4YBH | pdb_00004ybh

Crystal structure of the human RAGE ectodomain (VC1C2 fragment) in complex with human S100A6

PDB DOI: https://doi.org/10.2210/pdb4YBH/pdb

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

Deposited: 2015-02-18 Released: 2016-03-02
Deposition Author(s): Yatime, L., Andersen, G.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.233 (Depositor), 0.240 (DCC)
R-Value Work:
0.195 (Depositor), 0.201 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

The Structure of the RAGE:S100A6 Complex Reveals a Unique Mode of Homodimerization for S100 Proteins.

Yatime, L., Betzer, C., Jensen, R.K., Mortensen, S., Jensen, P.H., Andersen, G.R.

(2016) Structure 24: 2043-2052

PubMed: 27818100 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2016.09.011
Primary Citation Related Structures:
4P2Y, 4YBH

PubMed Abstract:
S100 proteins are calcium-dependent regulators of homeostatic processes. Upon cellular response to stress, and notably during tumorigenesis, they relocalize to the extracellular environment where they induce pro-inflammatory signals by activating the receptor for advanced glycation end products (RAGE), thereby facilitating tumor growth and metastasis. Despite its importance in sustaining inflammation, the structural basis for RAGE-S100 crosstalk is still unknown. Here we report two crystal structures of the RAGE:S100A6 complex encompassing a full-length RAGE ectodomain. The structures, in combination with a comprehensive interaction analysis, suggest that the primary S100A6 binding site is formed by the RAGE C1 domain. Complex formation with S100A6 induces a unique dimeric conformation of RAGE that appears suited for signal transduction and intracellular effector recruitment. Intriguingly, S100A6 adopts a dimeric conformation radically different from all known S100 dimers. We discuss the physiological relevance of this non-canonical homodimeric form in vivo.

Organizational Affiliation

Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark. Electronic address: laure.yatime@inserm.fr.

Macromolecule Content

Total Structure Weight: 43.89 kDa
Atom Count: 3,226
Modeled Residue Count: 391
Deposited Residue Count: 396
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Advanced glycosylation end product-specific receptor	A	304	Homo sapiens	Mutation(s): 0 Gene Names: AGER, RAGE
UniProt & NIH Common Fund Data Resources
Find proteins for Q15109 (Homo sapiens) Explore Q15109 Go to UniProtKB: Q15109
PHAROS: Q15109 GTEx: ENSG00000204305
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15109
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein S100-A6	B	92	Homo sapiens	Mutation(s): 0 Gene Names: S100A6, CACY
UniProt & NIH Common Fund Data Resources
Find proteins for P06703 (Homo sapiens) Explore P06703 Go to UniProtKB: P06703
PHAROS: P06703 GTEx: ENSG00000197956
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06703
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 P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] N [auth A] C [auth A], D [auth A], E [auth A], F [auth A], N [auth A], O [auth B], P [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A], M [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B]	R [auth B], S [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain R [auth B] Focus chain S [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A], J [auth A], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.233 (Depositor), 0.240 (DCC)
R-Value Work: 0.195 (Depositor), 0.201 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.98	α = 90
b = 112.53	β = 90
c = 139.89	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-03-02

Deposition Author(s):

Yatime, L.

Andersen, G.R.

Revision History (Full details and data files)

Version 1.0: 2016-03-02
Type: Initial release
Version 1.1: 2016-11-16
Changes: Database references
Version 1.2: 2016-11-23
Changes: Database references
Version 1.3: 2016-12-14
Changes: Database references
Version 1.4: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-11-13
Changes: Structure summary