3DMW

Crystal structure of human type III collagen G982-G1023 containing C-terminal cystine knot


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of human type III collagen Gly991-Gly1032 cystine knot-containing peptide shows both 7/2 and 10/3 triple helical symmetries.

Boudko, S.P.Engel, J.Okuyama, K.Mizuno, K.Bachinger, H.P.Schumacher, M.A.

(2008) J.Biol.Chem. 283: 32580-32589

  • DOI: 10.1074/jbc.M805394200

  • PubMed Abstract: 
  • Type III collagen is a critical collagen that comprises extensible connective tissue such as skin, lung, and the vascular system. Mutations in the type III collagen gene, COL3A1, are associated with the most severe forms of Ehlers-Danlos syndrome. A ...

    Type III collagen is a critical collagen that comprises extensible connective tissue such as skin, lung, and the vascular system. Mutations in the type III collagen gene, COL3A1, are associated with the most severe forms of Ehlers-Danlos syndrome. A characteristic feature of type III collagen is the presence of a stabilizing C-terminal cystine knot. Crystal structures of collagen triple helices reported so far contain artificial sequences like (Gly-Pro-Pro)(n) or (Gly-Pro-Hyp)(n). To gain insight into the structural properties exhibited by the natural type III collagen triple helix, we synthesized, crystallized, and determined the structure of a 12-triplet repeating peptide containing the natural type III collagen sequence from residues 991 to 1032 including the C-terminal cystine knot region, to 2.3A resolution. This represents the longest collagen triple helical structure determined to date with a native sequence. Strikingly, the Gly(991)-Gly(1032) structure reveals that the central non-imino acid-containing region adopts 10/3 superhelical properties, whereas the imino acid rich N- and C-terminal regions adhere to a 7/2 superhelical conformation. The structure is consistent with two models for the cystine knot; however, the poor density for the majority of this region suggests that multiple conformations may be adopted. The structure shows that the multiple non-imino acids make several types of direct intrahelical as well as interhelical contacts. The looser superhelical structure of the non-imino acid region of collagen triple helices combined with the extra contacts afforded by ionic and polar residues likely play a role in fibrillar assembly and interactions with other extracellular components.


    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(III) chain
A, B, C
42Homo sapiensMutation(s): 1 
Gene Names: COL3A1
Find proteins for P02461 (Homo sapiens)
Go to Gene View: COL3A1
Go to UniProtKB:  P02461
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
HYP
Query on HYP
A, B, C
L-PEPTIDE LINKINGC5 H9 N O3PRO
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.248 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 31.980α = 90.00
b = 21.520β = 92.58
c = 68.970γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
ADSCdata collection
SCALAdata scaling
MOSFLMdata reduction
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance