1JCC

Crystal Structure of a Novel Alanine-Zipper Trimer at 1.7 A Resolution, V13A,L16A,V20A,L23A,V27A,M30A,V34A mutations


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Zinc-Mediated Helix Capping in A Triple-Helical Protein

Liu, J.Dai, J.Lu, M.

(2003) Biochemistry 42: 5657-5664

  • DOI: 10.1021/bi026828a

  • PubMed Abstract: 
  • Specific sequence signals at alpha-helix termini can assist protein folding by punctuating and cueing secondary structural elements in the final native conformation. Here we report the crystallization of a 56-residue alanine-containing peptide, denot ...

    Specific sequence signals at alpha-helix termini can assist protein folding by punctuating and cueing secondary structural elements in the final native conformation. Here we report the crystallization of a 56-residue alanine-containing peptide, denoted Ala-10(56), in the presence of Zn(2+). The 1.7 A crystal structure shows that Ala-10(56) forms a parallel trimeric coiled coil with three zinc ions anchoring distinct capping conformations at the amino-terminal ends of the three helices. In each polypeptide chain, the free alpha-amino nitrogen and carbonyl oxygen of the amino-terminal Ser residue coordinate to a Zn(2+) ion to form a five-membered chelate, and the syn-unidentate interaction of the Asp7 side chain with the Zn(2+) cation leads to the formation of a unique docking arrangement for helix capping. Moreover, the coordination of the zinc ion involves a neighboring trimer molecule in the crystal. Consequently, the crystal contacts are stabilized by carboxylate-Zn(2+) interactions between four Ala-10(56) trimers in the crystal lattice. The observed synergy between the protein-zinc ion recognition and the helix-packing arrangements would contribute to the conformational specificity of the Ala-10(56) trimer.


    Organizational Affiliation

    Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MAJOR OUTER MEMBRANE LIPOPROTEIN
A, B, C
56Escherichia coli (strain K12)Gene Names: lpp (mlpA, mulI)
Find proteins for P69776 (Escherichia coli (strain K12))
Go to UniProtKB:  P69776
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 62.388α = 90.00
b = 33.322β = 102.55
c = 71.979γ = 90.00
Software Package:
Software NamePurpose
MADNESSdata collection
SCALEPACKdata scaling
AMoREphasing
MADNESSdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2001-06-08 
  • Released Date: 2003-06-17 
  • Deposition Author(s): Liu, J., Dai, J., Lu, M.

Revision History 

  • Version 1.0: 2003-06-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description