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- PDB-6jod: Angiotensin II type 2 receptor with ligand -

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Basic information

Entry
Database: PDB / ID: 6jod
TitleAngiotensin II type 2 receptor with ligand
Components
  • Angiotensin II
  • Heavy chain of 4A03Fab
  • Light chain of 4A03Fab
  • Soluble cytochrome b562,Soluble cytochrome b562
  • Type-2 angiotensin II receptor
KeywordsSIGNALING PROTEIN / G protein-coupled receptor / regulator of blood pressure
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-mediated vasodilation involved in regulation of systemic arterial blood pressure / angiotensin type II receptor activity / regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / type 2 angiotensin receptor binding / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of renal sodium excretion ...regulation of metanephros size / regulation of systemic arterial blood pressure by circulatory renin-angiotensin / brain renin-angiotensin system / angiotensin-mediated vasodilation involved in regulation of systemic arterial blood pressure / angiotensin type II receptor activity / regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / type 2 angiotensin receptor binding / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of renal sodium excretion / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / maintenance of blood vessel diameter homeostasis by renin-angiotensin / positive regulation of metanephric glomerulus development / regulation of extracellular matrix assembly / receptor antagonist activity / regulation of renal output by angiotensin / renin-angiotensin regulation of aldosterone production / renal system process / positive regulation of extracellular matrix assembly / positive regulation of branching involved in ureteric bud morphogenesis / : / type 1 angiotensin receptor binding / vasoconstriction / low-density lipoprotein particle remodeling / response to angiotensin / positive regulation of macrophage derived foam cell differentiation / positive regulation of extrinsic apoptotic signaling pathway / exploration behavior / positive regulation of epidermal growth factor receptor signaling pathway / negative regulation of heart rate / positive regulation of cardiac muscle hypertrophy / negative regulation of blood vessel endothelial cell migration / positive regulation of protein metabolic process / positive regulation of gap junction assembly / blood vessel remodeling / negative regulation of MAP kinase activity / regulation of cardiac conduction / regulation of vasoconstriction / positive regulation of epithelial to mesenchymal transition / Metabolism of Angiotensinogen to Angiotensins / nitric oxide-cGMP-mediated signaling / positive regulation of endothelial cell migration / Peptide ligand-binding receptors / positive regulation of cytokine production / kidney development / angiotensin-activated signaling pathway / regulation of cell growth / growth factor activity / serine-type endopeptidase inhibitor activity / electron transport chain / PPARA activates gene expression / negative regulation of cell growth / brain development / hormone activity / positive regulation of miRNA transcription / regulation of blood pressure / positive regulation of inflammatory response / positive regulation of fibroblast proliferation / positive regulation of reactive oxygen species metabolic process / positive regulation of NF-kappaB transcription factor activity / vasodilation / cell-cell signaling / regulation of cell population proliferation / : / G alpha (i) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / neuron apoptotic process / regulation of apoptotic process / G alpha (q) signalling events / blood microparticle / periplasmic space / electron transfer activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / inflammatory response / iron ion binding / heme binding / positive regulation of DNA-templated transcription / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Angiotensin II receptor type 2 / Angiotensin II receptor family / Angiotensinogen, serpin domain / Angiotensinogen / : / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain ...Angiotensin II receptor type 2 / Angiotensin II receptor family / Angiotensinogen, serpin domain / Angiotensinogen / : / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / 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) / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Angiotensinogen / Soluble cytochrome b562 / Type-2 angiotensin II receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsAsada, H. / Iwata, S. / Hirata, K. / Shimamura, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP18am0101070 Japan
CitationJournal: Structure / Year: 2020
Title: The Crystal Structure of Angiotensin II Type 2 Receptor with Endogenous Peptide Hormone.
Authors: Asada, H. / Inoue, A. / Ngako Kadji, F.M. / Hirata, K. / Shiimura, Y. / Im, D. / Shimamura, T. / Nomura, N. / Iwanari, H. / Hamakubo, T. / Kusano-Arai, O. / Hisano, H. / Uemura, T. / Suno, C. ...Authors: Asada, H. / Inoue, A. / Ngako Kadji, F.M. / Hirata, K. / Shiimura, Y. / Im, D. / Shimamura, T. / Nomura, N. / Iwanari, H. / Hamakubo, T. / Kusano-Arai, O. / Hisano, H. / Uemura, T. / Suno, C. / Aoki, J. / Iwata, S.
History
DepositionMar 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type-2 angiotensin II receptor
B: Angiotensin II
C: Soluble cytochrome b562,Soluble cytochrome b562
H: Heavy chain of 4A03Fab
L: Light chain of 4A03Fab


Theoretical massNumber of molelcules
Total (without water)92,5725
Polymers92,5725
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-44 kcal/mol
Surface area37820 Å2
Unit cell
Length a, b, c (Å)102.550, 426.430, 52.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Type-2 angiotensin II receptor / Angiotensin II type-2 receptor / AT2


Mass: 35733.621 Da / Num. of mol.: 1 / Mutation: S208A
Source method: isolated from a genetically manipulated source
Details: 1-34 and 347-363 deleted. / Source: (gene. exp.) Homo sapiens (human) / Gene: AGTR2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P50052
#2: Protein/peptide Angiotensin II


Mass: 1048.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Endogenous ligand of Angiotensin receptor / Source: (synth.) Homo sapiens (human) / References: UniProt: P01019*PLUS
#3: Protein Soluble cytochrome b562,Soluble cytochrome b562 / Cytochrome b-562


Mass: 9156.169 Da / Num. of mol.: 1 / Mutation: M1007W,R1098I,H1102I,R1106G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0ABE7
#4: Antibody Heavy chain of 4A03Fab


Mass: 23371.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#5: Antibody Light chain of 4A03Fab


Mass: 23262.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
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: 3.22 Å3/Da / Density % sol: 61.77 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 30% (v/v) PEG 300 0.1 M HEPES (pH 7.0) 100 mM Sodium phosphate dibasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: May 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→49.854 Å / Num. obs: 19767 / % possible obs: 99.89 % / Redundancy: 82.3 % / Biso Wilson estimate: 114.16 Å2 / Rpim(I) all: 0.0498 / Net I/σ(I): 17.47
Reflection shellResolution: 3.2→3.31 Å / Num. unique obs: 1933 / Rpim(I) all: 0.551

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5xjm, 1M6T

5xjm

1m6t


Resolution: 3.2→49.854 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.79
RfactorNum. reflection% reflection
Rfree0.2869 940 4.76 %
Rwork0.235 --
obs0.2375 19767 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 374.93 Å2 / Biso mean: 141.9422 Å2 / Biso min: 60.51 Å2
Refinement stepCycle: final / Resolution: 3.2→49.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6257 0 0 0 6257
Num. residues----805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036425
X-RAY DIFFRACTIONf_angle_d0.6098754
X-RAY DIFFRACTIONf_chiral_restr0.041999
X-RAY DIFFRACTIONf_plane_restr0.0051088
X-RAY DIFFRACTIONf_dihedral_angle_d13.0153798
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.2001-3.36880.44551330.381226252758
3.3688-3.57980.34261330.312326362769
3.5798-3.85610.33921360.27926382774
3.8561-4.2440.27691370.226626512788
4.244-4.85760.23931220.184927042826
4.8576-6.11830.25341330.221627182851
6.1183-49.85970.28731460.227828553001
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)
14.8296-1.35081.21853.504-1.31717.8398-1.15570.88811.12561.31340.16860.24531.04711.71151.01230.95850.3710.18210.89670.01041.565222.348634.798-3.016
22.6523.5564-4.38744.9766-4.83331.9867-1.203-0.957-2.74912.4033-0.7905-0.17040.51030.79960.09161.63160.51460.56630.08560.22152.89558.11957.9258-6.3851
35.79563.45330.27245.19280.58525.9170.49470.1889-0.6650.3542-0.64851.1381.0878-0.26490.19730.9628-0.09630.02210.6634-0.07941.380212.963928.60043.3496
42.7868-0.95534.42070.4802-1.99678.5318-0.53040.4313-0.9279-0.91780.5942-0.2159-2.979-1.6092-0.74453.4785-0.592-0.04142.20820.09751.3479.29210.39529.8111
51.4639-1.97140.14612.55260.18531.36331.1209-0.3014-0.24582.6531-1.73991.8122-0.2573-0.22220.1231.6518-0.01970.01341.1054-0.00371.57444.70428.94059.9381
63.9289-1.70370.68093.9362-2.26451.39210.0049-0.4654-0.27281.37510.29771.72570.3586-0.45490.24361.3305-0.26740.02740.8003-0.02511.275413.615343.950715.4438
71.0922-0.18381.70780.4239-0.96133.966-0.39820.3618-3.46310.0548-0.9445-0.03461.82191.8050.14842.01370.0120.50880.79970.15043.563524.89978.721516.7031
84.8930.6779-1.98861.4043-1.80583.4305-1.1368-0.0043-0.9358-0.37010.9977-0.95540.77160.94450.41751.11730.0389-0.02720.72060.19841.789226.909321.488211.8914
94.2408-1.5135-1.75352.9221-1.81827.2696-0.58910.73310.72720.5941.1894-0.3846-0.12360.949-0.06850.86550.1772-0.10590.7854-0.06721.854325.495235.08648.4478
101.93820.0174-0.22.143-2.68043.3376-0.61421.09351.6126-2.6570.7114-1.75690.39260.8457-0.38544.53430.0599-0.81290.3011-0.22982.856719.23629.2105-15.6659
114.4915-3.57590.18883.26520.98442.83690.9906-1.5955-0.6536-1.1925-0.627-0.9491-0.08061.81010.58871.55560.0227-0.0951.01920.06041.661117.524744.593710.7764
128.82175.24568.26394.76783.0759.8389-1.2683-1.2462.42111.51070.55981.08011.42122.7851.14481.6838-0.2657-0.15961.9631-0.35132.366237.717756.905127.5283
136.0095-3.5909-0.89083.28752.06012.36251.86073.6705-1.8585-0.2359-1.2893-1.13591.34380.46941.70583.23740.4351-0.13852.5074-0.25162.711839.248364.214833.8506
143.7063-0.63034.20793.48580.74865.55821.8151-2.71823.6408-0.49390.221-1.5366-0.46751.4256-1.57642.39320.27870.75072.4079-0.35462.748835.550669.255226.9765
157.6596-1.64611.34336.3849-2.43415.3507-0.3990.4424-0.30660.15350.1530.35380.5999-0.31430.32890.9383-0.1813-0.07220.6809-0.01820.75217.27968.4778-7.998
164.68543.64681.21298.0809-0.60842.65350.10691.034-0.4505-0.17140.4843-0.87680.00520.7563-0.48770.60580.0435-0.01961.1966-0.08240.642933.305595.2066-20.5645
173.97251.3531-0.68914.2869-0.10498.80540.23420.0313-0.9051-0.33-0.09750.0337-0.18730.5794-0.21650.82530.1283-0.12761.3008-0.14110.636134.767894.2962-21.4062
183.10573.6155-3.75075.7373-1.81358.60991.8148-0.66121.58621.4274-0.82390.8489-1.82320.4437-0.63111.4551-0.1065-0.07221.2520.27330.838829.721482.611411.3492
198.29973.0338-1.96074.18560.77377.97640.1076-0.1314-0.44230.9154-0.20190.3119-0.47780.5001-0.03571.17690.0581-0.17770.79920.1070.748129.514371.58017.9407
207.11453.566-3.38367.0165-0.61614.95121.044-1.1071-1.02282.7798-0.45070.65181.41220.46040.80992.43410.2655-0.55931.07840.29550.321729.874473.179815.569
218.86316.2906-3.07874.9358-0.61837.7725-0.379-0.0894-1.51110.30690.2784-0.79930.33881.7198-0.20111.5935-0.09610.0611.1021-0.01440.966133.043476.27986.477
229.65667.91531.46947.02592.66566.2666-0.34820.55431.59820.64090.14050.0461-1.00050.22050.20140.77730.20730.04770.7142-0.06930.942517.795172.7326.4385
230.9805-0.2850.47563.81440.27980.11880.1440.1393-0.449-0.061-0.42540.0637-0.4608-0.5127-0.19070.843-0.0006-0.1991.3880.01690.560236.6838100.4589-10.5701
242.17931.46532.02782.88382.64262.88030.0807-0.0626-0.50810.74180.29380.5371-0.1912-1.4537-0.49220.71140.14460.00271.2504-0.05520.50936.451101.158-7.1991
256.0355-2.17924.55574.21320.68856.5047-1.291-0.95031.6705-0.62712.4424-0.0843-1.0569-1.2769-0.03851.2989-0.11410.10571.3568-0.01550.80431.0716113.9737-7.0957
263.3731-4.57573.87886.5173-5.5984.79120.69891.0697-0.1139-2.09070.4042-0.3210.8720.1237-1.00851.1478-0.1355-0.00561.4295-0.25250.983734.370396.5066-5.2652
276.5555-3.43134.35988.1931-7.17588.87540.07990.33280.49030.7134-0.05610.6513-1.3950.5934-0.33751.0683-0.06260.03421.1504-0.09930.594430.5134112.8115-14.5034
287.8683-5.48955.72954.4905-5.186.0914-0.95040.56761.85060.4031-1.5575-1.8197-1.20240.48080.97321.2816-0.1397-0.06821.3515-0.02780.906440.839112.8398-9.2164
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 70 )A35 - 70
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 77 )A71 - 77
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 147 )A78 - 147
4X-RAY DIFFRACTION4chain 'A' and (resid 148 through 156 )A148 - 156
5X-RAY DIFFRACTION5chain 'A' and (resid 157 through 187 )A157 - 187
6X-RAY DIFFRACTION6chain 'A' and (resid 188 through 220 )A188 - 220
7X-RAY DIFFRACTION7chain 'A' and (resid 221 through 244 )A221 - 244
8X-RAY DIFFRACTION8chain 'A' and (resid 245 through 284 )A245 - 284
9X-RAY DIFFRACTION9chain 'A' and (resid 285 through 318 )A285 - 318
10X-RAY DIFFRACTION10chain 'A' and (resid 319 through 340 )A319 - 340
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 8 )B1 - 8
12X-RAY DIFFRACTION12chain 'C' and (resid 1008 through 1022 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 1023 through 1038 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 1039 through 1093 )C0
15X-RAY DIFFRACTION15chain 'H' and (resid 1 through 118 )H1 - 118
16X-RAY DIFFRACTION16chain 'H' and (resid 119 through 169 )H119 - 169
17X-RAY DIFFRACTION17chain 'H' and (resid 170 through 220 )H170 - 220
18X-RAY DIFFRACTION18chain 'L' and (resid 1 through 18 )L1 - 18
19X-RAY DIFFRACTION19chain 'L' and (resid 19 through 60 )L19 - 60
20X-RAY DIFFRACTION20chain 'L' and (resid 61 through 74 )L61 - 74
21X-RAY DIFFRACTION21chain 'L' and (resid 75 through 90 )L75 - 90
22X-RAY DIFFRACTION22chain 'L' and (resid 91 through 101 )L91 - 101
23X-RAY DIFFRACTION23chain 'L' and (resid 102 through 127 )L102 - 127
24X-RAY DIFFRACTION24chain 'L' and (resid 128 through 142 )L128 - 142
25X-RAY DIFFRACTION25chain 'L' and (resid 143 through 154 )L143 - 154
26X-RAY DIFFRACTION26chain 'L' and (resid 155 through 173 )L155 - 173
27X-RAY DIFFRACTION27chain 'L' and (resid 174 through 197 )L174 - 197
28X-RAY DIFFRACTION28chain 'L' and (resid 198 through 212 )L198 - 212

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