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- PDB-7c6a: Crystal structure of AT2R-BRIL and SRP2070_Fab complex -

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Basic information

Entry
Database: PDB / ID: 7c6a
TitleCrystal structure of AT2R-BRIL and SRP2070_Fab complex
Components
  • IgG Light Chain
  • IgG heavy chain
  • SAR1, ILE8-ANGIOTENSIN II
  • Type-2 angiotensin II receptor,Soluble cytochrome b562,Type-2 angiotensin II receptor
KeywordsSIGNALING PROTEIN / GPCR / BRIL / Crystallization / Antibody
Function / homology
Function and homology information


regulation of metanephros size / regulation of systemic arterial blood pressure by circulatory renin-angiotensin / brain renin-angiotensin system / regulation of blood volume by renin-angiotensin / angiotensin type II receptor activity / response to muscle activity involved in regulation of muscle adaptation / angiotensin-mediated vasodilation involved in regulation of systemic arterial blood pressure / 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 / regulation of blood volume by renin-angiotensin / angiotensin type II receptor activity / response to muscle activity involved in regulation of muscle adaptation / angiotensin-mediated vasodilation involved in regulation of systemic arterial blood pressure / 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 / positive regulation of extracellular matrix assembly / renin-angiotensin regulation of aldosterone production / renal system process / vasoconstriction / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of cholesterol metabolic process / type 1 angiotensin receptor binding / response to angiotensin / low-density lipoprotein particle remodeling / positive regulation of macrophage derived foam cell differentiation / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of epidermal growth factor receptor signaling pathway / negative regulation of heart rate / positive regulation of cardiac muscle hypertrophy / exploration behavior / negative regulation of MAP kinase activity / positive regulation of gap junction assembly / negative regulation of blood vessel endothelial cell migration / blood vessel remodeling / 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 / angiotensin-activated signaling pathway / growth factor activity / kidney development / regulation of cell growth / serine-type endopeptidase inhibitor activity / electron transport chain / PPARA activates gene expression / negative regulation of cell growth / hormone activity / brain development / positive regulation of miRNA transcription / regulation of blood pressure / vasodilation / positive regulation of reactive oxygen species metabolic process / positive regulation of fibroblast proliferation / positive regulation of inflammatory response / cell-cell signaling / regulation of cell population proliferation / : / neuron apoptotic process / regulation of apoptotic process / G alpha (i) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / blood microparticle / G alpha (q) signalling events / periplasmic space / electron transfer activity / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / iron ion binding / inflammatory response / heme binding / positive regulation of DNA-templated transcription / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Angiotensin II receptor type 2 / Angiotensinogen, serpin domain / Angiotensinogen / Angiotensin II receptor family / Serpin, conserved site / Serpins signature. / : / Serpin superfamily, domain 2 / Serpin family / Serpin domain ...Angiotensin II receptor type 2 / Angiotensinogen, serpin domain / Angiotensinogen / Angiotensin II receptor family / 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 speciesMus musculus (house mouse)
Homo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 Å
AuthorsSuzuki, M. / Miyagi, H. / Asada, H. / Yasunaga, M. / Suno, C. / Takahashi, Y. / Saito, J. / Iwata, S.
CitationJournal: Sci Rep / Year: 2020
Title: The discovery of a new antibody for BRIL-fused GPCR structure determination.
Authors: Miyagi, H. / Asada, H. / Suzuki, M. / Takahashi, Y. / Yasunaga, M. / Suno, C. / Iwata, S. / Saito, J.I.
History
DepositionMay 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IgG Light Chain
H: IgG heavy chain
A: Type-2 angiotensin II receptor,Soluble cytochrome b562,Type-2 angiotensin II receptor
B: SAR1, ILE8-ANGIOTENSIN II


Theoretical massNumber of molelcules
Total (without water)96,9784
Polymers96,9784
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.230, 131.040, 113.800
Angle α, β, γ (deg.)90.000, 97.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody IgG Light Chain


Mass: 23681.053 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)
#2: Antibody IgG heavy chain


Mass: 24240.152 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)
#3: 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: 48086.391 Da / Num. of mol.: 1 / Mutation: L93V, F133W, 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
#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 ligand of interestY
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: 3.07 Å3/Da / Density % sol: 59.93 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.05M POTASSIUM ACETATE, 0.1M MES PH6.5, 26-36% PEG300

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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: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→42.77 Å / Num. obs: 16178 / % possible obs: 100 % / Redundancy: 18.8 % / CC1/2: 0.985 / Rmerge(I) obs: 0.607 / Rpim(I) all: 0.14 / Rrim(I) all: 0.623 / Net I/σ(I): 5.1 / Num. measured all: 303868 / Scaling rejects: 44
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.4-3.6714.52.8134853133440.490.722.9071.1100
9-42.7721.20.184191008990.9910.040.18814.399.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.64 Å42.76 Å
Translation6.64 Å42.76 Å

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
PHASER2.6.1phasing
REFMAC5.8.0232refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZUD

4zud


Resolution: 3.4→40 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.869 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.634 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2853 795 4.9 %RANDOM
Rwork0.2352 ---
obs0.2378 15368 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 241.42 Å2 / Biso mean: 135.009 Å2 / Biso min: 89.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.93 Å2-0 Å21.69 Å2
2---2.72 Å2-0 Å2
3----0.61 Å2
Refinement stepCycle: final / Resolution: 3.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6352 0 0 0 6352
Num. residues----811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0136520
X-RAY DIFFRACTIONr_bond_other_d0.0350.0175965
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.6368877
X-RAY DIFFRACTIONr_angle_other_deg2.3471.56713856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6765803
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29922.877285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.043151056
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2381523
X-RAY DIFFRACTIONr_chiral_restr0.0490.2877
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027178
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021379
LS refinement shellResolution: 3.4→3.487 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 61 -
Rwork0.386 1113 -
all-1174 -
obs--99.58 %
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)
12.35960.53040.70482.65680.6993.296-0.3009-0.07190.37750.0649-0.17950.24640.30390.03110.48050.36160.12740.07010.6929-0.03560.13-20.0316.278113.27
22.9240.2269-0.32394.9501-2.09693.2504-0.2133-0.01630.5005-0.05750.0535-1.0355-0.22040.27340.15970.047-0.0144-0.00110.6667-0.03060.34380.75623.17135.974
32.0190.3296-0.92292.8678-0.74992.9343-0.0518-0.0265-0.19470.1802-0.0649-0.031-0.09960.05630.11680.19690.11220.00990.7246-0.02170.02050.277-13.52452.296
46.77070.1572-2.92363.65271.27512.215-0.080.1359-0.27730.0647-0.06490.08370.29310.07620.14490.54680.01320.02280.5765-0.05960.1217-29.938-10.83397.361
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 109
2X-RAY DIFFRACTION1H1 - 119
3X-RAY DIFFRACTION2H120 - 219
4X-RAY DIFFRACTION2L110 - 211
5X-RAY DIFFRACTION3A35 - 242
6X-RAY DIFFRACTION3A246 - 323
7X-RAY DIFFRACTION3B1 - 8
8X-RAY DIFFRACTION4A1001 - 1106

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