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- PDB-5xjm: Complex structure of angiotensin II type 2 receptor with Fab -

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Basic information

Entry
Database: PDB / ID: 5xjm
TitleComplex structure of angiotensin II type 2 receptor with Fab
Components
  • FabH
  • FabL
  • Sar1, Ile8-angiotensin II
  • Type-2 angiotensin II receptor,Soluble cytochrome b562,Type-2 angiotensin II receptor
KeywordsSIGNALING PROTEIN / class A GPCR / regulate human blood pressure / Angiotensin receptors
Function / homology
Function and homology information


angiotensin-mediated vasodilation involved in regulation of systemic arterial blood pressure / regulation of metanephros size / regulation of systemic arterial blood pressure by circulatory renin-angiotensin / brain renin-angiotensin system / 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 ...angiotensin-mediated vasodilation involved in regulation of systemic arterial blood pressure / regulation of metanephros size / regulation of systemic arterial blood pressure by circulatory renin-angiotensin / brain renin-angiotensin system / 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 macrophage derived foam cell differentiation / positive regulation of branching involved in ureteric bud morphogenesis / : / vasoconstriction / type 1 angiotensin receptor binding / low-density lipoprotein particle remodeling / response to angiotensin / 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 gap junction assembly / blood vessel remodeling / regulation of cardiac conduction / negative regulation of MAP kinase activity / regulation of vasoconstriction / positive regulation of epithelial to mesenchymal transition / Metabolism of Angiotensinogen to Angiotensins / nitric oxide-cGMP-mediated signaling / positive regulation of protein metabolic process / 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 / electron transport chain / serine-type endopeptidase inhibitor activity / PPARA activates gene expression / negative regulation of cell growth / brain development / hormone activity / regulation of blood pressure / positive regulation of miRNA transcription / positive regulation of inflammatory response / positive regulation of fibroblast proliferation / vasodilation / positive regulation of reactive oxygen species metabolic process / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / regulation of cell population proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / collagen-containing extracellular matrix / regulation of apoptotic process / neuron apoptotic process / G alpha (q) signalling events / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / electron transfer activity / cell surface receptor signaling pathway / periplasmic space / 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. / Horita, S. / Shimamura, T. / Iwata, S.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15J04343 Japan
Japan Society for the Promotion of Science15J04343 Japan
Japan Society for the Promotion of Science22590270 Japan
Japan Agency for Medical Research and DevelopmentA19170600003 Japan
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Crystal structure of the human angiotensin II type 2 receptor bound to an angiotensin II analog
Authors: Asada, H. / Horita, S. / Hirata, K. / Shiroishi, M. / Shiimura, Y. / Iwanari, H. / Hamakubo, T. / Shimamura, T. / Nomura, N. / Kusano-Arai, O. / Uemura, T. / Suno, C. / Kobayashi, T. / Iwata, S.
History
DepositionMay 2, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.2Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 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 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type-2 angiotensin II receptor,Soluble cytochrome b562,Type-2 angiotensin II receptor
H: FabH
L: FabL
B: Sar1, Ile8-angiotensin II


Theoretical massNumber of molelcules
Total (without water)95,6654
Polymers95,6654
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-46 kcal/mol
Surface area37700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)465.390, 48.650, 55.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 48061.383 Da / Num. of mol.: 1 / Fragment: UNP residues 35-242,UNP residues 246-346 / Mutation: M1007W, H1102I, R1106L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: AGTR2, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P50052, UniProt: P0ABE7
#2: Antibody FabH


Mass: 23371.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody FabL


Mass: 23262.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Protein/peptide Sar1, Ile8-angiotensin II


Mass: 970.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01019*PLUS
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: 3.5 Å3/Da / Density % sol: 64.87 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7
Details: 34%(v/v) PEG 300, 0.1 M HEPES pH 7.0, 0.5%(v/v) Tacsimate (pH7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→48.386 Å / Num. obs: 22033 / Biso Wilson estimate: 51.8 Å2
Reflection shellResolution: 3.2→3.38 Å / Mean I/σ(I) obs: 1.61 / Num. unique obs: 3410 / CC1/2: 0.508 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YAY, 1M6T

4yay

1m6t


Resolution: 3.2→48.386 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2751 1998 9.07 %
Rwork0.2259 20035 -
obs0.2304 22033 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 192.33 Å2 / Biso mean: 69.9193 Å2 / Biso min: 8.78 Å2
Refinement stepCycle: final / Resolution: 3.2→48.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6335 0 0 0 6335
Num. residues----815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026505
X-RAY DIFFRACTIONf_angle_d0.528864
X-RAY DIFFRACTIONf_chiral_restr0.0381010
X-RAY DIFFRACTIONf_plane_restr0.0041104
X-RAY DIFFRACTIONf_dihedral_angle_d12.0713850
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1999-3.27990.31721420.284314201562100
3.2799-3.36850.31451330.262713541487100
3.3685-3.46760.2941430.249414331576100
3.4676-3.57950.30731370.243713581495100
3.5795-3.70740.29191440.247514501594100
3.7074-3.85580.33931360.24313621498100
3.8558-4.03120.29831430.215214411584100
4.0312-4.24360.26461390.207213901529100
4.2436-4.50930.21631420.19814291571100
4.5093-4.85720.24761460.178914511597100
4.8572-5.34540.24731430.194714301573100
5.3454-6.11760.2751470.22714691616100
6.1176-7.70250.26111450.264314581603100
7.7025-48.39180.26861580.22771590174899
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)
11.4799-0.7148-0.24791.00890.04580.67510.10230.05310.4351-0.0704-0.04640.4152-0.2545-0.56280.01510.24030.1733-0.11191.52930.04521.636141.590525.41837.0986
21.4132-0.2185-0.67340.26840.14040.27150.005-0.2729-0.28710.30430.1360.54120.1533-0.16960.14930.23430.23510.07881.5460.03561.754745.89319.50617.964
31.395-0.4135-0.4651.6166-0.08890.55640.06810.24370.0222-0.5791-0.18940.6229-0.1264-0.7588-0.07350.28370.138-0.11730.564-0.01660.391580.725916.9679-8.3929
44.07931.6229-3.87992.335-1.71017.85470.15330.0380.0597-0.4649-0.22690.5319-0.077-0.3395-0.01770.25760.1466-0.19390.3183-0.01380.250784.751813.9075-4.8115
51.56590.07331.26243.9333-1.69333.11250.17220.2748-0.183-0.1927-0.1602-0.19220.162-0.1652-0.05030.26590.00880.00870.4238-0.02070.0412108.1095-2.8119-18.8423
61.9352-1.07230.3173.5271-0.63493.01990.33290.5598-0.2308-0.323-0.18550.08230.2767-0.32470.09380.26990.0285-0.01220.3608-0.22430.1733105.9974-7.1247-17.6726
72.05450.9949-0.35614.17661.11432.78690.0074-0.1776-0.18260.27920.126-0.46210.2038-0.1538-0.20270.1731-0.0064-0.0420.156-0.05590.160398.76379.075412.6065
80.850.365-0.2521.64390.62762.5868-0.0252-0.22810.15140.17580.07830.3180.3657-0.63250.07890.096-0.020.07990.4037-0.02020.181188.03829.231912.5622
93.1373-1.1670.00112.76740.88743.94210.0898-0.27960.0289-0.02410.09460.25460.6406-0.0275-0.23730.125-0.101-0.08860.42210.05110.170491.87514.842610.1778
100.41840.0791-0.06010.39480.00160.2198-0.07820.10890.04710.0031-0.02690.00810.2228-0.174-0.00910.2670.05380.02540.23030.01240.0104108.87971.0659-4.7133
116.67671.1939-3.89151.8074-1.87925.16960.03830.12540.1287-0.1909-0.03120.0073-0.0363-0.26370.02740.21630.0057-0.0480.1238-0.0180.0053116.2381.3068-5.6379
122.23360.3356-1.0621.3988-0.2622.0370.13540.26880.1615-0.3082-0.0825-0.1573-0.21470.1185-0.03320.37240.03990.08770.27940.09430.0667121.91823.3303-19.2364
131.8277-0.3139-0.38341.11820.85272.07430.13860.2221-0.04720.0225-0.0098-0.1819-0.13440.112-0.13450.20540.0998-0.03220.02080.01840.1581126.8369-3.6899-9.079
142.61521.9675-2.34254.28890.06163.2824-0.2075-0.2597-0.108-0.0410.18450.0328-0.1049-0.17360.06610.3457-0.1118-0.00021.3568-0.03591.376959.837422.499713.6093
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 180 )A35 - 180
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 320 )A181 - 320
3X-RAY DIFFRACTION3chain 'H' and (resid 1 through 84 )H1 - 84
4X-RAY DIFFRACTION4chain 'H' and (resid 85 through 118 )H85 - 118
5X-RAY DIFFRACTION5chain 'H' and (resid 119 through 162 )H119 - 162
6X-RAY DIFFRACTION6chain 'H' and (resid 163 through 220 )H163 - 220
7X-RAY DIFFRACTION7chain 'L' and (resid 1 through 18 )L1 - 18
8X-RAY DIFFRACTION8chain 'L' and (resid 19 through 74 )L19 - 74
9X-RAY DIFFRACTION9chain 'L' and (resid 75 through 90 )L75 - 90
10X-RAY DIFFRACTION10chain 'L' and (resid 91 through 142 )L91 - 142
11X-RAY DIFFRACTION11chain 'L' and (resid 143 through 173 )L143 - 173
12X-RAY DIFFRACTION12chain 'L' and (resid 174 through 186 )L174 - 186
13X-RAY DIFFRACTION13chain 'L' and (resid 187 through 212 )L187 - 212
14X-RAY DIFFRACTION14chain 'B' and (resid 2 through 8 )B2 - 8

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