6WVF

E.coli DsbB C104S with ubiquinone

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Aequorea victoria, Escherichia coli
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2020-05-05 Released: 2021-01-13 
  • Deposition Author(s): Liu, S., Li, W.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), Other private, National Institutes of Health/National Eye Institute (NIH/NEI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report



Literature

Termini restraining of small membrane proteins enables structure determination at near-atomic resolution.

Liu, S., Li, S., Yang, Y., Li, W.

(2020) Sci Adv 6

  • DOI: 10.1126/sciadv.abe3717
  • Primary Citation of Related Structures:  
    6WVF, 6WVE, 6WVD

  • PubMed Abstract: 

    • Small membrane proteins are difficult targets for structural characterization. Here, we stabilize their folding by restraining their amino and carboxyl termini with associable protein entities, exemplified by the two halves of a superfolder GFP. The term ...

    Small membrane proteins are difficult targets for structural characterization. Here, we stabilize their folding by restraining their amino and carboxyl termini with associable protein entities, exemplified by the two halves of a superfolder GFP. The termini-restrained proteins are functional and show improved stability during overexpression and purification. The reassembled GFP provides a versatile scaffold for membrane protein crystallization, enables diffraction to atomic resolution, and facilitates crystal identification, phase determination, and density modification. This strategy gives rise to 14 new structures of five vertebrate proteins from distinct functional families, bringing a substantial expansion to the structural database of small membrane proteins. Moreover, a high-resolution structure of bacterial DsbB reveals that this thiol oxidoreductase is activated through a catalytic triad, similar to cysteine proteases. Overall, termini restraining proves exceptionally effective for stabilization and structure determination of small membrane proteins.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA. weikai@wustl.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Green fluorescent protein,Disulfide bond formation protein B,Green fluorescent protein A399Aequorea victoria, Escherichia coliMutation(s): 4 
Gene Names: GFP, dsbB, roxB, ycgA, b1185, JW5182
Find proteins for P42212 (Aequorea victoria)
Explore P42212 
Go to UniProtKB:  P42212
Find proteins for P0A6M2 (Escherichia coli (strain K12))
Explore P0A6M2 
Go to UniProtKB:  P0A6M2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UQ1
Query on UQ1
Download Ideal Coordinates CCD File 
A
UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CRO
Query on CRO		AL-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.260 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.381α = 90
b = 53.381β = 90
c = 280.74γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-05-05 
  • Released Date: 2021-01-13 
    • Deposition Author(s): Liu, S., Li, W.
Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01 HL121718
Other privateUnited StatesForefront of Science Award
Other privateUnited StatesMCII 2020-854
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesR21 EY028705
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM131008
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30 GM124165

Revision History 

  • Version 1.0: 2021-01-13
    Type: Initial release