5CVB

Crystal structure of the type IX collagen NC2 hetero-trimerization domain with a guest fragment a1a1a1 of type I collagen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.249 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.227 

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:  

  • 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

    Research Department, Shriners Hospital for Children, Portland, Oregon 97239, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Collagen alpha-1(I) chain,Collagen alpha-1(IX) chain
A, D
71Homo sapiensMutation(s): 0 
Gene Names: COL1A1, COL9A1
Find proteins for P02452 (Homo sapiens)
Go to Gene View: COL1A1
Go to UniProtKB:  P02452
Find proteins for P20849 (Homo sapiens)
Go to Gene View: COL9A1
Go to UniProtKB:  P20849
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Collagen alpha-1(I) chain,Collagen alpha-2(IX) chain
B, E
71Homo sapiensMutation(s): 0 
Gene Names: COL9A2, COL1A1
Find proteins for Q14055 (Homo sapiens)
Go to Gene View: COL9A2
Go to UniProtKB:  Q14055
Find proteins for P02452 (Homo sapiens)
Go to Gene View: COL1A1
Go to UniProtKB:  P02452
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Collagen alpha-1(I) chain,Collagen alpha-3(IX) chain
C, F
72Homo sapiensMutation(s): 0 
Gene Names: COL9A3, COL1A1
Find proteins for Q14050 (Homo sapiens)
Go to Gene View: COL9A3
Go to UniProtKB:  Q14050
Find proteins for P02452 (Homo sapiens)
Go to Gene View: COL1A1
Go to UniProtKB:  P02452
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, C, F
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.249 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.770α = 90.00
b = 64.460β = 112.72
c = 65.390γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
PHENIXrefinement
PHENIXphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references, Derived calculations