5HLV

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

PDB DOI: https://doi.org/10.2210/pdb5HLV/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-01-15 Released: 2016-06-08
Deposition Author(s): Lin, H., Andersen, G.R., Yatime, L.

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 1.3 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

PubMed: 27251136 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/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. 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

Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000, Aarhus, Denmark.

Macromolecule Content

Total Structure Weight: 88.99 kDa
Atom Count: 6,199
Modelled Residue Count: 710
Deposited Residue Count: 752
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein S100-A8	A, B, C, D, E A, B, C, D, E, F, G, H	94	Homo sapiens	Mutation(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 GTEx: ENSG00000143546
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05109
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain FA [auth F] SDF format, chain GA [auth F] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C]	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		Interactions Focus chain FA [auth F] Focus chain GA [auth F] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain FA [auth F] Focus chain GA [auth F] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain KA [auth G] SDF format, chain M [auth A] SDF format, chain Q [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain KA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C]	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		Interactions Focus chain AA [auth D] Focus chain KA [auth G] Focus chain M [auth A] Focus chain Q [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain KA [auth G] Focus chain M [auth A] Focus chain Q [auth B] Focus chain W [auth C] Focus chain X [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain I [auth A] SDF format, chain IA [auth G] SDF format, chain J [auth A] SDF format, chain JA [auth G] SDF format, chain LA [auth H] SDF format, chain MA [auth H] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth G] MOL2 format, chain LA [auth H] MOL2 format, chain MA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D]	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		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain I [auth A] Focus chain IA [auth G] Focus chain J [auth A] Focus chain JA [auth G] Focus chain LA [auth H] Focus chain MA [auth H] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain I [auth A] Focus chain IA [auth G] Focus chain J [auth A] Focus chain JA [auth G] Focus chain LA [auth H] Focus chain MA [auth H] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain HA [auth F] SDF format, chain NA [auth H] MOL2 format, chain HA [auth F] MOL2 format, chain NA [auth H]	HA [auth F], NA [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain HA [auth F] Focus chain NA [auth H] Interactions & Density Focus chain HA [auth F] Focus chain NA [auth H]

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 = 50.93	α = 90
b = 85.09	β = 90
c = 197.2	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-06-08

Deposition Author(s):

Lin, H.

Andersen, G.R.

Yatime, L.

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
Version 1.3: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description