Crystal structure of human osteomodulin

Experimental Data Snapshot

  • Resolution: 2.17 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

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This is version 1.3 of the entry. See complete history


Molecular basis for governing the morphology of type-I collagen fibrils by Osteomodulin.

Tashima, T.Nagatoishi, S.Caaveiro, J.M.M.Nakakido, M.Sagara, H.Kusano-Arai, O.Iwanari, H.Mimuro, H.Hamakubo, T.Ohnuma, S.I.Tsumoto, K.

(2018) Commun Biol 1: 33-33

  • DOI: https://doi.org/10.1038/s42003-018-0038-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Small leucine-rich repeat proteoglycan (SLRP) proteins have an important role in the organization of the extracellular matrix, especially in the formation of collagen fibrils. However, the mechanism governing the shape of collagen fibrils is poorly understood. Here, we report that the protein Osteomodulin (OMD) of the SLRP family is a monomeric protein in solution that interacts with type-I collagen. This interaction is dominated by weak electrostatic forces employing negatively charged residues of OMD, in particular Glu284 and Glu303, and controlled by entropic factors. The protein OMD establishes a fast-binding equilibrium with collagen, where OMD may engage not only with individual collagen molecules, but also with the growing fibrils. This weak electrostatic interaction is carefully balanced so it modulates the shape of the fibrils without compromising their viability.

  • Organizational Affiliation

    Department of Chemistry & Biotechnology, School of Engineering, The University of Tokyo, Tokyo, 108-8639, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
430Homo sapiensMutation(s): 0 
Gene Names: OMDSLRR2CUNQ190/PRO216
UniProt & NIH Common Fund Data Resources
Find proteins for Q99983 (Homo sapiens)
Explore Q99983 
Go to UniProtKB:  Q99983
PHAROS:  Q99983
GTEx:  ENSG00000127083 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99983
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth B],
M [auth C],
N [auth C],
O [auth C],
P [auth D],
Q [auth D],
R [auth D]
C8 H15 N O6
Query on PO4

Download Ideal Coordinates CCD File 
L [auth B],
S [auth D]
O4 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.17 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.64α = 90
b = 110.7β = 106.97
c = 122.15γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-10-17
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description, Structure summary