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- PDB-7lmw: Receptor for Advanced Glycation End Products VC1 domain in comple... -

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Basic information

Entry
Database: PDB / ID: 7lmw
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 / neuron projection development / positive regulation of tumor necrosis factor production / 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 / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
ACETATE ION / Chem-Y6P / Advanced glycosylation end product-specific receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionFeb 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.2Aug 11, 2021Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Dec 15, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.5Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)48,04114
Polymers46,2632
Non-polymers1,77812
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-12 kcal/mol
Surface area22110 Å2
Unit cell
Length a, b, c (Å)101.885, 101.885, 102.306
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 51 or (resid 52...
d_2ens_1(chain "B" and (resid 20 through 36 or (resid 37...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYGLUA1 - 208
d_21ens_1GLYGLUB1 - 208

NCS oper: (Code: givenMatrix: (0.499801329889, 0.866139930126, 0.000502077895275), (0.86613978514, -0.499800603513, -0.00110874999045), (-0.000709393804183, 0.000989024360075, -0.999999259295)Vector: ...NCS oper: (Code: given
Matrix: (0.499801329889, 0.866139930126, 0.000502077895275), (0.86613978514, -0.499800603513, -0.00110874999045), (-0.000709393804183, 0.000989024360075, -0.999999259295)
Vector: -0.0113487649569, 0.0437254875479, 39.9176915972)

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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-Y6P / 7-methyl-3-(1~{H}-pyrazol-4-yl)-1~{H}-indole-2-carboxylic acid


Mass: 241.245 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C13H11N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 3.31 Å3/Da / Density % sol: 62.88 %
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-D / Wavelength: 1.0781 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 20999 / % possible obs: 99.81 % / Redundancy: 2.7 % / Biso Wilson estimate: 40.82 Å2 / Rpim(I) all: 0.037 / Rrim(I) all: 0.086 / Net I/av σ(I): 13 / Net I/σ(I): 13
Reflection shellResolution: 2.5→2.82 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 6412 / Rpim(I) all: 0.199 / Rrim(I) all: 0.461 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LP4

4lp4


Resolution: 2.5→33.41 Å / SU ML: 0.2934 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.9002
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2561 1084 5.16 %
Rwork0.2002 19915 -
obs0.2031 20999 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.62 Å2
Refinement stepCycle: LAST / Resolution: 2.5→33.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2967 0 129 40 3136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01163181
X-RAY DIFFRACTIONf_angle_d1.41144372
X-RAY DIFFRACTIONf_chiral_restr0.0698478
X-RAY DIFFRACTIONf_plane_restr0.0103577
X-RAY DIFFRACTIONf_dihedral_angle_d11.5656449
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.391811878839 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.610.28361350.24752475X-RAY DIFFRACTION100
2.61-2.750.29481460.21282475X-RAY DIFFRACTION99.96
2.75-2.920.35021320.26422492X-RAY DIFFRACTION99.96
2.92-3.140.28441380.22442472X-RAY DIFFRACTION100
3.14-3.460.28821210.22032508X-RAY DIFFRACTION100
3.46-3.960.22391500.18072453X-RAY DIFFRACTION99.47
3.96-4.980.23311320.16792515X-RAY DIFFRACTION99.92
4.99-33.410.2241300.19022525X-RAY DIFFRACTION99.22
Refinement TLS params.Method: refined / Origin x: -30.7033228783 Å / Origin y: -17.7833227908 Å / Origin z: 19.8555031182 Å
111213212223313233
T0.247050208947 Å20.0272296397274 Å20.0269919968969 Å2-0.213131915624 Å2-0.0609619742084 Å2--0.341730878789 Å2
L0.262291507904 °2-0.131446990777 °20.15905352972 °2-0.388899907825 °2-0.362573968505 °2--1.13454185494 °2
S0.0111072095668 Å °-0.0300909016549 Å °0.0414217768651 Å °-0.0107223105773 Å °0.0429030827609 Å °-0.0783699368345 Å °-0.117957622376 Å °0.208655335579 Å °-0.0562949913771 Å °
Refinement TLS groupSelection details: all

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