[English] 日本語
Yorodumi
- PDB-6xq5: Receptor for Advanced Glycation End Products VC1 domain in comple... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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)

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more