3HSH

Crystal structure of human collagen XVIII trimerization domain (Tetragonal crystal form)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Crystal structure of human collagen XVIII trimerization domain: A novel collagen trimerization Fold.

Boudko, S.P., Sasaki, T., Engel, J., Lerch, T.F., Nix, J., Chapman, M.S., Bachinger, H.P.

(2009) J Mol Biol 392: 787-802

  • DOI: 10.1016/j.jmb.2009.07.057
  • Primary Citation of Related Structures:  
    3HON, 3HSH

  • PubMed Abstract: 

    • Collagens contain a unique triple-helical structure with a repeating sequence -G-X-Y-, where proline and hydroxyproline are major constituents in X and Y positions, respectively. Folding of the collagen triple helix requires trimerization domains. Once trimerized, collagen chains are correctly aligned and the folding of the triple helix proceeds in a zipper-like fashion ...

    Collagens contain a unique triple-helical structure with a repeating sequence -G-X-Y-, where proline and hydroxyproline are major constituents in X and Y positions, respectively. Folding of the collagen triple helix requires trimerization domains. Once trimerized, collagen chains are correctly aligned and the folding of the triple helix proceeds in a zipper-like fashion. Here we report the isolation, characterization, and crystal structure of the trimerization domain of human type XVIII collagen, a member of the multiplexin family. This domain differs from all other known trimerization domains in other collagens and exhibits a high trimerization potential at picomolar concentrations. Strong chain association and high specificity of binding are needed for multiplexins, which are present at very low levels.

    Organizational Affiliation: 

    Research Department of Shriners Hospital for Children, Portland, OR 97239, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Collagen alpha-1(XVIII) chain
A, B, C, D, E, F
A, B, C, D, E, F
56Homo sapiensMutation(s): 1 
Gene Names: COL18A1
UniProt & NIH Common Fund Data Resources
Find proteins for P39060 (Homo sapiens)
Explore P39060 
Go to UniProtKB:  P39060
PHAROS:  P39060
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39060
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
AA [auth F],
BA [auth F],
G [auth A],
H [auth A],
I [auth A],
AA [auth F],
BA [auth F],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
N [auth B],
O [auth B],
P [auth B],
U [auth C],
V [auth C],
X [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
L [auth A],
M [auth A],
Q [auth B],
R [auth B],
S [auth B],
L [auth A],
M [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
W [auth C],
Y [auth D],
Z [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.179 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.745α = 90
b = 71.745β = 90
c = 134.723γ = 90
Software Package:
Software NamePurpose
JBluIce-EPICSdata collection
Blu-Icedata collection
PHENIXmodel building
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2021-10-13
    Changes: Database references, Derived calculations