1GR3 | pdb_00001gr3

Structure of the human collagen X NC1 trimer

• PDB DOI: https://doi.org/10.2210/pdb1GR3/pdb

• Classification: COLLAGEN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-12-12 Released: 2002-02-14 
• Deposition Author(s): Bogin, O., Kvansakul, M., Rom, E., Singer, J., Yayon, A., Hohenester, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.199 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Insight Into Schmid Metaphyseal Chondrodysplasia from the Crystal Structure of the Collagen X Nc1 Domain Trimer.

Bogin, O., Kvansakul, M., Rom, E., Singer, J., Yayon, A., Hohenester, E.

(2002) Structure 10: 165

• PubMed: 11839302 
• DOI: https://doi.org/10.1016/s0969-2126(02)00697-4
• Primary Citation of Related Structures:  
  1GR3


• PubMed Abstract: 
  

  Collagen X is expressed specifically in the growth plate of long bones. Its C1q-like C-terminal NC1 domain forms a stable homotrimer and is crucial for collagen X assembly. Mutations in the NC1 domain cause Schmid metaphyseal chondrodysplasia (SMCD). The crystal structure at 2.0 A resolution of the human collagen X NC1 domain reveals an intimate trimeric assembly strengthened by a buried cluster of calcium ions. Three strips of exposed aromatic residues on the surface of NC1 trimer are likely to be involved in the supramolecular assembly of collagen X. Most internal SMCD mutations probably prevent protein folding, whereas mutations of surface residues may affect the collagen X suprastructure in a dominant-negative manner.

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Organizational Affiliation: 

ProChon Biotech, P.O. Box 1482, Rehovot 76114, Israel.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 18.43 kDa 
• Atom Count: 1,126 
• Modeled Residue Count: 132 
• Deposited Residue Count: 160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COLLAGEN X	A	160	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q03692 (Homo sapiens) Explore Q03692  Go to UniProtKB:  Q03692
PHAROS:  Q03692 GTEx:  ENSG00000123500

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CPS	B [auth A]	3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE C32 H58 N2 O7 S UMCMPZBLKLEWAF-BCTGSCMUSA-N
CA	C [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.199 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.36	α = 90
b = 78.36	β = 90
c = 141.036	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-02-14 
Deposition Author(s): Bogin, O., Kvansakul, M., Rom, E., Singer, J., Yayon, A., Hohenester, E.

Revision History  

• Version 1.0: 2002-02-14
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-07-05
  Changes: Data collection
• Version 1.4: 2023-12-13
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description