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- PDB-6xq7: Receptor for Advanced Glycation End Products VC1 domain in comple... -

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Basic information

Entry
Database: PDB / ID: 6xq7
TitleReceptor for Advanced Glycation End Products VC1 domain in complex with Fragment 5
ComponentsAdvanced glycosylation end product-specific receptor
KeywordsSIGNALING PROTEIN / RAGE / IG-like domain / receptor / Advanced Glycation End Products
Function / homology
Function and homology information


advanced glycation end-product receptor activity / negative regulation of blood circulation / positive regulation of endothelin production / regulation of CD4-positive, alpha-beta T cell activation / glucose mediated signaling pathway / positive regulation of monocyte extravasation / regulation of T cell mediated cytotoxicity / positive regulation of DNA-templated DNA replication / positive regulation of dendritic cell differentiation / negative regulation of long-term synaptic depression ...advanced glycation end-product receptor activity / negative regulation of blood circulation / positive regulation of endothelin production / regulation of CD4-positive, alpha-beta T cell activation / glucose mediated signaling pathway / positive regulation of monocyte extravasation / regulation of T cell mediated cytotoxicity / positive regulation of DNA-templated DNA replication / positive regulation of dendritic cell differentiation / negative regulation of long-term synaptic depression / regulation of p38MAPK cascade / regulation of non-canonical NF-kappaB signal transduction / positive regulation of amyloid precursor protein catabolic process / induction of positive chemotaxis / transcytosis / positive regulation of monocyte chemotactic protein-1 production / positive regulation of heterotypic cell-cell adhesion / S100 protein binding / protein localization to membrane / regulation of long-term synaptic potentiation / positive regulation of p38MAPK cascade / negative regulation of connective tissue replacement involved in inflammatory response wound healing / regulation of spontaneous synaptic transmission / scavenger receptor activity / laminin receptor activity / positive regulation of double-strand break repair / 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 / negative regulation of long-term synaptic potentiation / phagocytic cup / phagocytosis / 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 / positive regulation of JNK cascade / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of non-canonical NF-kappaB signal transduction / regulation of synaptic plasticity / positive regulation of interleukin-6 production / response to wounding / fibrillar center / cellular response to amyloid-beta / neuron projection development / positive regulation of NF-kappaB transcription factor activity / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / cell junction / signaling receptor activity / amyloid-beta binding / regulation of inflammatory response / molecular adaptor activity / histone binding / learning or memory / response to hypoxia / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / postsynapse / apical plasma membrane / inflammatory response / protein-containing complex binding / cell surface / DNA binding / RNA binding / extracellular region / identical protein binding / nucleus / plasma membrane
Similarity search - Function
: / CD80-like, immunoglobulin C2-set / CD80-like C2-set 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. ...: / CD80-like, immunoglobulin C2-set / CD80-like C2-set 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
ACETATE ION / 5-bromo-3-methyl-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 / pdbx_initial_refinement_model
Revision 1.7Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)48,64420
Polymers46,2632
Non-polymers2,38118
Water3,819212
1
B: Advanced glycosylation end product-specific receptor
hetero molecules

B: Advanced glycosylation end product-specific receptor
hetero molecules

A: Advanced glycosylation end product-specific receptor
hetero molecules

A: Advanced glycosylation end product-specific receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,28840
Polymers92,5264
Non-polymers4,76236
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation3_655-x+y+1,-x,z+1/31
crystal symmetry operation6_555x-y,x,z+1/31
Buried area12980 Å2
ΔGint-93 kcal/mol
Surface area38810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.905, 102.905, 101.769
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-IDDetails
d_1ens_1(chain "A" and (resid 20 through 23 or resid 25...
d_2ens_1(chain "B" and (resid 20 through 23 or resid 25...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYALAA1 - 4
d_12ens_1ASNILEA8 - 9
d_13ens_1ALAGLYA13 - 16
d_14ens_1PROILEA20 - 78
d_15ens_1ASPASPA82
d_16ens_1GLYSERA86 - 102
d_17ens_1TYRVALA104 - 136
d_18ens_1GLUGLUA140 - 224
d_21ens_1GLYALAB1 - 4
d_22ens_1ASNILEB6 - 7
d_23ens_1ALAGLYB9 - 12
d_24ens_1PROILEB16 - 74
d_25ens_1ASPASPB78
d_26ens_1GLYSERB80 - 96
d_27ens_1TYRVALB100 - 132
d_28ens_1GLUGLUB134 - 218

NCS oper: (Code: givenMatrix: (0.499882420751, -0.866093125144, -0.000513812302748), (-0.866092386117, -0.499880967102, -0.00173131117168), (0.00124263171247, 0.00131046094287, -0.999998369278)Vector: ...NCS oper: (Code: given
Matrix: (0.499882420751, -0.866093125144, -0.000513812302748), (-0.866092386117, -0.499880967102, -0.00173131117168), (0.00124263171247, 0.00131046094287, -0.999998369278)
Vector: -0.0251249106346, -0.0340334981467, -27.7499239838)

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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.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-V6V / 5-bromo-3-methyl-1H-indole-2-carboxylic acid


Mass: 254.080 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H8BrNO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 63.42 %
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: ALS / Beamline: 12.3.1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 111660 / % possible obs: 99.81 % / Redundancy: 3.9 % / Biso Wilson estimate: 23.22 Å2 / Rpim(I) all: 0.025 / Rrim(I) all: 0.07 / Net I/σ(I): 17.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 7.83 / Num. unique obs: 11201 / Rpim(I) all: 0.11 / Rrim(I) all: 0.31 / % possible all: 99.63

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LP4

4lp4


Resolution: 1.8→45.92 Å / SU ML: 0.2083 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.0375
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.222 2800 4.95 %
Rwork0.1991 53742 -
obs0.2002 56542 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.5 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3062 0 136 212 3410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01833335
X-RAY DIFFRACTIONf_angle_d1.62194585
X-RAY DIFFRACTIONf_chiral_restr0.1105496
X-RAY DIFFRACTIONf_plane_restr0.0109609
X-RAY DIFFRACTIONf_dihedral_angle_d18.11381170
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.476859451273 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.29531670.23882545X-RAY DIFFRACTION95.53
1.83-1.860.28921180.22062696X-RAY DIFFRACTION100
1.86-1.90.20281310.21092707X-RAY DIFFRACTION100
1.9-1.940.22471190.19512700X-RAY DIFFRACTION99.93
1.94-1.980.27421370.19012693X-RAY DIFFRACTION100
1.98-2.030.24931340.2072689X-RAY DIFFRACTION100
2.03-2.080.22211590.20092664X-RAY DIFFRACTION100
2.08-2.130.24121420.19172675X-RAY DIFFRACTION100
2.13-2.20.24681470.19362719X-RAY DIFFRACTION100
2.2-2.270.19391600.20222646X-RAY DIFFRACTION100
2.27-2.350.20831540.21082693X-RAY DIFFRACTION100
2.35-2.440.261350.21292701X-RAY DIFFRACTION100
2.44-2.550.25921060.21812712X-RAY DIFFRACTION100
2.55-2.690.22841270.21462704X-RAY DIFFRACTION100
2.69-2.850.23881270.2192722X-RAY DIFFRACTION99.96
2.86-3.080.24531400.22062692X-RAY DIFFRACTION99.96
3.08-3.380.22681530.21372690X-RAY DIFFRACTION100
3.38-3.870.20971500.17892704X-RAY DIFFRACTION100
3.87-4.880.18631520.16562704X-RAY DIFFRACTION99.9
4.88-45.920.20421420.19722686X-RAY DIFFRACTION97.52

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