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- PDB-4oi8: RAGE is a nucleic acid receptor that promotes inflammatory respon... -

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Basic information

Entry
Database: PDB / ID: 4oi8
TitleRAGE is a nucleic acid receptor that promotes inflammatory responses to DNA.
Components
  • 5'-D(*CP*CP*AP*TP*GP*AP*CP*TP*GP*TP*AP*GP*GP*AP*AP*AP*CP*TP*CP*TP*AP*GP*A)-3'
  • 5'-D(*CP*TP*CP*TP*AP*GP*AP*GP*TP*TP*TP*CP*CP*TP*AP*CP*AP*GP*TP*CP*AP*TP*G)-3'
  • Advanced glycosylation end product-specific receptor
KeywordsTRANSPORT PROTEIN / SIGNALING PROTEIN/DNA / Ig fold / DNA binding / 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 / 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 / transcytosis / induction of positive chemotaxis / positive regulation of heterotypic cell-cell adhesion / S100 protein binding / positive regulation of p38MAPK cascade / protein localization to membrane / positive regulation of monocyte chemotactic protein-1 production / regulation of long-term synaptic potentiation / 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 / phagocytosis / phagocytic cup / 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 / positive regulation of non-canonical NF-kappaB signal transduction / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of NF-kappaB transcription factor activity / 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 / molecular adaptor activity / histone binding / response to hypoxia / learning or memory / early endosome / 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
DNA / DNA (> 10) / Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.101 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: 3S59
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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*CP*AP*TP*GP*AP*CP*TP*GP*TP*AP*GP*GP*AP*AP*AP*CP*TP*CP*TP*AP*GP*A)-3'
F: 5'-D(*CP*TP*CP*TP*AP*GP*AP*GP*TP*TP*TP*CP*CP*TP*AP*CP*AP*GP*TP*CP*AP*TP*G)-3'


Theoretical massNumber of molelcules
Total (without water)62,4714
Polymers62,4714
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-28 kcal/mol
Surface area31460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.560, 78.560, 224.801
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) / References: UniProt: Q15109
#2: DNA chain 5'-D(*CP*CP*AP*TP*GP*AP*CP*TP*GP*TP*AP*GP*GP*AP*AP*AP*CP*TP*CP*TP*AP*GP*A)-3'


Mass: 7073.599 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*TP*CP*TP*AP*GP*AP*GP*TP*TP*TP*CP*CP*TP*AP*CP*AP*GP*TP*CP*AP*TP*G)-3'


Mass: 7006.533 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.21 Å3/Da / Density % sol: 61.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M HEPES, pH 7.4, 5% PEG6000, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.03 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 27, 2013
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(220) / 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. obs: 13924 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 79.2 Å2
Reflection shellHighest resolution: 3.1 Å

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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 / Resolution: 3.101→43.329 Å / σ(F): 1.36 / Phase error: 29.25 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2667 1410 10.13 %
Rwork0.2246 --
obs0.2288 13920 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.101→43.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3274 934 0 25 4233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084411
X-RAY DIFFRACTIONf_angle_d0.9146184
X-RAY DIFFRACTIONf_dihedral_angle_d19.9411744
X-RAY DIFFRACTIONf_chiral_restr0.067676
X-RAY DIFFRACTIONf_plane_restr0.006652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1019-3.21270.34251180.32141060X-RAY DIFFRACTION75
3.2127-3.34120.29881390.28931213X-RAY DIFFRACTION86
3.3412-3.49320.36151410.27741284X-RAY DIFFRACTION90
3.4932-3.67710.33561400.26331282X-RAY DIFFRACTION90
3.6771-3.90720.27571430.24481283X-RAY DIFFRACTION90
3.9072-4.20850.29321430.22621246X-RAY DIFFRACTION90
4.2085-4.63110.27111440.20671298X-RAY DIFFRACTION90
4.6311-5.29920.19891440.19611268X-RAY DIFFRACTION90
5.2992-6.66870.23451460.20681279X-RAY DIFFRACTION90
6.6687-34.79210.25771450.19861289X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: 38.3424 Å / Origin y: -22.4392 Å / Origin z: -10.8533 Å
111213212223313233
T0.4562 Å20.0421 Å20.0325 Å2-0.4485 Å20.0778 Å2--0.4324 Å2
L0.6355 °2-0.2659 °2-0.0917 °2-0.3589 °2-0.142 °2--0.8633 °2
S0.1251 Å °-0.1018 Å °-0.0078 Å °-0.117 Å °0.0127 Å °-0.0261 Å °-0.289 Å °-0.2804 Å °-0.0647 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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