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- PDB-4oi7: RAGE recognizes nucleic acids and promotes inflammatory responses... -

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Basic information

Entry
Database: PDB / ID: 4oi7
TitleRAGE recognizes nucleic acids and promotes inflammatory responses to DNA
Components
  • 5'-D(*CP*AP*CP*GP*TP*TP*CP*GP*TP*AP*GP*CP*AP*TP*CP*GP*TP*TP*GP*CP*AP*G)-3'
  • 5'-D(*CP*TP*GP*CP*AP*AP*CP*GP*AP*TP*GP*CP*TP*AP*CP*GP*AP*AP*CP*GP*TP*G)-3'
  • Advanced glycosylation end product-specific receptor
KeywordsTRANSPORT PROTEIN / SIGNALING PROTEIN/DNA / protein-DNA complex / Ig fold / DNA binding / extracellular receptor / SIGNALING PROTEIN-DNA complex
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 / negative regulation of long-term synaptic depression / positive regulation of dendritic cell differentiation ...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 / negative regulation of long-term synaptic depression / positive regulation of dendritic cell differentiation / regulation of p38MAPK cascade / regulation of non-canonical NF-kappaB signal transduction / positive regulation of amyloid precursor protein catabolic process / transcytosis / induction of positive chemotaxis / positive regulation of heterotypic cell-cell adhesion / positive regulation of monocyte chemotactic protein-1 production / S100 protein binding / positive regulation of p38MAPK cascade / regulation of long-term synaptic potentiation / protein localization to membrane / regulation of spontaneous synaptic transmission / negative regulation of connective tissue replacement involved in inflammatory response wound healing / scavenger receptor activity / laminin receptor activity / negative regulation of interleukin-10 production / positive regulation of double-strand break repair / 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 / phagocytosis / phagocytic cup / transport across blood-brain barrier / positive regulation of chemokine production / positive regulation of interleukin-12 production / astrocyte activation / positive regulation of interleukin-1 beta production / positive regulation of JNK cascade / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / TAK1-dependent IKK and NF-kappa-B activation / 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 tumor necrosis factor production / cell junction / transmembrane signaling receptor activity / signaling receptor activity / amyloid-beta binding / regulation of inflammatory response / histone binding / molecular adaptor activity / learning or memory / early endosome / 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/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin ...: / CD80-like, immunoglobulin C2-set / CD80-like C2-set 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.104 Å
AuthorsJin, T. / Jiang, J. / Xiao, T.
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 19, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionApr 30, 2014ID: 3S58
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 9, 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: Advanced glycosylation end product-specific receptor
E: 5'-D(*CP*TP*GP*CP*AP*AP*CP*GP*AP*TP*GP*CP*TP*AP*CP*GP*AP*AP*CP*GP*TP*G)-3'
F: 5'-D(*CP*AP*CP*GP*TP*TP*CP*GP*TP*AP*GP*CP*AP*TP*CP*GP*TP*TP*GP*CP*AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1448
Polymers61,8964
Non-polymers2484
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-16 kcal/mol
Surface area30470 Å2
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

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Components

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


Mass: 24195.580 Da / Num. of mol.: 2 / Fragment: UNP residues 23-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGER, RAGE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q15109
#2: DNA chain 5'-D(*CP*TP*GP*CP*AP*AP*CP*GP*AP*TP*GP*CP*TP*AP*CP*GP*AP*AP*CP*GP*TP*G)-3'


Mass: 6761.380 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*AP*CP*GP*TP*TP*CP*GP*TP*AP*GP*CP*AP*TP*CP*GP*TP*TP*GP*CP*AP*G)-3'


Mass: 6743.352 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
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: 3.18 Å3/Da / Density % sol: 61.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / 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

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 22, 2010
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 13957 / Num. obs: 13817 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.14
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 6 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 1.97 / Num. unique all: 575 / % possible all: 85.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_1448)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3O3U

3o3u


Resolution: 3.104→43.138 Å / σ(F): 1.38 / Phase error: 26.77 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 687 4.99 %RANDOM
Rwork0.2153 ---
obs0.2174 13758 98.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.104→43.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3274 896 16 42 4228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054381
X-RAY DIFFRACTIONf_angle_d0.976128
X-RAY DIFFRACTIONf_dihedral_angle_d23.8361728
X-RAY DIFFRACTIONf_chiral_restr0.054668
X-RAY DIFFRACTIONf_plane_restr0.005650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1066-3.34490.30561420.27882476X-RAY DIFFRACTION90
3.3449-3.67860.29641360.26062617X-RAY DIFFRACTION95
3.6786-4.20440.2411430.22222604X-RAY DIFFRACTION95
4.2044-5.27280.20891350.18552634X-RAY DIFFRACTION95
5.2728-17.45670.2171290.19272645X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 38.0286 Å / Origin y: -22.2532 Å / Origin z: -12.1861 Å
111213212223313233
T0.3571 Å2-0.0148 Å20.0302 Å2-0.3667 Å20.1149 Å2--0.39 Å2
L0.2473 °2-0.2419 °2-0.0076 °2-0.1217 °2-0.0532 °2--0.2953 °2
S0.1019 Å °-0.148 Å °-0.089 Å °-0.1392 Å °0.0236 Å °-0.0642 Å °-0.0921 Å °-0.1458 Å °-0.0428 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( chain A or chain B )A23 - 233
2X-RAY DIFFRACTION1( chain A or chain B )B21 - 235

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