1IRJ | pdb_00001irj

Crystal Structure of the MRP14 complexed with CHAPS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.274 (Depositor) 
  • R-Value Work: 
    0.245 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

The crystal structure of human MRP14 (S100A9), a Ca(2+)-dependent regulator protein in inflammatory process.

Itou, H.Yao, M.Fujita, I.Watanabe, N.Suzuki, M.Nishihira, J.Tanaka, I.

(2002) J Mol Biology 316: 265-276

  • DOI: https://doi.org/10.1006/jmbi.2001.5340
  • Primary Citation Related Structures: 
    1IRJ

  • PubMed Abstract: 

    Human MRP14 (hMRP14) is a Ca(2+)-binding protein from the S100 family of proteins. This protein is co-expressed with human MRP8 (hMRP8), a homologue protein in myeloid cells, and plays an indispensable role in Ca(2+)-dependent functions during inflammation. This role includes the activation of Mac-1, the beta(2) integrin which is involved in neutrophil adhesion to endothelial cells. The crystal structure of the holo form of hMRP14 was analyzed at 2.1 A resolution. hMRP14 is distinguished from other S100 member proteins by its long C-terminal region, and its structure shows that the region is extensively flexible. In this crystal structure of hMRP14, Chaps molecules bind to the hinge region that connects two EF-hand motifs, which suggests that this region is a target-binding site of this protein. Based on a structural comparison of hMRP14 with hMRP8 and human S100A12 (hS100A12) that is another homologue protein, the character of MRP8/14 hetero-complex and the functional significance of the flexibility of the C-terminal region of hMRP14 are discussed.


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

Macromolecule Content 

  • Total Structure Weight: 108.16 kDa 
  • Atom Count: 5,871 
  • Modeled Residue Count: 670 
  • Deposited Residue Count: 904 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Migration Inhibitory Factor-Related Protein 14
A, B, C, D, E
A, B, C, D, E, F, G, H
113Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P06702 (Homo sapiens)
Explore P06702 
Go to UniProtKB:  P06702
PHAROS:  P06702
GTEx:  ENSG00000163220 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06702
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CPS

Query on CPS



Download:Ideal Coordinates CCD File
M [auth B],
R [auth D],
S [auth D],
Z [auth G]
3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
C32 H58 N2 O7 S
UMCMPZBLKLEWAF-BCTGSCMUSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
AA [auth H]
BA [auth H]
I [auth A]
J [auth A]
K [auth B]
AA [auth H],
BA [auth H],
I [auth A],
J [auth A],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
P [auth D],
Q [auth D],
T [auth E],
U [auth E],
V [auth F],
W [auth F],
X [auth G],
Y [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.274 (Depositor) 
  • R-Value Work:  0.245 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.59α = 90
b = 178.44β = 113.17
c = 61.23γ = 90
Software Package:
Software NamePurpose
SHELXSphasing
SHARPphasing
CNSrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations