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- PDB-6xq1: Receptor for Advanced Glycation End Products VC1 domain in comple... -

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Basic information

Entry
Database: PDB / ID: 6xq1
TitleReceptor for Advanced Glycation End Products VC1 domain in complex with 3-(3-((4-(4-carboxyphenoxy)benzyl)oxy)phenyl)-1H-indole-2-carboxylic acid
ComponentsAdvanced glycosylation end product-specific receptor
KeywordsSIGNALING PROTEIN / RAGE / inhibitor / receptor / Advanced Glycation End Products
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 / Immunoglobulin subtype / Immunoglobulin ...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 / Immunoglobulin subtype / Immunoglobulin / Immunoglobulins and major histocompatibility complex proteins signature. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
ACETATE ION / Chem-V74 / Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsSalay, L.E. / Kozlyuk, N. / Gilston, B.A. / Gogliotti, R.D. / Christov, P.P. / Kim, K. / Ovee, M. / Waterson, A.G. / Chazin, W.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI101171 United States
CitationJournal: Proteins / Year: 2021
Title: A fragment-based approach to discovery of Receptor for Advanced Glycation End products inhibitors.
Authors: Kozlyuk, N. / Gilston, B.A. / Salay, L.E. / Gogliotti, R.D. / Christov, P.P. / Kim, K. / Ovee, M. / Waterson, A.G. / Chazin, W.J.
History
DepositionJul 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Aug 4, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Aug 11, 2021Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Dec 15, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.6Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_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

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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)47,73413
Polymers46,2632
Non-polymers1,47111
Water8,305461
1
A: Advanced glycosylation end product-specific receptor
hetero molecules

A: Advanced glycosylation end product-specific receptor
hetero molecules

B: Advanced glycosylation end product-specific receptor
hetero molecules

B: Advanced glycosylation end product-specific receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,46826
Polymers92,5264
Non-polymers2,94222
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
crystal symmetry operation2_454-y-1,x-y,z-1/31
crystal symmetry operation5_554y,-x+y,z-1/31
Buried area12520 Å2
ΔGint-76 kcal/mol
Surface area38950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.180, 102.180, 102.407
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYMETMET(chain 'A' and (resid 20 through 23 or resid 25...AA20 - 221 - 3
12ASNASNILEILE(chain 'A' and (resid 20 through 23 or resid 25...AA25 - 306 - 11
13PROPROLYSLYS(chain 'A' and (resid 20 through 23 or resid 25...AA33 - 3714 - 18
14GLYGLYGLUGLU(chain 'A' and (resid 20 through 23 or resid 25...AA40 - 5021 - 31
15LEULEUGLUGLU(chain 'A' and (resid 20 through 23 or resid 25...AA53 - 5934 - 40
16LYSLYSVALVAL(chain 'A' and (resid 20 through 23 or resid 25...AA62 - 6343 - 44
17PROPROVALVAL(chain 'A' and (resid 20 through 23 or resid 25...AA66 - 7547 - 56
18VALVALSERSER(chain 'A' and (resid 20 through 23 or resid 25...AA78 - 12959 - 110
19LEULEUCYSCYS(chain 'A' and (resid 20 through 23 or resid 25...AA133 - 144114 - 125
110GLUGLUTHRTHR(chain 'A' and (resid 20 through 23 or resid 25...AA147 - 154128 - 135
111TRPTRPGLYGLY(chain 'A' and (resid 20 through 23 or resid 25...AA157 - 170138 - 151
112VALVALGLNGLN(chain 'A' and (resid 20 through 23 or resid 25...AA173 - 176154 - 157
113HISHISTHRTHR(chain 'A' and (resid 20 through 23 or resid 25...AA180 - 187161 - 168
114LEULEUSERSER(chain 'A' and (resid 20 through 23 or resid 25...AA192 - 207173 - 188
115PROPROARGARG(chain 'A' and (resid 20 through 23 or resid 25...AA212 - 228193 - 209
116GLUGLUGLUGLU(chain 'A' and (resid 20 through 23 or resid 25...AA231212
217GLYGLYMETMET(chain 'B' and (resid 20 through 23 or resid 25...BB20 - 221 - 3
218ASNASNILEILE(chain 'B' and (resid 20 through 23 or resid 25...BB25 - 306 - 11
219PROPROLYSLYS(chain 'B' and (resid 20 through 23 or resid 25...BB33 - 3714 - 18
220GLYGLYGLUGLU(chain 'B' and (resid 20 through 23 or resid 25...BB40 - 5021 - 31
221LEULEUGLUGLU(chain 'B' and (resid 20 through 23 or resid 25...BB53 - 5934 - 40
222LYSLYSVALVAL(chain 'B' and (resid 20 through 23 or resid 25...BB62 - 6343 - 44
223PROPROVALVAL(chain 'B' and (resid 20 through 23 or resid 25...BB66 - 7547 - 56
224VALVALSERSER(chain 'B' and (resid 20 through 23 or resid 25...BB78 - 12959 - 110
225LEULEUCYSCYS(chain 'B' and (resid 20 through 23 or resid 25...BB133 - 144114 - 125
226GLUGLUTHRTHR(chain 'B' and (resid 20 through 23 or resid 25...BB147 - 154128 - 135
227TRPTRPGLYGLY(chain 'B' and (resid 20 through 23 or resid 25...BB157 - 170138 - 151
228VALVALGLNGLN(chain 'B' and (resid 20 through 23 or resid 25...BB173 - 176154 - 157
229HISHISTHRTHR(chain 'B' and (resid 20 through 23 or resid 25...BB180 - 187161 - 168
230LEULEUSERSER(chain 'B' and (resid 20 through 23 or resid 25...BB192 - 207173 - 188
231PROPROARGARG(chain 'B' and (resid 20 through 23 or resid 25...BB212 - 228193 - 209
232GLUGLUGLUGLU(chain 'B' and (resid 20 through 23 or resid 25...BB231212

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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: VC1 domain, resdues 23-231
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: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-V74 / 3-[3-({[3-(4-carboxyphenoxy)phenyl]methoxy}methyl)phenyl]-1H-indole-2-carboxylic acid


Mass: 493.507 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H23NO6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.34 Å3/Da / Density % sol: 63.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 2.5 M NaOAc (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.51→33.45 Å / Num. obs: 95300 / % possible obs: 99.83 % / Redundancy: 4.7 % / Biso Wilson estimate: 21.16 Å2 / CC1/2: 0.965 / Rpim(I) all: 0.02 / Rrim(I) all: 0.061 / Net I/σ(I): 16.4
Reflection shellResolution: 1.51→1.55 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.19 / Num. unique obs: 9586 / CC1/2: 0.808 / Rpim(I) all: 0.284 / Rrim(I) all: 0.783 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LP4

4lp4


Resolution: 1.51→33.45 Å / SU ML: 0.1618 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7479
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1965 4640 4.87 %
Rwork0.172 90641 -
obs0.1732 95281 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.12 Å2
Refinement stepCycle: LAST / Resolution: 1.51→33.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3177 0 104 461 3742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01723557
X-RAY DIFFRACTIONf_angle_d1.46044889
X-RAY DIFFRACTIONf_chiral_restr0.0994513
X-RAY DIFFRACTIONf_plane_restr0.0096653
X-RAY DIFFRACTIONf_dihedral_angle_d20.4467519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.520.29881520.27032879X-RAY DIFFRACTION95.31
1.52-1.540.29731770.25342962X-RAY DIFFRACTION100
1.54-1.560.28031630.23323007X-RAY DIFFRACTION99.94
1.56-1.580.27341860.20972974X-RAY DIFFRACTION99.94
1.58-1.60.21921770.20463011X-RAY DIFFRACTION100
1.6-1.620.18981430.19763069X-RAY DIFFRACTION100
1.62-1.650.22551790.18012970X-RAY DIFFRACTION100
1.65-1.670.21511340.1783042X-RAY DIFFRACTION100
1.67-1.70.2251510.17183004X-RAY DIFFRACTION100
1.7-1.730.22891280.17623006X-RAY DIFFRACTION100
1.73-1.750.18611320.17373065X-RAY DIFFRACTION99.94
1.75-1.790.19881350.17673070X-RAY DIFFRACTION99.91
1.79-1.820.22031610.18212980X-RAY DIFFRACTION100
1.82-1.860.23811540.18413072X-RAY DIFFRACTION100
1.86-1.90.19921730.17812963X-RAY DIFFRACTION100
1.9-1.940.22631330.16443033X-RAY DIFFRACTION100
1.94-1.990.1811630.16823029X-RAY DIFFRACTION99.97
1.99-2.050.21411710.1693037X-RAY DIFFRACTION99.97
2.05-2.110.1981390.16393000X-RAY DIFFRACTION100
2.11-2.170.19661510.16613058X-RAY DIFFRACTION100
2.17-2.250.19561570.17742996X-RAY DIFFRACTION99.94
2.25-2.340.21591440.17953042X-RAY DIFFRACTION100
2.34-2.450.21370.17793057X-RAY DIFFRACTION100
2.45-2.580.21321670.18293011X-RAY DIFFRACTION100
2.58-2.740.17951510.17623041X-RAY DIFFRACTION100
2.74-2.950.21451650.19173039X-RAY DIFFRACTION100
2.95-3.250.21291720.18153000X-RAY DIFFRACTION100
3.25-3.720.1611350.16083075X-RAY DIFFRACTION100
3.72-4.680.16291420.14173076X-RAY DIFFRACTION100
4.68-33.450.18331680.16693073X-RAY DIFFRACTION99.69
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)
11.8056703492-0.378022182195-0.1335623631382.175294768250.1655362619272.17398074079-0.101541572857-0.2590629575920.01033937291160.3466283828690.1274838226980.02041088330530.2187012136120.145233659605-0.0133508375760.2335018502750.0881098477096-0.01040347977770.143454794719-0.006879312183880.166520011465-44.4977881461-11.840301321122.1339384919
22.465308181930.87617522111-2.18171214311.76433411796-0.2377454224543.79946592383-0.0178726093278-0.037568566030.0934674792727-0.2149542393520.280824834655-0.328384899436-0.04922159780660.647185977739-0.1319587704590.20128993913-0.02167724511960.06596660396820.301841056576-0.08384019817180.270093234139-26.2273595013-6.0940416894-12.7674290355
31.77554694566-0.412567913161-0.026205646482.020922388290.1919018618812.133319334520.1114396163490.223475851025-0.0181466185861-0.361800103927-0.0835165340020.00342075591524-0.22844786295-0.107952490383-0.01553260431450.2405736855450.08084371715070.008642047718610.1321877912640.007141760889070.164957257999-32.3438551018-32.700596026217.826622311
42.702017614960.5620221631291.371930018371.671071768161.952602427344.17533107430.066579730386-0.2668847095840.2428597902-0.08578394241850.208494343906-0.250107940121-0.5725249738080.426487988024-0.1399708464660.268670449738-0.05959153407780.04305173290860.246361446909-0.10080678980.266811607464-18.0988357452-19.292411100952.8630642859
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 20:118 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 119:231 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 20:118 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 119:231 )

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