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- PDB-4of5: Refinement of RAGE-DNA complex in 3S59 without DNA -

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Basic information

Entry
Database: PDB / ID: 4of5
TitleRefinement of RAGE-DNA complex in 3S59 without DNA
ComponentsAdvanced glycosylation end product-specific receptor
KeywordsSIGNALING PROTEIN / membrane / SIGNALING PROTEINIg domain / receptor / S100 proteins Ab oligomer AGE DNA
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 / positive regulation of dendritic cell differentiation ...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 / 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 / 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 / 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 / regulation of synaptic plasticity / 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 / positive regulation of tumor necrosis factor production / neuron projection development / cell junction / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / regulation of inflammatory response / postsynapse / 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 / protein-containing complex binding / cell surface / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype ...CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / 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 / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsYatime, L. / Andersen, G.R.
CitationJournal: J.Exp.Med. / Year: 2014
Title: The specificity of DNA recognition by the RAGE receptor.
Authors: Yatime, L. / Andersen, G.R.
History
DepositionJan 14, 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
Remark 0THE ENTRY PDB ID 4OF5 REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA OF ENTRY PDB ID 3S59

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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)79.121, 79.121, 224.045
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and resid 1:117
21chain B and resid 1:117
12chain A and resid 119:240
22chain B and resid 119:240

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and resid 1:117A1 - 117
211chain B and resid 1:117B1 - 117
112chain A and resid 119:240A119 - 240
212chain B and resid 119:240B119 - 240

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.499223, -0.866471, -0.001884), (-0.866472, -0.499225, 0.000549), (-0.001416, 0.001358, -0.999998)-0.013141, 0.04265, -24.963499
2given(0.50579, -0.862656, 0.001256), (-0.862654, -0.505792, -0.001809), (0.002196, -0.000169, -0.999998)-0.12424, -0.311711, -25.1273

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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

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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: 4.33 Å3/Da / Density % sol: 71.57 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 3S59
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 10% 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 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Details: THE ENTRY USES THE SF FILE FROM ENTRY PDB ID 3S59
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S59

3s59
PDB Unreleased entry


Resolution: 2.803→39.56 Å / FOM work R set: 0.8013 / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.72 / Stereochemistry target values: ML / Details: AUTHOR USED THE SF DATA FROM ENTRY 3S58
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 990 5.15 %The same R-free set as in 3S59
Rwork0.2199 ---
obs0.2208 19224 98.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 219.73 Å2 / Biso mean: 85.8 Å2 / Biso min: 36.52 Å2
Refinement stepCycle: LAST / Resolution: 2.803→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3267 0 0 0 3267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023358
X-RAY DIFFRACTIONf_angle_d0.6274564
X-RAY DIFFRACTIONf_chiral_restr0.027492
X-RAY DIFFRACTIONf_plane_restr0.004605
X-RAY DIFFRACTIONf_dihedral_angle_d13.4351290
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A738X-RAY DIFFRACTIONPOSITIONAL0.01
12B738X-RAY DIFFRACTIONPOSITIONAL0.01
21A872X-RAY DIFFRACTIONPOSITIONAL0.001
22B872X-RAY DIFFRACTIONPOSITIONAL0.001
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.803-2.95080.33821330.27642544267796
2.9508-3.13560.28061490.269326012750100
3.1356-3.37760.30211420.259226172759100
3.3776-3.71720.22321520.220626152767100
3.7172-4.25460.20411330.205826202753100
4.2546-5.35820.19351510.179426342785100
5.3582-39.56440.25181300.23012603273397
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)
14.59920.2857-1.08255.732-0.87585.70510.2923-0.43620.0940.6369-0.2801-0.1247-0.6436-0.1042-0.10640.61210.09280.06070.47380.04680.432536.5941-7.9839-8.7892
24.04551.2542-0.68364.9788-1.16065.5119-0.27710.368-0.0979-0.78850.3430.07970.1762-0.579-0.04940.3955-0.00560.01360.65710.0680.418725.2603-27.8472-16.2805
33.919-2.1536-3.74934.25650.99269.72950.67340.19770.2013-0.6531-0.2593-0.1093-0.38740.0808-0.23140.79280.1610.17790.63670.07510.501853.5142-12.3436-45.9972
44.2997-0.65631.39832.5577-3.0238.3560.1355-0.8699-0.2479-0.0060.3550.19210.2284-0.3012-0.05360.57780.0212-0.03880.90370.18420.542837.5378-40.434721.418
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 22:118 )B22 - 118
3X-RAY DIFFRACTION3( CHAIN A AND RESID 119:233 )A119 - 233
4X-RAY DIFFRACTION4( CHAIN B AND RESID 119:235 )B119 - 235

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