5HLV

Crystal structure of calcium and zinc-bound human S100A8 in space group P212121

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of human S100A8 in complex with zinc and calcium.

Lin, H., Andersen, G.R., Yatime, L.

(2016) BMC Struct Biol 16: 8-8

  • DOI: 10.1186/s12900-016-0058-4
  • Primary Citation of Related Structures:  
    5HLO, 5HLV

  • PubMed Abstract: 

    • S100 proteins are a large family of calcium binding proteins present only in vertebrates. They function intra- and extracellularly both as regulators of homeostatic processes and as potent effectors during inflammation. Among these, S100A8 and S100A9 are two major constituents of neutrophils that can assemble into homodimers, heterodimers and higher oligomeric species, including fibrillary structures found in the ageing prostate ...

    S100 proteins are a large family of calcium binding proteins present only in vertebrates. They function intra- and extracellularly both as regulators of homeostatic processes and as potent effectors during inflammation. Among these, S100A8 and S100A9 are two major constituents of neutrophils that can assemble into homodimers, heterodimers and higher oligomeric species, including fibrillary structures found in the ageing prostate. Each of these forms assumes specific functions and their formation is dependent on divalent cations, notably calcium and zinc. In particular, zinc appears as a major regulator of S100 protein function in a disease context. Despite this central role, no structural information on how zinc bind to S100A8/S100A9 and regulates their quaternary structure is yet available.

    Organizational Affiliation: 

    Present address: DIMNP - UMR5235, University of Montpellier, Place Eugène Bataillon, Bât. 24 cc107, 34095, Montpellier Cedex 5, France. laure.yatime@inserm.fr.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein S100-A8
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
94Homo sapiensMutation(s): 0 
Gene Names: S100A8, CAGA, CFAG, MRP8
UniProt & NIH Common Fund Data Resources
Find proteins for P05109 (Homo sapiens)
Explore P05109 
Go to UniProtKB:  P05109
PHAROS:  P05109
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05109
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
FA [auth F],
GA [auth F],
K [auth A],
L [auth A],
P [auth B],
FA [auth F],
GA [auth F],
K [auth A],
L [auth A],
P [auth B],
R [auth B],
U [auth C],
V [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
AA [auth D],
KA [auth G],
M [auth A],
Q [auth B],
W [auth C],
AA [auth D],
KA [auth G],
M [auth A],
Q [auth B],
W [auth C],
X [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
BA [auth E],
CA [auth E],
DA [auth F],
EA [auth F],
I [auth A],
BA [auth E],
CA [auth E],
DA [auth F],
EA [auth F],
I [auth A],
IA [auth G],
J [auth A],
JA [auth G],
LA [auth H],
MA [auth H],
N [auth B],
O [auth B],
S [auth C],
T [auth C],
Y [auth D],
Z [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
HA [auth F],
NA [auth H]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.93α = 90
b = 85.09β = 90
c = 197.2γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2016-07-27
    Changes: Database references
  • Version 1.2: 2018-01-17
    Changes: Data collection