1MR8

MIGRATION INHIBITORY FACTOR-RELATED PROTEIN 8 FROM HUMAN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structure of human MRP8, a member of the S100 calcium-binding protein family, by MAD phasing at 1.9 A resolution.

Ishikawa, K.Nakagawa, A.Tanaka, I.Suzuki, M.Nishihira, J.

(2000) Acta Crystallogr D Biol Crystallogr 56: 559-566

  • DOI: https://doi.org/10.1107/s0907444900002833
  • Primary Citation of Related Structures:  
    1MR8

  • PubMed Abstract: 

    The structure of human MRP8 in the calcium-bound form was determined at 1.9 A resolution by X-ray crystallography. The structure was initially solved by MAD phasing of an ytterbium-substituted crystal and was refined against data obtained from a Ca(2+)-bound crystal. The dimeric form of MRP8 was stabilized by hydrophobic interactions between mutually wrapped helices. There were two EF-hand motifs per monomer and each EF-hand bound one Ca(2+) with a different affinity [the affinity of the C-terminal EF-hand (EF-2) for Ca(2+) was stronger than that of the N-terminal EF-hand (EF-1)]. Furthermore, replacement with Yb(3+) occurred in the C-terminal EF-hand only, suggesting a more flexible nature for EF-2 than for EF-1. This, combined with previous observations that the helix in EF-2 (helix III) undergoes a large conformational change upon calcium binding, suggests that the C-terminal EF-hand (EF-2) plays a role as a trigger for Ca(2+)-induced conformational change.


  • Organizational Affiliation

    Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MIGRATION INHIBITORY FACTOR-RELATED PROTEIN 8
A, B
93Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P05109 (Homo sapiens)
Explore P05109 
Go to UniProtKB:  P05109
PHAROS:  P05109
GTEx:  ENSG00000143546 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05109
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.5α = 90
b = 52.5β = 90
c = 128.6γ = 120
Software Package:
Software NamePurpose
SHARPphasing
X-PLORrefinement
DENZOdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-05-17
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations