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: 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 ...

    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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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Collagen alpha-2(I) chain,Collagen alpha-1(IX) chainA, D71Homo sapiensMutation(s): 0 
Gene Names: COL1A2
Find proteins for P20849 (Homo sapiens)
Explore P20849 
Go to UniProtKB:  P20849
NIH Common Fund Data Resources
PHAROS  P20849
GTEx  ENSG00000112280
Find proteins for P08123 (Homo sapiens)
Explore P08123 
Go to UniProtKB:  P08123
NIH Common Fund Data Resources
PHAROS  P08123
GTEx  ENSG00000164692
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Collagen alpha-1(I) chain,Collagen alpha-2(IX) chainB, E71Homo sapiensMutation(s): 0 
Gene Names: COL1A1
Find proteins for P02452 (Homo sapiens)
Explore P02452 
Go to UniProtKB:  P02452
NIH Common Fund Data Resources
PHAROS  P02452
GTEx  ENSG00000108821
Find proteins for Q14055 (Homo sapiens)
Explore Q14055 
Go to UniProtKB:  Q14055
NIH Common Fund Data Resources
PHAROS  Q14055
GTEx  ENSG00000049089
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Collagen alpha-1(I) chain,Collagen alpha-3(IX) chainC, F72Homo sapiensMutation(s): 0 
Gene Names: COL1A1
Find proteins for P02452 (Homo sapiens)
Explore P02452 
Go to UniProtKB:  P02452
NIH Common Fund Data Resources
PHAROS  P02452
GTEx  ENSG00000108821
Find proteins for Q14050 (Homo sapiens)
Explore Q14050 
Go to UniProtKB:  Q14050
NIH Common Fund Data Resources
PHAROS  Q14050
GTEx  ENSG00000092758
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
A, F
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A,DL-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

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Shriners Hospitals for ChildrenUnited States--

Revision History 

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