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- PDB-4lp4: Crystal structure of the human RAGE VC1 fragment in space group P62 -

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Basic information

Entry
Database: PDB / ID: 4lp4
TitleCrystal structure of the human RAGE VC1 fragment in space group P62
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 / 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 / molecular replacement / Resolution: 2.4 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: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.5Sep 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_conn / struct_ncs_dom_lim / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3556
Polymers46,2632
Non-polymers924
Water4,414245
1
A: Advanced glycosylation end product-specific receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1542
Polymers23,1311
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Advanced glycosylation end product-specific receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2004
Polymers23,1311
Non-polymers693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.000, 102.000, 103.400
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A AND (RESSEQ 20:231 )
21CHAIN B AND (RESSEQ 20:231 )

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 20 - 231 / Label seq-ID: 1 - 212

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1CHAIN A AND (RESSEQ 20:231 )AA
2CHAIN B AND (RESSEQ 20:231 )BB

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Components

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


Mass: 23131.494 Da / Num. of mol.: 2
Fragment: V and C1 domains (VC1 fragment), ectodomain fragment (UNP residues 23-231)
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
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O

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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: 3.36 Å3/Da / Density % sol: 63.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.5 M sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 18, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.4→35 Å / Num. all: 23876 / Num. obs: 23876 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 22.72
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.4-2.50.4944.77274432763100
2.5-2.60.3636.52234012340100
2.6-2.80.23110.15372513721100
2.8-30.1514.51283032827100
3-3.50.08125.33452334524100
3.5-40.06633.4223458247597.4
4-50.04443.95247482545100
5-60.04144.56110751129100
6-80.03945.158813895100
8-100.0352.823109323100
10-120.02457.01138714599.3
12-200.02355.891462156100
200.02540.572223371.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MAR345data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3O3U

3o3u


Resolution: 2.4→33.387 Å / Occupancy max: 1 / Occupancy min: 0.67 / FOM work R set: 0.8473 / SU ML: 0.25 / σ(F): 2 / σ(I): 2 / Phase error: 22.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 1212 5.08 %RANDOM (5% of all reflections)
Rwork0.1785 ---
obs0.1805 23854 99.62 %-
all-23854 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.04 Å2 / Biso mean: 44.4319 Å2 / Biso min: 14.53 Å2
Refinement stepCycle: LAST / Resolution: 2.4→33.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 4 245 3501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063340
X-RAY DIFFRACTIONf_angle_d0.9744534
X-RAY DIFFRACTIONf_chiral_restr0.063486
X-RAY DIFFRACTIONf_plane_restr0.005602
X-RAY DIFFRACTIONf_dihedral_angle_d12.8961282
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1626X-RAY DIFFRACTIONTORTIONAL0.008
12B1626X-RAY DIFFRACTIONTORTIONAL0.008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.49610.2461290.210725352664100
2.4961-2.60960.25261340.195324932627100
2.6096-2.74710.23291350.187325322667100
2.7471-2.91920.24831390.194125052644100
2.9192-3.14440.23621410.19825062647100
3.1444-3.46050.22461360.18425192655100
3.4605-3.96060.22681320.19522458259098
3.9606-4.98730.1571330.14325352668100
4.9873-33.39060.22311330.16742559269299
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)
13.6848-0.61310.13153.10580.14773.0732-0.2097-0.4670.1060.4580.2118-0.01680.08940.04960.0320.33460.081-0.02890.1939-0.02870.2709-44.4255-11.784422.3117
24.46250.9146-4.0582.3215-0.81046.14190.0852-0.1847-0.0007-0.18550.1172-0.4285-0.23560.8244-0.13020.2986-0.04110.03140.3588-0.12190.3621-25.7555-6.0996-12.862
33.1428-0.2641-0.29743.5962-0.04552.47770.12370.304-0.0959-0.6026-0.1027-0.0478-0.0892-0.048-0.01090.30660.09240.020.2220.00840.2675-32.4094-32.580517.7126
43.45971.01171.80172.77732.18934.72690.0052-0.16630.3429-0.05820.2251-0.199-0.52150.5405-0.1130.3004-0.0410.08210.3474-0.09010.3383-18.1587-19.26552.893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 20:118 )A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 119:231 )A0
3X-RAY DIFFRACTION3CHAIN B AND (RESID 20:118 )B0
4X-RAY DIFFRACTION4CHAIN B AND (RESID 119:231 )B0

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