1MR8

MIGRATION INHIBITORY FACTOR-RELATED PROTEIN 8 FROM HUMAN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.,Sect.D 56: 559-566


  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MIGRATION INHIBITORY FACTOR-RELATED PROTEIN 8
A, B
93Homo sapiensGene Names: S100A8 (CAGA, CFAG, MRP8)
Find proteins for P05109 (Homo sapiens)
Go to Gene View: S100A8
Go to UniProtKB:  P05109
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.193 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 52.500α = 90.00
b = 52.500β = 90.00
c = 128.600γ = 120.00
Software Package:
Software NamePurpose
SHARPphasing
CCP4data scaling
X-PLORrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-17
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance