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- PDB-4ofv: Refinement of RAGE-DNA complex in 3S58 without DNA -

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Basic information

Entry
Database: PDB / ID: 4ofv
TitleRefinement of RAGE-DNA complex in 3S58 without DNA
ComponentsAdvanced glycosylation end product-specific receptor
KeywordsPROTEIN BINDING / Ig domain / receptor / S100 proteins advanced glycation end products Ab oligomers DNA / membrane
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 / 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 / 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 / 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 / fibrillar center / cellular response to amyloid-beta / neuron projection development / positive regulation of NF-kappaB transcription factor activity / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / cell junction / 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 / protein-containing complex binding / cell surface / DNA binding / RNA binding / extracellular region / identical protein binding / nucleus / plasma membrane
Similarity search - Function
: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 / Mainly Beta
Similarity search - Domain/homology
Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.1 Å
AuthorsYatime, L. / Andersen, G.R.
CitationJournal: J.Exp.Med. / Year: 2013
Title: RAGE is a nucleic acid receptor that promotes inflammatory responses to DNA.
Authors: Sirois, C.M. / Jin, T. / Miller, A.L. / Bertheloot, D. / Nakamura, H. / Horvath, G.L. / Mian, A. / Jiang, J. / Schrum, J. / Bossaller, L. / Pelka, K. / Garbi, N. / Brewah, Y. / Tian, J. / ...Authors: Sirois, C.M. / Jin, T. / Miller, A.L. / Bertheloot, D. / Nakamura, H. / Horvath, G.L. / Mian, A. / Jiang, J. / Schrum, J. / Bossaller, L. / Pelka, K. / Garbi, N. / Brewah, Y. / Tian, J. / Chang, C. / Chowdhury, P.S. / Sims, G.P. / Kolbeck, R. / Coyle, A.J. / Humbles, A.A. / Xiao, T.S. / Latz, E.
History
DepositionJan 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.5Mar 12, 2025Group: Database references / Category: citation / citation_author
Remark 0THE ENTRY PDB ID 4OFV REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA OF ENTRY PDB ID 3S58

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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: Advanced glycosylation end product-specific receptor


Theoretical massNumber of molelcules
Total (without water)48,3912
Polymers48,3912
Non-polymers00
Water00
1
A: Advanced glycosylation end product-specific receptor


Theoretical massNumber of molelcules
Total (without water)24,1961
Polymers24,1961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Advanced glycosylation end product-specific receptor


Theoretical massNumber of molelcules
Total (without water)24,1961
Polymers24,1961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.920, 77.920, 224.387
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and resid 1:117
211chain B and resid 1:117
112chain A and resid 119:233
212chain B and resid 119:233

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.491606, -0.87081, -0.003618), (-0.870817, -0.491601, -0.002298), (0.000223, 0.00428, -0.999991)0.063846, 0.287838, -24.7736
2given(0.503308, -0.864104, 0.002295), (-0.864107, -0.503309, -4.17635), (0.001191, -0.001962, -0.999997)-0.094826, -0.258608, -25.0128

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Components

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


Mass: 24195.580 Da / Num. of mol.: 2 / Fragment: VC1 fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGER, RAGE / Production host: Escherichia coli (E. coli) / References: UniProt: Q15109
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: 4.19 Å3/Da / Density % sol: 70.61 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 3S58
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.4
Details: 12% PEG6000, 0.1 M Tris-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Details: THE ENTRY USES THE SF FILE FROM ENTRY PDB ID 3S58
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 13817 / % possible obs: 99 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 76.7 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3S58

3s58
PDB Unreleased entry


Resolution: 3.1→43.14 Å / SU ML: 0.45 / σ(F): 1.29 / Phase error: 28.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 683 4.98 %
Rwork0.22 --
obs0.221 13727 98.7 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.76 Å2
Refinement stepCycle: LAST / Resolution: 3.1→43.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3274 0 0 0 3274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023365
X-RAY DIFFRACTIONf_angle_d0.6734574
X-RAY DIFFRACTIONf_dihedral_angle_d12.9161292
X-RAY DIFFRACTIONf_chiral_restr0.028494
X-RAY DIFFRACTIONf_plane_restr0.004606
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A738X-RAY DIFFRACTIONPOSITIONAL
12B738X-RAY DIFFRACTIONPOSITIONAL0.01
21A872X-RAY DIFFRACTIONPOSITIONAL
22B872X-RAY DIFFRACTIONPOSITIONAL0.001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.104-3.34360.32711410.2692481X-RAY DIFFRACTION95
3.3436-3.67990.30291360.24532630X-RAY DIFFRACTION100
3.6799-4.2120.22591440.20752634X-RAY DIFFRACTION100
4.212-5.30510.19441350.18872644X-RAY DIFFRACTION100
5.3051-43.1420.23771270.22922655X-RAY DIFFRACTION99
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)
15.8141.1068-0.77017.32230.59565.86540.4338-0.48650.15330.695-0.3493-0.303-0.65620.0794-0.39870.8040.05590.07740.60270.08960.700936.1235-7.8076-8.6239
25.05031.2740.59825.431-0.58395.5792-0.28150.3349-0.2996-0.77590.25520.13430.2929-0.35430.03320.6115-0.04750.02050.82290.09450.727824.8597-27.6528-16.2887
32.3467-1.1603-2.31344.6673-0.4926.33230.68740.2340.2165-0.5265-0.2401-0.0864-0.3610.2157-0.15190.87450.18820.20360.77660.09080.773352.6745-11.8842-46.0145
44.40120.76360.75862.4733-2.67136.27590.1137-0.9474-0.24480.0390.44710.21090.2233-0.428-0.27490.67620.0592-0.031.06830.21420.786236.6343-39.812821.3353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 23:118 )A23 - 118
2X-RAY DIFFRACTION2( CHAIN B AND RESID 23:118 )B23 - 118
3X-RAY DIFFRACTION3( CHAIN A AND RESID 119:233 )A119 - 233
4X-RAY DIFFRACTION4( CHAIN B AND RESID 119:234 )B119 - 234

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