5CVA

Crystal structure of the type IX collagen NC2 hetero-trimerization domain with a guest fragment a1a2a1 of type I collagen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insight for chain selection and stagger control in collagen.

Boudko, S.P.Bachinger, H.P.

(2016) Sci Rep 6: 37831-37831

  • DOI: https://doi.org/10.1038/srep37831
  • Primary Citation of Related Structures:  
    5CTD, 5CTI, 5CVA, 5CVB

  • PubMed Abstract: 

    Collagen plays a fundamental role in all known metazoans. In collagens three polypeptides form a unique triple-helical structure with a one-residue stagger to fit every third glycine residue in the inner core without disturbing the poly-proline type II helical conformation of each chain. There are homo- and hetero-trimeric types of collagen consisting of one, two or three distinct chains. Thus there must be mechanisms that control composition and stagger during collagen folding. Here, we uncover the structural basis for both chain selection and stagger formation of a collagen molecule. Three distinct chains (α1, α2 and α3) of the non-collagenous domain 2 (NC2) of type IX collagen are assembled to guide triple-helical sequences in the leading, middle and trailing positions. This unique domain opens the door for generating any fragment of collagen in its native composition and stagger.


  • Organizational Affiliation

    Department of Molecular Biology and Biochemistry, Oregon Health and Science University, Portland, Oregon 97239, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Collagen alpha-2(I) chain,Collagen alpha-1(IX) chain
A, D
71Homo sapiensMutation(s): 0 
Gene Names: COL1A2COL9A1
UniProt & NIH Common Fund Data Resources
Find proteins for P20849 (Homo sapiens)
Explore P20849 
Go to UniProtKB:  P20849
PHAROS:  P20849
GTEx:  ENSG00000112280 
Find proteins for P08123 (Homo sapiens)
Explore P08123 
Go to UniProtKB:  P08123
PHAROS:  P08123
GTEx:  ENSG00000164692 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP08123P20849
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Collagen alpha-1(I) chain,Collagen alpha-2(IX) chain
B, E
71Homo sapiensMutation(s): 0 
Gene Names: COL1A1COL9A2
UniProt & NIH Common Fund Data Resources
Find proteins for P02452 (Homo sapiens)
Explore P02452 
Go to UniProtKB:  P02452
PHAROS:  P02452
GTEx:  ENSG00000108821 
Find proteins for Q14055 (Homo sapiens)
Explore Q14055 
Go to UniProtKB:  Q14055
PHAROS:  Q14055
GTEx:  ENSG00000049089 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ14055P02452
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Collagen alpha-1(I) chain,Collagen alpha-3(IX) chain
C, F
72Homo sapiensMutation(s): 0 
Gene Names: COL1A1COL9A3
UniProt & NIH Common Fund Data Resources
Find proteins for P02452 (Homo sapiens)
Explore P02452 
Go to UniProtKB:  P02452
PHAROS:  P02452
GTEx:  ENSG00000108821 
Find proteins for Q14050 (Homo sapiens)
Explore Q14050 
Go to UniProtKB:  Q14050
PHAROS:  Q14050
GTEx:  ENSG00000092758 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ14050P02452
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.238 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.41α = 90
b = 63.98β = 112.75
c = 65.37γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Shriners Hospitals for ChildrenUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2017-07-12
    Changes: Database references, Derived calculations