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- PDB-6xq8: Receptor for Advanced Glycation End Products VC1 domain in comple... -

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Basic information

Entry
Database: PDB / ID: 6xq8
TitleReceptor for Advanced Glycation End Products VC1 domain in complex with Fragments 1 & 11
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 / 7-methyl-3-phenyl-1H-indole-2-carboxylic acid / 3-phenoxyphenol / Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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)47,74915
Polymers46,2632
Non-polymers1,48613
Water3,171176
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)95,49930
Polymers92,5264
Non-polymers2,97326
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation2_544-y,x-y-1,z-1/31
crystal symmetry operation5_554y,-x+y,z-1/31
Buried area10750 Å2
ΔGint-66 kcal/mol
Surface area37550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.017, 102.017, 102.779
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 60 or resid 62 through 145 or resid 147 through 231))
d_2ens_1(chain "B" and (resid 20 through 60 or resid 62...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYALAA1 - 41
d_12ens_1LYSVALA45 - 128
d_13ens_1GLUGLUA132 - 209
d_21ens_1GLYALAB1 - 41
d_22ens_1LYSVALB45 - 128
d_23ens_1GLUPROB132 - 197
d_24ens_1LEUGLUB199 - 210

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 189 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: 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
#4: Chemical ChemComp-V6P / 3-phenoxyphenol


Mass: 186.207 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C12H10O2
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.34 Å3/Da / Density % sol: 63.14 %
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: Feb 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 107292 / % possible obs: 99.94 % / Redundancy: 4.2 % / Biso Wilson estimate: 24.37 Å2 / Rpim(I) all: 0.019 / Rrim(I) all: 0.056 / Net I/σ(I): 19.22
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 5.05 / Num. unique obs: 10717 / Rpim(I) all: 0.107 / Rrim(I) all: 0.309

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Processing

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

4lp4


Resolution: 1.82→45.69 Å / SU ML: 0.1429 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.9303
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2183 2730 5.02 %
Rwork0.1984 51605 -
obs0.1994 54335 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.91 Å2
Refinement stepCycle: LAST / Resolution: 1.82→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2997 0 106 176 3279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01953216
X-RAY DIFFRACTIONf_angle_d1.50394403
X-RAY DIFFRACTIONf_chiral_restr0.109477
X-RAY DIFFRACTIONf_plane_restr0.0108582
X-RAY DIFFRACTIONf_dihedral_angle_d19.13991130
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.458180071343 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.850.2281280.21682551X-RAY DIFFRACTION99.11
1.85-1.880.21661350.20442588X-RAY DIFFRACTION100
1.88-1.920.24731160.2042585X-RAY DIFFRACTION100
1.92-1.960.19851590.18882558X-RAY DIFFRACTION100
1.96-20.2041030.19152600X-RAY DIFFRACTION100
2-2.050.22311460.19172548X-RAY DIFFRACTION100
2.05-2.10.17841560.1832553X-RAY DIFFRACTION100
2.1-2.160.20581580.18252574X-RAY DIFFRACTION100
2.16-2.220.1941340.18582573X-RAY DIFFRACTION100
2.22-2.290.22871320.19262577X-RAY DIFFRACTION100
2.29-2.370.23861590.20382565X-RAY DIFFRACTION100
2.37-2.470.20981190.20942574X-RAY DIFFRACTION100
2.47-2.580.23241400.20662582X-RAY DIFFRACTION100
2.58-2.720.21171210.21412593X-RAY DIFFRACTION100
2.72-2.890.23481440.22332585X-RAY DIFFRACTION100
2.89-3.110.22811210.2252591X-RAY DIFFRACTION100
3.11-3.420.28871040.20452625X-RAY DIFFRACTION100
3.42-3.920.21231360.19242595X-RAY DIFFRACTION100
3.92-4.940.21831510.17242581X-RAY DIFFRACTION100
4.94-45.690.18941680.2022607X-RAY DIFFRACTION99.5

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