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- PDB-6xq5: Receptor for Advanced Glycation End Products VC1 domain in comple... -

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Basic information

Entry
Database: PDB / ID: 6xq5
TitleReceptor for Advanced Glycation End Products VC1 domain in complex with Fragment 1
ComponentsAdvanced glycosylation end product-specific receptor
KeywordsSIGNALING PROTEIN / RAGE / IG-like domain / 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 / 7-methyl-3-phenyl-1H-indole-2-carboxylic acid / Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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)47,25013
Polymers46,2632
Non-polymers98711
Water6,521362
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)94,50026
Polymers92,5264
Non-polymers1,97422
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 area12130 Å2
ΔGint-84 kcal/mol
Surface area38380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.735, 101.735, 101.812
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 26...AA20 - 221 - 3
12ILEILEGLUGLU(chain 'A' and (resid 20 through 23 or resid 26...AA26 - 507 - 31
13LEULEUGLUGLU(chain 'A' and (resid 20 through 23 or resid 26...AA53 - 5934 - 40
14LYSLYSASNASN(chain 'A' and (resid 20 through 23 or resid 26...AA62 - 8143 - 62
15LEULEUASNASN(chain 'A' and (resid 20 through 23 or resid 26...AA84 - 11265 - 93
16TYRTYRALAALA(chain 'A' and (resid 20 through 23 or resid 26...AA118 - 13099 - 111
17LEULEUCYSCYS(chain 'A' and (resid 20 through 23 or resid 26...AA133 - 144114 - 125
18GLUGLUSERSER(chain 'A' and (resid 20 through 23 or resid 26...AA147 - 156128 - 137
19LEULEUGLNGLN(chain 'A' and (resid 20 through 23 or resid 26...AA159 - 176140 - 157
110ARGARGHISHIS(chain 'A' and (resid 20 through 23 or resid 26...AA179 - 180160 - 161
111THRTHRTHRTHR(chain 'A' and (resid 20 through 23 or resid 26...AA183 - 187164 - 168
112LEULEUPROPRO(chain 'A' and (resid 20 through 23 or resid 26...AA192 - 196173 - 177
113GLYGLYSERSER(chain 'A' and (resid 20 through 23 or resid 26...AA199 - 207180 - 188
114PROPROPROPRO(chain 'A' and (resid 20 through 23 or resid 26...AA212 - 224193 - 205
115PROPROARGARG(chain 'A' and (resid 20 through 23 or resid 26...AA227 - 228208 - 209
116GLUGLUGLUGLU(chain 'A' and (resid 20 through 23 or resid 26...AA231212
217GLYGLYMETMET(chain 'B' and (resid 20 through 23 or resid 26...BB20 - 221 - 3
218ILEILEGLUGLU(chain 'B' and (resid 20 through 23 or resid 26...BB26 - 507 - 31
219LEULEUGLUGLU(chain 'B' and (resid 20 through 23 or resid 26...BB53 - 5934 - 40
220LYSLYSASNASN(chain 'B' and (resid 20 through 23 or resid 26...BB62 - 8143 - 62
221LEULEUASNASN(chain 'B' and (resid 20 through 23 or resid 26...BB84 - 11265 - 93
222TYRTYRALAALA(chain 'B' and (resid 20 through 23 or resid 26...BB118 - 13099 - 111
223LEULEUCYSCYS(chain 'B' and (resid 20 through 23 or resid 26...BB133 - 144114 - 125
224GLUGLUSERSER(chain 'B' and (resid 20 through 23 or resid 26...BB147 - 156128 - 137
225LEULEUGLNGLN(chain 'B' and (resid 20 through 23 or resid 26...BB159 - 176140 - 157
226ARGARGHISHIS(chain 'B' and (resid 20 through 23 or resid 26...BB179 - 180160 - 161
227THRTHRTHRTHR(chain 'B' and (resid 20 through 23 or resid 26...BB183 - 187164 - 168
228LEULEUPROPRO(chain 'B' and (resid 20 through 23 or resid 26...BB192 - 196173 - 177
229GLYGLYSERSER(chain 'B' and (resid 20 through 23 or resid 26...BB199 - 207180 - 188
230PROPROPROPRO(chain 'B' and (resid 20 through 23 or resid 26...BB212 - 224193 - 205
231PROPROARGARG(chain 'B' and (resid 20 through 23 or resid 26...BB227 - 228208 - 209
232GLUGLUGLUGLU(chain 'B' and (resid 20 through 23 or resid 26...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-V6M / 7-methyl-3-phenyl-1H-indole-2-carboxylic acid


Mass: 251.280 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C16H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.29 Å3/Da / Density % sol: 62.59 %
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-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 55196 / % possible obs: 97.23 % / Redundancy: 4.4 % / Biso Wilson estimate: 20.29 Å2 / Rpim(I) all: 0.024 / Rrim(I) all: 0.067 / Net I/σ(I): 15.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 7.96 / Num. unique obs: 5530 / Rpim(I) all: 0.128 / Rrim(I) all: 0.356

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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: 1.8→45.5 Å / SU ML: 0.1512 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.9146
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1963 2639 4.91 %
Rwork0.1731 51109 -
obs0.1743 53748 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.94 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3144 0 68 362 3574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01583492
X-RAY DIFFRACTIONf_angle_d1.35924809
X-RAY DIFFRACTIONf_chiral_restr0.1011513
X-RAY DIFFRACTIONf_plane_restr0.0093646
X-RAY DIFFRACTIONf_dihedral_angle_d22.1158514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.23221420.20282700X-RAY DIFFRACTION98.24
1.83-1.870.22811130.17632743X-RAY DIFFRACTION98.72
1.87-1.910.17891300.17532706X-RAY DIFFRACTION98.51
1.91-1.950.19011390.1612718X-RAY DIFFRACTION98.45
1.95-1.990.23071380.17352747X-RAY DIFFRACTION98.4
1.99-2.040.1791370.17222683X-RAY DIFFRACTION98.33
2.04-2.10.21041650.16942693X-RAY DIFFRACTION98.18
2.1-2.160.22941450.16552695X-RAY DIFFRACTION98
2.16-2.230.19351590.17112681X-RAY DIFFRACTION98.07
2.23-2.310.23981440.17822696X-RAY DIFFRACTION97.76
2.31-2.40.21361440.17492691X-RAY DIFFRACTION97.62
2.4-2.510.2176960.1822740X-RAY DIFFRACTION97.39
2.51-2.640.1811390.18162690X-RAY DIFFRACTION97.15
2.64-2.810.21381290.18282701X-RAY DIFFRACTION96.92
2.81-3.030.2311180.19272680X-RAY DIFFRACTION96.55
3.03-3.330.20521570.18082648X-RAY DIFFRACTION96.16
3.33-3.810.21111530.16152642X-RAY DIFFRACTION95.62
3.81-4.80.15381490.15152650X-RAY DIFFRACTION95.07
4.81-45.50.16991420.18112605X-RAY DIFFRACTION92.52
Refinement TLS params.Method: refined / Origin x: -30.3174392463 Å / Origin y: -17.3807116615 Å / Origin z: 19.6791336306 Å
111213212223313233
T0.143597343757 Å20.086944610539 Å20.0254145855586 Å2-0.0463105793077 Å2-0.0430329303476 Å2--0.0922925104104 Å2
L0.15769371052 °20.158858666434 °20.0804959900155 °2-0.0142395652497 °2-0.14832974469 °2--0.165215378059 °2
S0.0348050385336 Å °-0.0218091059955 Å °0.0232239492376 Å °-0.0269786583952 Å °0.0656794615271 Å °-0.0399347042327 Å °-0.0582319862182 Å °0.106237886181 Å °0.0439980512056 Å °
Refinement TLS groupSelection details: all

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