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- PDB-4im8: low resolution crystal structure of mouse RAGE -

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Basic information

Entry
Database: PDB / ID: 4im8
Titlelow resolution crystal structure of mouse RAGE
ComponentsAdvanced glycation end-products receptor
KeywordsSIGNALING PROTEIN / heparan sulfate
Function / homology
Function and homology information


positive regulation of signaling / high mobility group box 1 binding / advanced glycation end-product binding / negative regulation of advanced glycation end-product receptor activity / positive regulation of advanced glycation end-product receptor activity / positive regulation of chemokine production => GO:0032722 / positive regulation of tumor necrosis factor production => GO:0032760 / Advanced glycosylation endproduct receptor signaling / regulation of DNA binding / : ...positive regulation of signaling / high mobility group box 1 binding / advanced glycation end-product binding / negative regulation of advanced glycation end-product receptor activity / positive regulation of advanced glycation end-product receptor activity / positive regulation of chemokine production => GO:0032722 / positive regulation of tumor necrosis factor production => GO:0032760 / Advanced glycosylation endproduct receptor signaling / regulation of DNA binding / : / negative regulation of signaling / regulation of CD4-positive, alpha-beta T cell activation / : / negative regulation of blood circulation / regulation of T cell mediated cytotoxicity / positive regulation of potassium ion transmembrane transporter activity / positive regulation of endothelin production / glucose mediated signaling pathway / negative regulation of long-term synaptic depression / positive regulation of monocyte extravasation / TRAF6 mediated NF-kB activation / positive regulation of type B pancreatic cell apoptotic process / positive regulation of dendritic cell differentiation / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / regulation of p38MAPK cascade / TAK1-dependent IKK and NF-kappa-B activation / negative regulation of collagen biosynthetic process / positive regulation of phagocytosis, engulfment / astrocyte development / induction of positive chemotaxis / transcytosis / negative regulation of cell adhesion / positive regulation of endothelial cell apoptotic process / protein localization to membrane / positive regulation of monocyte chemotactic protein-1 production / negative regulation of endothelial cell migration / positive regulation of fibroblast migration / negative regulation of connective tissue replacement involved in inflammatory response wound healing / S100 protein binding / regulation of long-term synaptic potentiation / regulation of spontaneous synaptic transmission / positive regulation of heterotypic cell-cell adhesion / positive regulation of p38MAPK cascade / negative regulation of interleukin-10 production / negative regulation of endothelial cell proliferation / positive regulation of activated T cell proliferation / positive regulation of smooth muscle cell migration / negative regulation of long-term synaptic potentiation / cell surface receptor signaling pathway via JAK-STAT / response to amyloid-beta / transport across blood-brain barrier / positive regulation of epithelial to mesenchymal transition / calcium ion homeostasis / positive regulation of autophagy / positive regulation of JUN kinase activity / positive regulation of interleukin-12 production / basal plasma membrane / negative regulation of cell migration / negative regulation of protein phosphorylation / positive regulation of interleukin-1 beta production / astrocyte activation / microglial cell activation / positive regulation of JNK cascade / positive regulation of smooth muscle cell proliferation / fibrillar center / positive regulation of inflammatory response / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / neuron projection development / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / positive regulation of reactive oxygen species metabolic process / positive regulation of fibroblast proliferation / signaling receptor activity / cell junction / amyloid-beta binding / positive regulation of NF-kappaB transcription factor activity / regulation of inflammatory response / membrane => GO:0016020 / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / learning or memory / positive regulation of cell migration / inflammatory response / positive regulation of protein phosphorylation / positive regulation of apoptotic process / apical plasma membrane / axon / external side of plasma membrane / neuronal cell body / protein-containing complex binding / positive regulation of gene expression / cell surface / extracellular space / extracellular region / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site ...CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Advanced glycosylation end product-specific receptor / Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.503 Å
AuthorsXu, D. / Young, J.H. / Krahn, J.M. / Song, D. / Corbett, K.D. / Chazin, W.J. / Pedersen, L.C. / Esko, J.D.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Stable RAGE-Heparan Sulfate Complexes Are Essential for Signal Transduction.
Authors: Xu, D. / Young, J.H. / Krahn, J.M. / Song, D. / Corbett, K.D. / Chazin, W.J. / Pedersen, L.C. / Esko, J.D.
History
DepositionJan 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Feb 26, 2014Group: Database references
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Advanced glycation end-products receptor


Theoretical massNumber of molelcules
Total (without water)22,9261
Polymers22,9261
Non-polymers00
Water0
1
A: Advanced glycation end-products receptor
x 6


Theoretical massNumber of molelcules
Total (without water)137,5586
Polymers137,5586
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation14_444-y-1/4,-x-1/4,-z-1/41
crystal symmetry operation19_444-x-1/4,-z-1/4,-y-1/41
crystal symmetry operation24_444-z-1/4,-y-1/4,-x-1/41
2
A: Advanced glycation end-products receptor

A: Advanced glycation end-products receptor


Theoretical massNumber of molelcules
Total (without water)45,8532
Polymers45,8532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation24_444-z-1/4,-y-1/4,-x-1/41
3
A: Advanced glycation end-products receptor
x 6


Theoretical massNumber of molelcules
Total (without water)137,5586
Polymers137,5586
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
crystal symmetry operation13_455y-1/4,x+1/4,-z+1/41
crystal symmetry operation18_445-x-3/4,z-1/4,y+1/41
crystal symmetry operation24_444-z-1/4,-y-1/4,-x-1/41
Buried area12580 Å2
ΔGint-95 kcal/mol
Surface area60670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.810, 115.810, 115.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Advanced glycation end-products receptor / Advanced glycosylation end product-specific receptor / Advanced glycosylation end product-specific ...Advanced glycosylation end product-specific receptor / Advanced glycosylation end product-specific receptor / isoform CRA_b / RAGE


Mass: 22926.318 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ager, RAGE, mCG_5497 / Production host: Escherichia coli (E. coli) / References: UniProt: O35444, UniProt: Q62151*PLUS

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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: 2.82 Å3/Da / Density % sol: 56.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris pH 8.5, 200mM MgCl2 and 22% PEG 400. Protein was purified on gel filtration in the presence of excess dodecasaccharide heparan sulfate that caused a shift in the elution profile ...Details: 0.1M Tris pH 8.5, 200mM MgCl2 and 22% PEG 400. Protein was purified on gel filtration in the presence of excess dodecasaccharide heparan sulfate that caused a shift in the elution profile from monomer to hexamer, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 4, 2012
RadiationMonochromator: Sagitally Focused Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 3672 / Num. obs: 3672 / % possible obs: 99.5 % / Observed criterion σ(F): 48106 / Observed criterion σ(I): 48106 / Redundancy: 13.1 % / Rsym value: 0.107 / Net I/σ(I): 8.1
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 4 / Num. unique all: 348 / Rsym value: 0.702 / % possible all: 100

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CJJ

3cjj


Resolution: 3.503→23.162 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 36.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3361 183 5.02 %Random
Rwork0.2583 ---
all0.26 3672 --
obs0.2624 3645 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.503→23.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1357 0 0 0 1357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161398
X-RAY DIFFRACTIONf_angle_d1.7561925
X-RAY DIFFRACTIONf_dihedral_angle_d13.539462
X-RAY DIFFRACTIONf_chiral_restr0.098238
X-RAY DIFFRACTIONf_plane_restr0.006251
Refinement TLS params.

S33: 0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0210.0255-0.02660.0090.00220.0064-0.14190.15840.11530.21430.1218-0.2786-0.26380.05640.64270.05210.09460.632-0.10440.7777-20.3967-9.33385.5377
20.0147-0.04010.01010.0278-0.0155-0.0459-0.6585-0.1030.15320.1024-0.3448-0.1986-0.14460.0282-1.46651.42830.7834-0.5211-0.3493-0.1114-23.9844-44.148822.2305
30.0010.0021-0.00310.00450.01050.0108-0.1022-0.0236-0.0290.0036-0.1865-0.0210.00240.06961.00280.2348-0.25631.12880.10821.1686-8.8986-20.603824.7423
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 22:117)
2X-RAY DIFFRACTION2chain 'A' and (resseq 118:214)
3X-RAY DIFFRACTION3chain 'A' and (resseq 215:228)

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