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- PDB-4lp5: Crystal structure of the full-length human RAGE extracellular dom... -

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Basic information

Entry
Database: PDB / ID: 4lp5
TitleCrystal structure of the full-length human RAGE extracellular domain (VC1C2 fragment)
ComponentsAdvanced glycosylation end product-specific receptor
KeywordsSIGNALING PROTEIN / Immunoglobulin fold / pattern recognition receptor / signaling receptor / Membrane
Function / homology
Function and homology information


regulation of CD4-positive, alpha-beta T cell activation / advanced glycation end-product receptor activity / negative regulation of blood circulation / regulation of T cell mediated cytotoxicity / positive regulation of endothelin production / glucose mediated signaling pathway / negative regulation of long-term synaptic depression / positive regulation of monocyte extravasation / positive regulation of dendritic cell differentiation / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process ...regulation of CD4-positive, alpha-beta T cell activation / advanced glycation end-product receptor activity / negative regulation of blood circulation / regulation of T cell mediated cytotoxicity / positive regulation of endothelin production / glucose mediated signaling pathway / negative regulation of long-term synaptic depression / positive regulation of monocyte extravasation / positive regulation of dendritic cell differentiation / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / regulation of p38MAPK cascade / regulation of non-canonical NF-kappaB signal transduction / scavenger receptor activity / induction of positive chemotaxis / transcytosis / laminin receptor activity / protein localization to membrane / positive regulation of monocyte chemotactic protein-1 production / 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 / positive regulation of activated T cell proliferation / TRAF6 mediated NF-kB activation / negative regulation of long-term synaptic potentiation / response to amyloid-beta / Advanced glycosylation endproduct receptor signaling / 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 / microglial cell activation / positive regulation of JNK cascade / regulation of synaptic plasticity / TAK1-dependent IKK and NF-kappa-B activation / fibrillar center / response to wounding / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / neuron projection development / cellular response to amyloid-beta / transmembrane signaling receptor activity / positive regulation of tumor necrosis factor production / signaling receptor activity / cell junction / amyloid-beta binding / positive regulation of NF-kappaB transcription factor activity / regulation of inflammatory response / postsynapse / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / learning or memory / cell surface receptor signaling pathway / molecular adaptor activity / 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 domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin ...CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin / 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 / 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 / molecular replacement / Resolution: 3.8 Å
AuthorsYatime, L. / Andersen, G.R.
CitationJournal: Febs J. / Year: 2013
Title: Structural insights into the oligomerization mode of the human receptor for advanced glycation end-products.
Authors: Yatime, L. / Andersen, G.R.
History
DepositionJul 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3Dec 18, 2013Group: Database references
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 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
B: Advanced glycosylation end product-specific receptor
A: Advanced glycosylation end product-specific receptor


Theoretical massNumber of molelcules
Total (without water)65,3612
Polymers65,3612
Non-polymers00
Water0
1
B: Advanced glycosylation end product-specific receptor


Theoretical massNumber of molelcules
Total (without water)32,6801
Polymers32,6801
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Advanced glycosylation end product-specific receptor


Theoretical massNumber of molelcules
Total (without water)32,6801
Polymers32,6801
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)180.010, 180.010, 48.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 32680.297 Da / Num. of mol.: 2
Fragment: V, C1 and C2 domains (VC1C2 fragment), full-length ectodomain (UNP residues 23-323)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGER, RAGE / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle T7 Express / 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: 3.5 Å3/Da / Density % sol: 64.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris, 10% Ethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→80 Å / Num. all: 8902 / Num. obs: 8902 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.8 % / Biso Wilson estimate: 136 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 23.23
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.8-3.90.8432.94172.3
3.9-40.6023.87177.2
4-4.10.3995.51199.8
4.1-4.30.2398.871100
4.3-4.50.15712.481100
4.5-50.09818.361100
5-5.50.08223.121100
5.5-60.06628.191100
6-70.06132.021100
7-80.04346.41100
8-100.03258.871100
10-150.02965.251100
15-200.03159.34199
200.03412.16196.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
RemDAqdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LP4

4lp4


Resolution: 3.8→31.179 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.55 / σ(F): 2 / Phase error: 36.66 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2859 890 10.11 %
Rwork0.2422 --
obs0.2467 8799 95.53 %
all-8803 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 130.558 Å2
Refinement stepCycle: LAST / Resolution: 3.8→31.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3902 0 0 0 3902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054013
X-RAY DIFFRACTIONf_angle_d0.985467
X-RAY DIFFRACTIONf_dihedral_angle_d16.2891533
X-RAY DIFFRACTIONf_chiral_restr0.056598
X-RAY DIFFRACTIONf_plane_restr0.006726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-4.03820.39911110.34761019X-RAY DIFFRACTION75
4.0382-4.34920.36081340.26551382X-RAY DIFFRACTION100
4.3492-4.78540.29141470.24011379X-RAY DIFFRACTION100
4.7854-5.47470.2821680.23711364X-RAY DIFFRACTION100
5.4747-6.88530.30061690.27851358X-RAY DIFFRACTION100
6.8853-31.17970.24711610.21011407X-RAY DIFFRACTION98
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)
14.39740.91440.82098.587-2.55158.28480.4781-1.88140.56631.0052-0.4231.18440.61980.16670.22791.06110.16360.40721.11150.00141.051356.781-42.18476.5373
25.00720.7179-2.96693.3487-0.23638.48510.60080.37640.7025-0.56620.28710.4245-0.80270.2722-1.04530.9127-0.01290.14571.35570.20941.195384.8956-30.0762-19.872
36.8455-1.725-0.42415.30240.358.99570.566-1.50422.77430.7906-0.30450.6483-0.78461.6553-0.0981.1533-0.12110.47341.0447-0.45472.774755.0311-18.3187.2659
46.88651.7470.75182.34261.55631.19990.3813-0.79761.1333-0.08550.11070.28770.1833-0.53930.13520.8705-0.02680.45560.8291-0.05662.967217.5706-31.642-0.3564
57.89031.8282-0.38622.2462-2.47398.86310.52840.26250.2079-0.39140.3713-1.33730.0901-0.8364-0.54770.5911-0.08950.07610.9097-0.34641.2641127.9787-29.5181-46.7347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 23:117
2X-RAY DIFFRACTION2CHAIN A AND RESID 118:231
3X-RAY DIFFRACTION3CHAIN B AND RESID 23:117
4X-RAY DIFFRACTION4CHAIN B AND RESID 118:231
5X-RAY DIFFRACTION5CHAIN A AND RESID 232:321

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