[English] 日本語
Yorodumi
- PDB-7jni: Crystal structure of the angiotensin II type 2 receptoror (AT2R) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jni
TitleCrystal structure of the angiotensin II type 2 receptoror (AT2R) in complex with EMA401
ComponentsSoluble cytochrome b562,Type-2 angiotensin II receptor
KeywordsMEMBRANE PROTEIN / angiotensin II type 2 receptor / AT2R / EMA401 / PD-126055 / G protein-coupled receptor / GPCR / BRIL fusion / Glioblastoma / GBM / LCP
Function / homology
Function and homology information


regulation of metanephros size / regulation of systemic arterial blood pressure by circulatory renin-angiotensin / brain renin-angiotensin system / angiotensin type II receptor activity / angiotensin-mediated vasodilation involved in regulation of systemic arterial blood pressure / negative regulation of neurotrophin TRK receptor signaling pathway / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / positive regulation of metanephric glomerulus development / receptor antagonist activity / positive regulation of branching involved in ureteric bud morphogenesis ...regulation of metanephros size / regulation of systemic arterial blood pressure by circulatory renin-angiotensin / brain renin-angiotensin system / angiotensin type II receptor activity / angiotensin-mediated vasodilation involved in regulation of systemic arterial blood pressure / negative regulation of neurotrophin TRK receptor signaling pathway / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / positive regulation of metanephric glomerulus development / receptor antagonist activity / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of extrinsic apoptotic signaling pathway / negative regulation of heart rate / exploration behavior / negative regulation of blood vessel endothelial cell migration / blood vessel remodeling / nitric oxide-cGMP-mediated signaling / Peptide ligand-binding receptors / electron transport chain / negative regulation of cell growth / brain development / regulation of blood pressure / vasodilation / neuron apoptotic process / G alpha (i) signalling events / periplasmic space / electron transfer activity / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / inflammatory response / iron ion binding / heme binding / positive regulation of DNA-templated transcription / plasma membrane
Similarity search - Function
Angiotensin II receptor type 2 / Angiotensin II receptor family / : / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
FORMIC ACID / HEXANE-1,6-DIOL / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Olodanrigan / Soluble cytochrome b562 / Type-2 angiotensin II receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCherezov, V. / Shaye, H. / Han, G.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Inhibition of the angiotensin II type 2 receptor AT 2 R is a novel therapeutic strategy for glioblastoma.
Authors: Perryman, R. / Renziehausen, A. / Shaye, H. / Kostagianni, A.D. / Tsiailanis, A.D. / Thorne, T. / Chatziathanasiadou, M.V. / Sivolapenko, G.B. / El Mubarak, M.A. / Han, G.W. / Zarzycka, B. / ...Authors: Perryman, R. / Renziehausen, A. / Shaye, H. / Kostagianni, A.D. / Tsiailanis, A.D. / Thorne, T. / Chatziathanasiadou, M.V. / Sivolapenko, G.B. / El Mubarak, M.A. / Han, G.W. / Zarzycka, B. / Katritch, V. / Lebon, G. / Lo Nigro, C. / Lattanzio, L. / Morse, S.V. / Choi, J.J. / O'Neill, K. / Kanaki, Z. / Klinakis, A. / Crook, T. / Cherezov, V. / Tzakos, A.G. / Syed, N.
History
DepositionAug 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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: Soluble cytochrome b562,Type-2 angiotensin II receptor
B: Soluble cytochrome b562,Type-2 angiotensin II receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,73413
Polymers93,3552
Non-polymers3,37911
Water724
1
A: Soluble cytochrome b562,Type-2 angiotensin II receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,26610
Polymers46,6781
Non-polymers2,5899
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Soluble cytochrome b562,Type-2 angiotensin II receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4683
Polymers46,6781
Non-polymers7902
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.658, 68.090, 89.171
Angle α, β, γ (deg.)90.000, 104.650, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 42 through 43 and (name N...
21(chain B and (resid 42 through 246 or (resid 247...
12(chain A and (resid 1001 through 1014 or (resid 1015...
22(chain B and (resid 1001 through 1103 or (resid 1104...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSPHEPHE(chain A and ((resid 42 through 43 and (name N...AA42 - 333119 - 410
121LYSLYSPHEPHE(chain A and ((resid 42 through 43 and (name N...AA42 - 333119 - 410
131LYSLYSPHEPHE(chain A and ((resid 42 through 43 and (name N...AA42 - 333119 - 410
141LYSLYSPHEPHE(chain A and ((resid 42 through 43 and (name N...AA42 - 333119 - 410
211LYSLYSPHEPHE(chain B and (resid 42 through 246 or (resid 247...BB42 - 333119 - 410
221LYSLYSPHEPHE(chain B and (resid 42 through 246 or (resid 247...BB42 - 333119 - 410
231LYSLYSPHEPHE(chain B and (resid 42 through 246 or (resid 247...BB42 - 333119 - 410
241LYSLYSPHEPHE(chain B and (resid 42 through 246 or (resid 247...BB42 - 333119 - 410
251LYSLYSPHEPHE(chain B and (resid 42 through 246 or (resid 247...BB42 - 333119 - 410
261LYSLYSPHEPHE(chain B and (resid 42 through 246 or (resid 247...BB42 - 333119 - 410
112ALAALALEULEU(chain C and (resid 1001 through 1014 or (resid 1015...AA1001 - 11062 - 107
122ALAALALEULEU(chain C and (resid 1001 through 1014 or (resid 1015...AA1001 - 11062 - 107
132ALAALALEULEU(chain C and (resid 1001 through 1014 or (resid 1015...AA1001 - 11062 - 107
142ALAALALEULEU(chain C and (resid 1001 through 1014 or (resid 1015...AA1001 - 11062 - 107
152ALAALALEULEU(chain C and (resid 1001 through 1014 or (resid 1015...AA1001 - 11062 - 107
162ALAALALEULEU(chain C and (resid 1001 through 1014 or (resid 1015...AA1001 - 11062 - 107
212ALAALALEULEU(chain D and (resid 1001 through 1103 or (resid 1104...BB1001 - 11062 - 107
222ALAALALEULEU(chain D and (resid 1001 through 1103 or (resid 1104...BB1001 - 11062 - 107
232ALAALALEULEU(chain D and (resid 1001 through 1103 or (resid 1104...BB1001 - 11062 - 107
242ALAALALEULEU(chain D and (resid 1001 through 1103 or (resid 1104...BB1001 - 11062 - 107
252TYRTYRLEULEU(chain D and (resid 1001 through 1103 or (resid 1104...BB1101 - 1106102 - 107
262TYRTYRLEULEU(chain D and (resid 1001 through 1103 or (resid 1104...BB1101 - 1106102 - 107

NCS ensembles :
ID
1
2
DetailsThe authors state that the biological unit is unknown

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Soluble cytochrome b562,Type-2 angiotensin II receptor / Cytochrome b-562 / Angiotensin II type-2 receptor / AT2


Mass: 46677.695 Da / Num. of mol.: 2 / Mutation: M29W,H124I,R128L in cyt b562
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: cybC, AGTR2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0ABE7, UniProt: P50052

-
Non-polymers , 6 types, 15 molecules

#2: Chemical ChemComp-VFD / Olodanrigan / EMA401 / (3S)-5-(benzyloxy)-2-(diphenylacetyl)-6-methoxy-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid


Mass: 507.576 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H29NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: Tris-HCl pH 8.0, Potassium Formate, PEG400, and 1,6-hexanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3→32.72 Å / Num. obs: 17858 / % possible obs: 97.8 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 7
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 1 / Num. unique obs: 844 / CC star: 0.68 / % possible all: 95.4

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 5UNH

5unh


Resolution: 3→32.72 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2726 862 4.83 %
Rwork0.2343 16968 -
obs0.2361 17830 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 239.83 Å2 / Biso mean: 96.1298 Å2 / Biso min: 38.54 Å2
Refinement stepCycle: final / Resolution: 3→32.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6342 0 226 4 6572
Biso mean--76.26 55.88 -
Num. residues----805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026728
X-RAY DIFFRACTIONf_angle_d0.5519106
X-RAY DIFFRACTIONf_dihedral_angle_d17.5812403
X-RAY DIFFRACTIONf_chiral_restr0.0381023
X-RAY DIFFRACTIONf_plane_restr0.0031127
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2646X-RAY DIFFRACTION12.523TORSIONAL
12B2646X-RAY DIFFRACTION12.523TORSIONAL
21A956X-RAY DIFFRACTION12.523TORSIONAL
22B956X-RAY DIFFRACTION12.523TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3-3.180.34981430.3315263992
3.18-3.430.34961520.29286899
3.43-3.770.31521410.2536283698
3.77-4.310.24991490.2265286898
4.31-5.430.23031340.2129286398
5.43-32.720.26011430.2113289497
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.1016-0.2763-0.30252.3927-0.27753.19630.1656-0.36610.00940.1598-0.0797-0.01490.23760.0704-00.56660.0320.01580.393-0.02390.536634.8781-12.27478.9229
20.5092-0.16710.18190.9180.71540.5578-0.5271-1.27942.35920.15380.4556-1.3375-0.46120.8598-0.01870.7497-0.0358-0.06711.2529-0.33141.156749.2338-0.99421.2639
30.04970.4106-0.42612.3179-0.11432.042-0.0950.0149-0.00810.21320.33690.33580.1713-0.3603-00.60110.0336-0.03080.58780.00330.727519.05421.87358.2723
40.89870.29570.37332.3653-0.46991.9230.17530.23560.1182-0.292-0.1301-0.44210.01850.252100.59080.02980.04060.38810.0260.598642.9846-1.2611-1.285
50.14880.0665-0.00770.16070.08590.01780.3691-0.8530.92140.5842-0.028-0.9465-0.22071.53530.00930.8732-0.0454-0.10031.20180.15121.234361.6364-10.95237.8396
61.191-0.3289-1.60411.42990.03513.0267-0.3189-1.1418-0.53820.3830.57180.3720.53310.0052-0.00130.81570.17330.11171.12990.36220.835830.4746-27.911733.7194
70.22550.2364-0.56731.5505-0.53411.3839-0.8369-0.50450.5245-0.59830.10280.8374-0.3545-0.4309-0.00080.7310.0307-0.04640.81030.00590.951720.3626-20.168817.4394
80.17420.1330.60460.69690.03921.156-0.1958-1.2759-0.18720.57990.00120.04120.8319-0.1419-0.00410.7550.1203-0.06891.6640.13280.67848.8784-16.986832.0881
90.5877-0.2278-1.11223.81260.28592.4569-0.4406-1.4582-0.49620.52450.55850.38750.10660.4765-0.02180.7710.30860.10251.58940.08730.5225.1182-12.330838.5052
100.0889-0.07350.05320.0558-0.0250.02490.2584-0.38170.0006-0.7332-0.58120.62450.27320.7443-0.00011.0438-0.04310.18421.23190.11671.47265.5718-21.194631.7792
111.39471.29860.06113.3817-1.32071.2222-0.11760.04020.437-0.191-0.0723-0.7067-0.26110.30500.7473-0.00370.00240.71360.02050.98422.288518.36116.2067
121.5330.84860.95022.2875-0.43691.1524-0.24080.7398-0.8797-0.31870.04950.2360.4544-0.4250.00010.75570.0983-0.0810.8903-0.09840.8337-3.11310.9933-2.534
130.64380.14310.66031.65750.03920.730.0806-0.33760.29050.05770.074-0.7971-0.05710.21820.00010.76930.1580.11150.87570.08010.92181.09398.378.2597
140.509-0.01160.38641.34270.74260.68720.3545-1.1439-0.18160.5630.2390.6726-0.8004-1.4406-0.00121.10190.04220.09921.4210.16450.847662.87597.114842.8845
150.486-0.09630.1170.4060.42720.4777-0.6428-0.6725-0.7878-0.0834-0.3577-0.53311.42870.77720.00011.1186-0.0037-0.05371.07120.22761.277568.594-3.309346.4174
160.3129-0.6176-0.07491.65080.27440.0464-0.0938-0.2621-0.22280.9618-0.46110.2106-0.04750.00910.00730.9927-0.1678-0.08641.50720.0340.894361.1228-0.6635.914
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 39 through 147 )A39 - 147
2X-RAY DIFFRACTION2chain 'A' and (resid 148 through 174 )A148 - 174
3X-RAY DIFFRACTION3chain 'A' and (resid 175 through 220 )A175 - 220
4X-RAY DIFFRACTION4chain 'A' and (resid 221 through 318 )A221 - 318
5X-RAY DIFFRACTION5chain 'A' and (resid 319 through 334 )A319 - 334
6X-RAY DIFFRACTION6chain 'B' and (resid 42 through 147 )B42 - 147
7X-RAY DIFFRACTION7chain 'B' and (resid 148 through 174 )B148 - 174
8X-RAY DIFFRACTION8chain 'B' and (resid 175 through 220 )B175 - 220
9X-RAY DIFFRACTION9chain 'B' and (resid 221 through 318 )B221 - 318
10X-RAY DIFFRACTION10chain 'B' and (resid 319 through 333 )B319 - 333
11X-RAY DIFFRACTION11chain 'A' and (resid 1001 through 1048 )A1001 - 1048
12X-RAY DIFFRACTION12chain 'A' and (resid 1049 through 1080 )A1049 - 1080
13X-RAY DIFFRACTION13chain 'A' and (resid 1081 through 1106 and resid 900 through 903 and resid 35)A1081 - 35
14X-RAY DIFFRACTION14chain 'B' and (resid 1001 through 1048 )B1001 - 1048
15X-RAY DIFFRACTION15chain 'B' and (resid 1049 through 1080 )B1049 - 1080
16X-RAY DIFFRACTION16chain 'B' and (resid 1081 through 1106 )B1081 - 1106

+
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://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