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: 1.70 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.4 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
  • Primary Citation of Related Structures:  
    1JCC

  • 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, denoted Ala-10(56), in the presence of Zn(2+) ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MAJOR OUTER MEMBRANE LIPOPROTEINA, B, C56Escherichia coliMutation(s): 7 
UniProt
Find proteins for P69776 (Escherichia coli (strain K12))
Explore P69776 
Go to UniProtKB:  P69776
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69776
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 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
b = 33.322β = 102.55
c = 71.979γ = 90
Software Package:
Software NamePurpose
MADNESSdata collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
MADNESSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2021-10-27
    Changes: Database references, Derived calculations