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- PDB-4p2y: Crystal structure of the human RAGE ectodomain (fragment VC1C2) i... -

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Basic information

Entry
Database: PDB / ID: 4p2y
TitleCrystal structure of the human RAGE ectodomain (fragment VC1C2) in complex with mouse S100A6
Components
  • Advanced glycosylation end product-specific receptor
  • Protein S100-A6
KeywordsSIGNALING PROTEIN / signaling complex / pattern recognition receptor / dimerization / EF-hand calcium binding protein
Function / homology
Function and homology information


advanced glycation end-product receptor activity / negative regulation of blood circulation / positive regulation of endothelin production / regulation of CD4-positive, alpha-beta T cell activation / glucose mediated signaling pathway / positive regulation of monocyte extravasation / regulation of T cell mediated cytotoxicity / positive regulation of DNA-templated DNA replication / positive regulation of dendritic cell differentiation / negative regulation of long-term synaptic depression ...advanced glycation end-product receptor activity / negative regulation of blood circulation / positive regulation of endothelin production / regulation of CD4-positive, alpha-beta T cell activation / glucose mediated signaling pathway / positive regulation of monocyte extravasation / regulation of T cell mediated cytotoxicity / positive regulation of DNA-templated DNA replication / positive regulation of dendritic cell differentiation / negative regulation of long-term synaptic depression / monoatomic ion transmembrane transporter activity / regulation of p38MAPK cascade / regulation of non-canonical NF-kappaB signal transduction / positive regulation of amyloid precursor protein catabolic process / induction of positive chemotaxis / transcytosis / positive regulation of monocyte chemotactic protein-1 production / positive regulation of heterotypic cell-cell adhesion / S100 protein binding / protein localization to membrane / regulation of long-term synaptic potentiation / positive regulation of p38MAPK cascade / negative regulation of connective tissue replacement involved in inflammatory response wound healing / regulation of spontaneous synaptic transmission / scavenger receptor activity / laminin receptor activity / positive regulation of double-strand break repair / negative regulation of interleukin-10 production / tropomyosin binding / positive regulation of activated T cell proliferation / response to amyloid-beta / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / negative regulation of long-term synaptic potentiation / phagocytic cup / phagocytosis / transport across blood-brain barrier / positive regulation of chemokine production / ruffle / positive regulation of interleukin-12 production / 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 / positive regulation of non-canonical NF-kappaB signal transduction / regulation of synaptic plasticity / positive regulation of interleukin-6 production / response to wounding / cytoplasmic side of plasma membrane / fibrillar center / cellular response to amyloid-beta / neuron projection development / calcium-dependent protein binding / positive regulation of NF-kappaB transcription factor activity / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / cell junction / nuclear envelope / signaling receptor activity / amyloid-beta binding / regulation of inflammatory response / : / molecular adaptor activity / histone binding / learning or memory / response to hypoxia / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / postsynapse / apical plasma membrane / inflammatory response / calcium ion binding / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / DNA binding / RNA binding / extracellular region / zinc ion binding / identical protein binding / nucleus / plasma membrane / 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 ...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 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 subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / 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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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
DepositionMar 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Refinement description / Category: citation / software / Item: _citation.journal_id_CSD
Revision 1.3Sep 27, 2023Group: 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.ptnr2_auth_asym_id / _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_symmetry
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)43,97223
Polymers42,8732
Non-polymers1,09921
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-259 kcal/mol
Surface area22530 Å2
MethodPISA
2
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

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)175,88792
Polymers171,4928
Non-polymers4,39584
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area31060 Å2
ΔGint-1338 kcal/mol
Surface area74340 Å2
MethodPISA
3
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)87,94346
Polymers85,7464
Non-polymers2,19742
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area11970 Å2
ΔGint-616 kcal/mol
Surface area40730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.780, 113.390, 140.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
DetailsThe biological assembly is a heterotetramer generated from the heterodimer in the asymmetric unit by the operation: -x, y, -z.

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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 (E. coli) / Strain (production host): Shuffle T7 Express / References: UniProt: Q15109
#2: Protein Protein S100-A6 / 5B10 / Calcyclin / Prolactin receptor-associated protein / S100 calcium-binding protein A6


Mass: 10192.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: S100a6, Cacy / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14069

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Non-polymers , 5 types, 207 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / 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.: 186 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.61 Å3/Da / Density % sol: 65.9 %
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: MAX II / Beamline: I911-2 / Wavelength: 1.041 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 19, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.041 Å / Relative weight: 1
ReflectionResolution: 2.3→35 Å / Num. obs: 27554 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 44.57 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.08 / Χ2: 1.032 / Net I/σ(I): 15.56
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.3-2.367.20.9370.4354.1214865204820480.469100
2.36-2.430.9540.3465.0715219209220920.373100
2.43-2.50.9720.2836.1713871190519050.305100
2.5-2.60.980.2147.9816993234323430.23100
2.6-2.70.9870.1789.7314774203620360.191100
2.7-2.850.9910.13912.3218266253725370.15100
2.85-30.9930.11214.8814673204220420.121100
3-3.20.9950.09217.915537219121890.09999.9
3.2-3.50.9960.07321.816822242124210.079100
3.5-40.9970.06524.4717456258625840.07199.9
4-4.50.9970.05926.310505158115800.06499.9
4.5-50.9980.05526.976745101110080.0699.7
5-5.50.9980.05327.1946866936920.05799.9
5.5-70.9970.05526.727175108610830.0699.7
7-90.9970.04927.1434355415360.05499.1
9-120.9940.05426.8416332922780.05995.2
12-150.9950.05325.19514108970.05989.8
15-200.9910.05824.0326872550.06576.4
200.9960.06217.1610157280.0749.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LP5, 1K96

4lp5

1k96


Resolution: 2.3→27.242 Å / FOM work R set: 0.8478 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2067 1355 5.01 %random selection
Rwork0.1866 25709 --
obs0.1877 27064 98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.91 Å2 / Biso mean: 52.48 Å2 / Biso min: 17.59 Å2
Refinement stepCycle: final / Resolution: 2.3→27.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2974 0 42 186 3202
Biso mean--56.75 46 -
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043081
X-RAY DIFFRACTIONf_angle_d0.8754182
X-RAY DIFFRACTIONf_chiral_restr0.059463
X-RAY DIFFRACTIONf_plane_restr0.003557
X-RAY DIFFRACTIONf_dihedral_angle_d14.741170
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.30.27521310.2279252097
2.38220.25961270.2188250797
2.47750.2751350.2065250997
2.59020.2441310.2022254498
2.72660.27471360.2045252898
2.89720.23441240.2181258099
3.12060.19421450.1944257799
3.43410.19871450.1731262499
3.92980.16061430.149262399
4.9463-27.24390.19991380.1934269797
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)
15.25861.3576-0.85326.23481.3175.5520.0424-0.71480.39240.79790.017-0.0176-0.25830.1279-0.02550.27130.0264-0.03520.3278-0.05350.24455.7784131.096333.1544
21.06190.01620.31265.9863.80463.5627-0.0417-0.08120.01410.30180.168-0.39390.20080.3851-0.15050.14780.0026-0.00590.29870.0110.259412.5367106.702913.7986
32.3074-2.3078-0.83262.62071.8923.7491-0.2407-0.096-0.58760.5576-0.24831.07940.6888-0.51680.4850.5915-0.06760.28380.5948-0.16690.746822.559871.4764-29.0933
41.23010.9628-0.18191.14740.9429.25230.18480.1715-0.3187-0.1810.0013-0.18141.01790.9888-0.17690.4040.08470.08190.2663-0.07230.37299.201279.3921-9.1961
54.697-2.6336-0.13517.3386-0.14744.3816-0.06990.3665-1.0798-0.7550.14320.37361.4669-0.4051-0.060.8158-0.12590.07750.3298-0.11580.5179-2.692271.4549-15.5723
63.2449-1.30260.79468.0662-4.69665.3045-0.0631-0.086-0.26340.47690.12940.33570.4278-0.171-0.06730.5125-0.07220.05590.2682-0.06570.2953-3.653677.266-6.3623
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 21:94)A21 - 94
2X-RAY DIFFRACTION2chain 'A' and (resseq 95:230)A95 - 230
3X-RAY DIFFRACTION3chain 'A' and (resseq 231:321)A231 - 321
4X-RAY DIFFRACTION4chain 'B' and (resseq 2:30)B2 - 30
5X-RAY DIFFRACTION5chain 'B' and (resseq 31:60)B31 - 60
6X-RAY DIFFRACTION6chain 'B' and (resseq 61:89)B61 - 89

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