5YQ5

Crystal structure of human osteomodulin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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 1.2 of the entry. See complete history. 


Literature

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: 10.1038/s42003-018-0038-2
  • Primary Citation of Related Structures:  
    5YQ5

  • 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 ...

    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: 

    Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan. tsumoto@bioeng.t.u-tokyo.ac.jp.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
OsteomodulinA, B, C, D430Homo sapiensMutation(s): 0 
Gene Names: OMD, SLRR2C, UNQ190/PRO216
UniProt & NIH Common Fund Data Resources
Find proteins for Q99983 (Homo sapiens)
Explore Q99983 
Go to UniProtKB:  Q99983
PHAROS:  Q99983
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99983
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
JSPSJapan16H02420
JSPSJapan15K06962

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