3HR2

Low resolution, molecular envelope structure of type I collagen in situ determined by fiber diffraction. Single type I collagen molecule, post rigid body refinement, 'relaxed'


Experimental Data Snapshot

  • Method: FIBER DIFFRACTION
  • Resolution: 5.16 Å
  • R-Value Work: 0.042 
  • R-Value Observed: 0.042 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Microfibrillar Structure of Type I Collagen in Situ.

Orgel, J.P.Irving, T.C.Miller, A.Wess, T.J.

(2006) Proc Natl Acad Sci U S A 103: 9001-9005

  • DOI: 10.1073/pnas.0502718103
  • Primary Citation of Related Structures:  
    3HQV, 3HR2

  • PubMed Abstract: 
  • The fibrous collagens are ubiquitous in animals and form the structural basis of all mammalian connective tissues, including those of the heart, vasculature, skin, cornea, bones, and tendons. However, in comparison with what is known of their product ...

    The fibrous collagens are ubiquitous in animals and form the structural basis of all mammalian connective tissues, including those of the heart, vasculature, skin, cornea, bones, and tendons. However, in comparison with what is known of their production, turnover and physiological structure, very little is understood regarding the three-dimensional arrangement of collagen molecules in naturally occurring fibrils. This knowledge may provide insight into key biological processes such as fibrillo-genesis and tissue remodeling and into diseases such as heart disease and cancer. Here we present a crystallographic determination of the collagen type I supermolecular structure, where the molecular conformation of each collagen segment found within the naturally occurring crystallographic unit cell has been defined (P1, a approximately 40.0 A, b approximately 27.0 A, c approximately 678 A, alpha approximately 89.2 degrees , beta approximately 94.6 degrees , gamma approximately 105.6 degrees ; reflections: 414, overlapping, 232, and nonoverlapping, 182; resolution, 5.16 A axial and 11.1 A equatorial). This structure shows that the molecular packing topology of the collagen molecule is such that packing neighbors are arranged to form a supertwisted (discontinuous) right-handed microfibril that interdigitates with neighboring microfibrils. This interdigitation establishes the crystallographic superlattice, which is formed of quasihexagonally packed collagen molecules. In addition, the molecular packing structure of collagen shown here provides information concerning the potential modes of action of two prominent molecules involved in human health and disease: decorin and the Matrix Metallo-Proteinase (MMP) collagenase.


    Organizational Affiliation

    Center for Synchrotron Radiation Research and Instrumentation, Department of Biological, Chemical, and Physical Sciences, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, IL 60616, USA. orgel@lit.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Collagen alpha-1(I) chainAC1056Rattus norvegicusMutation(s): 0 
Gene Names: Col1a1
Find proteins for P02454 (Rattus norvegicus)
Explore P02454 
Go to UniProtKB:  P02454
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Collagen alpha-2(I) chainB1028Rattus norvegicusMutation(s): 0 
Gene Names: Col1a2
Find proteins for P02466 (Rattus norvegicus)
Explore P02466 
Go to UniProtKB:  P02466
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
HYP
Query on HYP
A,CL-PEPTIDE LINKINGC5 H9 N O3PRO
LYZ
Query on LYZ
A,CL-PEPTIDE LINKINGC6 H14 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: FIBER DIFFRACTION
  • Resolution: 5.16 Å
  • R-Value Work: 0.042 
  • R-Value Observed: 0.042 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.97α = 89.24
b = 26.95β = 94.59
c = 677.9γ = 105.58
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-06-08 
  • Released Date: 2009-07-14 
  • Deposition Author(s): Orgel, J.P.
  • This entry supersedes: 1Y0F

Revision History 

  • Version 1.0: 2009-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance