1TGG

RH3 DESIGNED RIGHT-HANDED COILED COIL TRIMER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural test of the parameterized-backbone method for protein design

Plecs, J.J.Harbury, P.B.Kim, P.S.Alber, T.

(2004) J.Mol.Biol. 342: 289-297

  • DOI: 10.1016/j.jmb.2004.06.051

  • PubMed Abstract: 
  • Designing new protein folds requires a method for simultaneously optimizing the conformation of the backbone and the side-chains. One approach to this problem is the use of a parameterized backbone, which allows the systematic exploration of families ...

    Designing new protein folds requires a method for simultaneously optimizing the conformation of the backbone and the side-chains. One approach to this problem is the use of a parameterized backbone, which allows the systematic exploration of families of structures. We report the crystal structure of RH3, a right-handed, three-helix coiled coil that was designed using a parameterized backbone and detailed modeling of core packing. This crystal structure was determined using another rationally designed feature, a metal-binding site that permitted experimental phasing of the X-ray data. RH3 adopted the intended fold, which has not been observed previously in biological proteins. Unanticipated structural asymmetry in the trimer was a principal source of variation within the RH3 structure. The sequence of RH3 differs from that of a previously characterized right-handed tetramer, RH4, at only one position in each 11 amino acid sequence repeat. This close similarity indicates that the design method is sensitive to the core packing interactions that specify the protein structure. Comparison of the structures of RH3 and RH4 indicates that both steric overlap and cavity formation provide strong driving forces for oligomer specificity.


    Related Citations: 
    • Repacking Protein Cores with Backbone Freedom: Structure Prediction for Coiled Coils
      Harbury, P.B.,Tidor, B.,Kim, P.S.
      (1995) Proc.Natl.Acad.Sci.USA 92: 8408
    • High-Resolution Design with Backbone Freedom
      Harbury, P.B.,Plecs, J.J.,Tidor, B.,Alber, T.,Kim, P.S.
      (1998) Science 282: 1462


    Organizational Affiliation

    Department of Physics, University of California, Berkeley, 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
right-handed coiled coil trimer
A, B, C
34N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
IIL
Query on IIL
A, B, C
L-PEPTIDE LINKINGC6 H13 N O2ILE
CGU
Query on CGU
A, B, C
L-PEPTIDE LINKINGC6 H9 N O6GLU
ACE
Query on ACE
A, B, C
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.233 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 25.420α = 90.00
b = 25.420β = 90.00
c = 141.340γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling
SCALAdata scaling
MLPHAREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance