding module.

Matsumoto, Y., Xu, Q., Miyazaki, S., Kaito, C., Farr, C.L., Axelrod, H.L., Chiu, H.J., Klock, H.E., Knuth, M.W., Miller, M.D., Elsliger, M.A., Deacon, A.M., Godzik, A., Lesley, S.A., Sekimizu, K., Wilson, I.A.

(2010) Structure 18: 537-547

• PubMed: 20399190 
• DOI: 10.1016/j.str.2010.02.007
• Structures With Same Primary Citation


• PubMed Abstract: 
  

CvfB is a conserved regulatory protein important for the virulence of Staphylococcus aureus. We show here that CvfB binds RNA. The crystal structure of the CvfB ortholog from Streptococcus pneumoniae at 1.4 A resolution reveals a unique RNA binding protein that is formed from a concatenation of well-known structural modules that bind nucleic acids: three consecutive S1 RNA binding domains and a winged helix (WH) domain. The third S1 and the WH domains are required for cooperative RNA binding and form a continuous surface that likely contributes to the RNA interaction. The WH domain is critical to CvfB function and contains a unique sequence motif. Thus CvfB represents a novel assembly of modules for binding RNA.

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Organizational Affiliation: 

Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Multidomain protein with S1 RNA-binding domains	A	285	Streptococcus pneumoniae TIGR4	Mutation(s): 0  Gene Names: NP_345429.1, SP_0946
Find proteins for A0A0H2UPM3 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Go to UniProtKB:  A0A0H2UPM3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.175 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 
• Space Group: P 3₂ 2 1
• Diffraction Data DOI: 3GO5 Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.56	α = 90
b = 62.56	β = 90
c = 160.2	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-03-18 
• Released Date: 2009-04-07 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History 

• Version 1.0: 2009-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description