Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 126972.81 
• Atom Count: 8476 
• Residue Count: 1092 
• Unique protein chains: 1

1GQM

The structure of S100A12 in a hexameric form and its proposed role in receptor signalling

• DOI: 10.2210/pdb1GQM/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Homo sapiens


• Deposited: 2001-11-26 Released: 2002-02-28 
• Deposition Author(s): Moroz, O.V., Antson, A.A., Dodson, E.G., Burrel, H.J., Grist, S.J., Lloyd, R.M., Maitland, N.J., Dodson, G.G., Wilson, K.S., Lukanidin, E., Bronstein, I.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.281 
• R-Value Work: 0.217 

Literature

The Structure of S100A12 in a Hexameric Form and its Proposed Role in Receptor Signalling

Moroz, O.V., Antson, A.A., Dodson, E.J., Burrell, H.J., Grist, S.J., Lloyd, R.M., Maitland, N.J., Dodson, G.G., Wilson, K.S., Lukanidin, E., Bronstein, I.B.

(2002) Acta Crystallogr.,Sect.D 58: 407

• PubMed: 11856825 
• Also Cited By: 2WCF, 2WCE, 2WCB, 2WC8


• PubMed Abstract: 
  

S100A12 is a member of the S100 subfamily of EF-hand calcium-binding proteins; it has been shown to be one of the ligands of the 'receptor for advanced glycation end products' (RAGE) that belongs to the immunoglobulin superfamily and is involved in diabetes, Alzheimer's disease, inflammation and tumour invasion. The structure of the dimeric form of native S100A12 from human granulocytes in the presence of calcium in space group R3 has previously been reported. Here, the structure of a second crystal form in space group P2(1) (unit-cell parameters a = 53.9, b = 100.5, c = 112.7A, beta = 94.6 degrees) solved at 2.7A resolution by molecular replacement using the R3 structure as a search model is reported. Like most S100 proteins, S100A12 is a dimer. However, in the P2(1) crystal form dimers of S100A12 are arranged in a spherical hexameric assembly with an external diameter of about 55 A stabilized by calcium ions bound between adjacent dimers. The putative target-binding sites of S100A12 are located at the outer surface of the hexamer, making it possible for the hexamer to bind several targets. It is proposed that the S100A12 hexameric assembly might interact with three extracellular domains of the receptor, bringing them together into large trimeric assemblies.

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Related Citations: 

• Crystallization and Preliminary X-Ray Diffraction Analysis of Human Calcium-Binding Protein S100A12
  Moroz, O.V.,Antson, A.A.,Dodson, G.G.,Wilson, K.S.,Skibshoj, I.,Lukanidin, E.,Bronstein, I.
  (2000) Acta Crystallogr.,Sect.D 56: 189
• The Three-Dimensional Structure of Human S100A12
  Moroz, O.V.,Antson, A.A.,Murshudov, G.N.,Maitland, N.J.,Dodson, G.G.,Wilson, K.S.,Skibshoj, I.,Lukanidin, E.M.,Bronstein, I.B.
  (2001) Acta Crystallogr.,Sect.D 57: 20




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Organizational Affiliation: 

Department of Chemistry, University of York, York YO10 5DD, England.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CALGRANULIN C	A, B, C, D, E, F, G, H, I, J, K, L	91	Homo sapiens	Mutation(s): 0  Gene Names: S100A12
Find proteins for P80511 (Homo sapiens) Go to Gene View: S100A12 Go to UniProtKB:  P80511

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	A, B, C, D, E, F, G, H, I, J, K, L	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.281 
• R-Value Work: 0.217 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 53.875	α = 90.00
b = 100.501	β = 94.55
c = 112.687	γ = 90.00

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-11-26 
• Released Date: 2002-02-28 
• Deposition Author(s): Moroz, O.V., Antson, A.A., Dodson, E.G., Burrel, H.J., Grist, S.J., Lloyd, R.M., Maitland, N.J., Dodson, G.G., Wilson, K.S., Lukanidin, E., Bronstein, I.B.

Revision History 

• Version 1.0: 2002-02-28
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Advisory, Version format compliance
• Version 1.2: 2011-09-28
  Type: Atomic model, Derived calculations, Non-polymer description
• Version 1.3: 2019-05-08
  Type: Advisory, Data collection, Experimental preparation, Other