[English] 日本語
Yorodumi
- PDB-7c6a: Crystal structure of AT2R-BRIL and SRP2070_Fab complex -

+
Open data


ID or keywords:

Loading...

-
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 IICOPII
  • 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


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 / angiotensin type II receptor activity / brain renin-angiotensin system / regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / regulation of renal sodium excretion / : / type 2 angiotensin receptor binding ...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 / angiotensin type II receptor activity / brain renin-angiotensin system / regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / regulation of renal sodium excretion / : / type 2 angiotensin receptor binding / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / positive regulation of metanephric glomerulus development / regulation of extracellular matrix assembly / receptor antagonist activity / positive regulation of activation of Janus kinase activity / regulation of renal output by angiotensin / positive regulation of NAD(P)H oxidase activity / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / renin-angiotensin regulation of aldosterone production / renal system process / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of CoA-transferase activity / positive regulation of extracellular matrix assembly / positive regulation of macrophage derived foam cell differentiation / low-density lipoprotein particle remodeling / vasoconstriction / type 1 angiotensin receptor binding / 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 / positive regulation of phosphoprotein phosphatase activity / regulation of vasoconstriction / regulation of cardiac conduction / positive regulation of epithelial to mesenchymal transition / blood vessel remodeling / positive regulation of protein tyrosine kinase activity / Metabolism of Angiotensinogen to Angiotensins / nitric oxide mediated signal transduction / positive regulation of protein metabolic process / Peptide ligand-binding receptors / negative regulation of MAP kinase activity / positive regulation of endothelial cell migration / kidney development / positive regulation of nitric-oxide synthase activity / regulation of cell growth / positive regulation of cytokine production / angiotensin-activated signaling pathway / brain development / growth factor activity / serine-type endopeptidase inhibitor activity / hormone activity / negative regulation of cell growth / PPARA activates gene expression / regulation of blood pressure / positive regulation of inflammatory response / positive regulation of miRNA transcription / vasodilation / positive regulation of reactive oxygen species metabolic process / positive regulation of nitric oxide biosynthetic process / positive regulation of fibroblast proliferation / cell-cell signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / regulation of cell population proliferation / G alpha (i) signalling events / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / neuron apoptotic process / regulation of apoptotic process / electron transfer activity / periplasmic space / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / intracellular signal transduction / inflammatory response / iron ion binding / G protein-coupled receptor signaling pathway / heme binding / positive regulation of DNA-templated transcription / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytosol
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 / Serpin superfamily ...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)
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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 / COPII


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
Phasing

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

-
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

+
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