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- PDB-4ybh: Crystal structure of the human RAGE ectodomain (VC1C2 fragment) i... -

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Basic information

Entry
Database: PDB / ID: 4ybh
TitleCrystal structure of the human RAGE ectodomain (VC1C2 fragment) in complex with human S100A6
Components
  • Advanced glycosylation end product-specific receptor
  • Protein S100-A6
KeywordsSIGNALING PROTEIN / signaling complex / pattern recognition receptor / dimerization / EF-hand calcium binding protein / immunoglobulin domain
Function / homology
Function and homology information


regulation of CD4-positive, alpha-beta T cell activation / negative regulation of blood circulation / advanced glycation end-product receptor activity / positive regulation of endothelin production / regulation of T cell mediated cytotoxicity / glucose mediated signaling pathway / negative regulation of long-term synaptic depression / positive regulation of monocyte extravasation / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / monoatomic ion transmembrane transporter activity ...regulation of CD4-positive, alpha-beta T cell activation / negative regulation of blood circulation / advanced glycation end-product receptor activity / positive regulation of endothelin production / regulation of T cell mediated cytotoxicity / glucose mediated signaling pathway / negative regulation of long-term synaptic depression / positive regulation of monocyte extravasation / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / monoatomic ion transmembrane transporter activity / positive regulation of dendritic cell differentiation / regulation of p38MAPK cascade / regulation of non-canonical NF-kappaB signal transduction / scavenger receptor activity / induction of positive chemotaxis / transcytosis / protein localization to membrane / positive regulation of monocyte chemotactic protein-1 production / positive regulation of heterotypic cell-cell adhesion / S100 protein binding / regulation of long-term synaptic potentiation / regulation of spontaneous synaptic transmission / laminin receptor activity / positive regulation of p38MAPK cascade / negative regulation of interleukin-10 production / positive regulation of activated T cell proliferation / tropomyosin binding / response to amyloid-beta / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / transport across blood-brain barrier / negative regulation of long-term synaptic potentiation / positive regulation of chemokine production / ruffle / positive regulation of interleukin-12 production / axonogenesis / positive regulation of interleukin-1 beta production / astrocyte activation / positive regulation of JNK cascade / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / regulation of synaptic plasticity / cytoplasmic side of plasma membrane / fibrillar center / response to wounding / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to amyloid-beta / transmembrane signaling receptor activity / positive regulation of interleukin-6 production / calcium-dependent protein binding / positive regulation of tumor necrosis factor production / neuron projection development / positive regulation of fibroblast proliferation / cell junction / nuclear envelope / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / regulation of inflammatory response / postsynapse / collagen-containing extracellular matrix / molecular adaptor activity / learning or memory / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / inflammatory response / positive regulation of protein phosphorylation / apical plasma membrane / calcium ion binding / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / signal transduction / protein homodimerization activity / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Protein S100-A6 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin ...Protein S100-A6 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / EF-hand / Recoverin; domain 1 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / Immunoglobulins and major histocompatibility complex proteins signature. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Protein S100-A6 / Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsYatime, L. / Andersen, G.R.
CitationJournal: Structure / Year: 2016
Title: The Structure of the RAGE:S100A6 Complex Reveals a Unique Mode of Homodimerization for S100 Proteins.
Authors: Yatime, L. / Betzer, C. / Jensen, R.K. / Mortensen, S. / Jensen, P.H. / Andersen, G.R.
History
DepositionFeb 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Nov 23, 2016Group: Database references
Revision 1.3Dec 14, 2016Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Advanced glycosylation end product-specific receptor
B: Protein S100-A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,89519
Polymers43,0022
Non-polymers89217
Water3,747208
1
A: Advanced glycosylation end product-specific receptor
B: Protein S100-A6
hetero molecules

A: Advanced glycosylation end product-specific receptor
B: Protein S100-A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,78938
Polymers86,0044
Non-polymers1,78534
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_657-x+1,y,-z+21
Buried area10240 Å2
ΔGint-655 kcal/mol
Surface area41270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.980, 112.530, 139.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-665-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Advanced glycosylation end product-specific receptor / Receptor for advanced glycosylation end products


Mass: 32680.297 Da / Num. of mol.: 1
Fragment: V, C1 and C2 domains (VC1C2 module), full-length ectodomain, UNP residues 23-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGER, RAGE / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15109
#2: Protein Protein S100-A6 / Calcyclin / Growth factor-inducible protein 2A9 / MLN 4 / Prolactin receptor-associated protein / ...Calcyclin / Growth factor-inducible protein 2A9 / MLN 4 / Prolactin receptor-associated protein / PRA / S100 calcium-binding protein A6


Mass: 10321.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A6, CACY / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P06703

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Non-polymers , 5 types, 225 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Zn acetate, 0.1 M Na cacodylate pH 6.5, 10% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 23764 / Num. obs: 23764 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 43.18 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.093 / Χ2: 0.945 / Net I/σ(I): 14.21 / Num. measured all: 110920
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.4-2.50.6690.7232.0612450274527380.81999.7
2.5-2.60.8190.4992.9210976227222680.5699.8
2.6-2.70.880.3913.869784199919960.43999.8
2.7-2.850.9270.2965.0211929246424540.33299.6
2.85-30.9610.2196.649584201620080.24699.6
3-3.20.9820.1469.569849212421130.16499.5
3.2-3.50.9920.08714.7410544238323650.09899.2
3.5-40.9970.05521.8311669254525440.062100
4-4.50.9980.0430.847438154615460.045100
4.5-50.9990.03433.41472110009950.03999.5
5-5.50.9990.03533.2830346576530.0499.4
5.5-70.9980.0430.254509106810520.04598.5
7-90.9990.02839.2822635365310.03299.1
9-120.9990.02551.9313002842810.02898.9
12-150.9990.02253.514411051040.02599
15-2010.02154.5228170680.02497.1
200.9990.02348.6214857480.02784.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1839)refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P2Y

4p2y


Resolution: 2.4→46.799 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1169 5.07 %random selection
Rwork0.1947 ---
obs0.1967 23037 96.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→46.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2992 0 26 208 3226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063113
X-RAY DIFFRACTIONf_angle_d0.7014183
X-RAY DIFFRACTIONf_dihedral_angle_d13.8431174
X-RAY DIFFRACTIONf_chiral_restr0.026464
X-RAY DIFFRACTIONf_plane_restr0.004554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50920.35121430.29392598X-RAY DIFFRACTION93
2.5092-2.64150.30321380.24782667X-RAY DIFFRACTION95
2.6415-2.8070.27431460.22912657X-RAY DIFFRACTION96
2.807-3.02370.26341300.23832744X-RAY DIFFRACTION97
3.0237-3.32790.25831560.20712706X-RAY DIFFRACTION97
3.3279-3.80930.2311410.18672779X-RAY DIFFRACTION98
3.8093-4.79850.18931580.15782817X-RAY DIFFRACTION99
4.7985-46.80770.21011570.17782900X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.46360.76760.70485.2614-1.06384.998-0.0223-0.4221-0.33950.74180.1056-0.03740.2853-0.0614-0.09020.32950.01250.03030.29590.03110.271232.0882-130.131173.0606
20.60740.0176-0.50654.1151-2.57612.8775-0.0314-0.0444-0.02170.10460.05460.31390.0215-0.2123-0.10410.2259-0.04350.00270.3604-0.00260.32824.691-107.7002153.9669
31.1078-0.43210.59274.3857-3.69645.28-0.251-0.17010.17470.35870.23230.1419-0.5709-0.57990.02540.2030.0438-0.04720.3348-0.02890.320325.3021-94.08145.338
40.998-1.0455-0.15922.84380.3161.7938-0.0403-0.12450.28050.4679-0.1467-0.7808-0.46020.26740.2180.7272-0.0641-0.26450.59470.14570.744715.676-69.6006109.8272
52.32020.81480.35312.2855-0.43957.99710.03840.11910.3238-0.03280.05310.1035-0.6902-0.6884-0.1830.41010.07-0.05830.3080.07640.427728.6508-78.4961130.6451
65.5305-0.344-0.1972.0680.91367.16070.14740.28890.5753-0.26610.2211-0.2711-1.14360.6595-0.22880.7481-0.1013-0.01920.35620.050.494240.6855-70.6918124.2623
71.67660.340.5844.24721.44670.7447-0.04650.02820.00340.2757-0.0045-0.1299-0.30040.16430.00740.4827-0.0647-0.02780.38610.04670.321241.6728-76.0355133.6915
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 94 )
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 205 )
3X-RAY DIFFRACTION3chain 'A' and (resid 206 through 238 )
4X-RAY DIFFRACTION4chain 'A' and (resid 239 through 322 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 30 )
6X-RAY DIFFRACTION6chain 'B' and (resid 31 through 60 )
7X-RAY DIFFRACTION7chain 'B' and (resid 61 through 90 )

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