[English] 日本語
Yorodumi
- PDB-5ung: XFEL structure of human angiotensin II type 2 receptor (Orthorhom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ung
TitleXFEL structure of human angiotensin II type 2 receptor (Orthorhombic form) in complex with compound 1 (N-benzyl-N-(2-ethyl-4-oxo-3-{[2'-(2H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl] methyl}-3,4-dihydroquinazolin-6-yl)thiophene-2-carboxamide)
ComponentsChimera protein of Type-2 angiotensin II receptor and Soluble cytochrome b562
KeywordsSIGNALING PROTEIN / human Angiotensin II receptor complex / GPCR signaling / GPCR / BRIL / membrane protein / LCP / XFEL / blood pressure regulation / orthorhombic crystal / compound 1 (cpd 1)
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 / negative regulation of cell growth / electron transport chain / 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 / iron ion binding / inflammatory response / heme binding / positive regulation of DNA-templated transcription / plasma membrane
Similarity search - Function
Angiotensin II receptor type 2 / Angiotensin II receptor family / Cytochrome c/b562 / : / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Angiotensin II receptor type 2 / Angiotensin II receptor family / Cytochrome c/b562 / : / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-8ES / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Soluble cytochrome b562 / Type-2 angiotensin II receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhang, H. / Han, G.W. / Batyuk, A. / Ishchenko, A. / White, K.L. / Patel, N. / Sadybekov, A. / Zamlynny, B. / Rudd, M.T. / Hollenstein, K. ...Zhang, H. / Han, G.W. / Batyuk, A. / Ishchenko, A. / White, K.L. / Patel, N. / Sadybekov, A. / Zamlynny, B. / Rudd, M.T. / Hollenstein, K. / Tolstikova, A. / White, T.A. / Hunter, M.S. / Weierstall, U. / Liu, W. / Babaoglu, K. / Moore, E.L. / Katz, R.D. / Shipman, J.M. / Garcia-Calvo, M. / Sharma, S. / Sheth, P. / Soisson, S.M. / Stevens, R.C. / Katritch, V. / Cherezov, V.
CitationJournal: Nature / Year: 2017
Title: Structural basis for selectivity and diversity in angiotensin II receptors.
Authors: Zhang, H. / Han, G.W. / Batyuk, A. / Ishchenko, A. / White, K.L. / Patel, N. / Sadybekov, A. / Zamlynny, B. / Rudd, M.T. / Hollenstein, K. / Tolstikova, A. / White, T.A. / Hunter, M.S. / ...Authors: Zhang, H. / Han, G.W. / Batyuk, A. / Ishchenko, A. / White, K.L. / Patel, N. / Sadybekov, A. / Zamlynny, B. / Rudd, M.T. / Hollenstein, K. / Tolstikova, A. / White, T.A. / Hunter, M.S. / Weierstall, U. / Liu, W. / Babaoglu, K. / Moore, E.L. / Katz, R.D. / Shipman, J.M. / Garcia-Calvo, M. / Sharma, S. / Sheth, P. / Soisson, S.M. / Stevens, R.C. / Katritch, V. / Cherezov, V.
History
DepositionJan 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Data collection / Database references
Revision 1.2Nov 28, 2018Group: Data collection
Category: diffrn / pdbx_serial_crystallography_data_reduction ...diffrn / pdbx_serial_crystallography_data_reduction / pdbx_serial_crystallography_measurement / pdbx_serial_crystallography_sample_delivery
Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.3Oct 4, 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 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Chimera protein of Type-2 angiotensin II receptor and Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7694
Polymers46,5071
Non-polymers1,2633
Water181
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-4 kcal/mol
Surface area20630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.260, 78.790, 93.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

-
Components

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


Mass: 46506.535 Da / Num. of mol.: 1
Fragment: UNP P0ABE7 residues 23-128 and UNP P50052 35-335 linked via LINKER resdiues GSGS
Mutation: M1007W, H1102I, R1106L
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) / Strain (production host): sf9 / References: UniProt: P0ABE7, UniProt: P50052
#2: Chemical ChemComp-8ES / N-benzyl-N-(2-ethyl-4-oxo-3-{[2'-(2H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl]methyl}-3,4-dihydroquinazolin-6-yl)thiophene-2-carboxamide


Mass: 623.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H29N7O2S
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8
Details: 100 mM Tris-HCl, pH 8.0, 25 mM potassium formate, 25% (v/v) PEG400, and 0.3% (v/v) (+/-)-2-Methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 294 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Dec 9, 2015 / Details: K-B mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 2.8→28.96 Å / Num. obs: 13330 / % possible obs: 100 % / Redundancy: 85.5 % / Biso Wilson estimate: 80.91 Å2 / Rmerge(I) obs: 0.148 / Net I/σ(I): 4.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 27.2 % / Rmerge(I) obs: 1.24 / Mean I/σ(I) obs: 1 / % possible all: 100
Serial crystallography measurementPhotons per pulse: 1011 Tphotons/pulse / Pulse duration: 40 fsec. / Pulse energy: 1.8 µJ / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography data reductionCrystal hits: 175241 / Frames indexed: 15804 / Frames total: 2701530

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YAY, 4ZUD

4yay

4zud


Resolution: 2.8→28.96 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.881 / SU R Cruickshank DPI: 2.685 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.894 / SU Rfree Blow DPI: 0.357 / SU Rfree Cruickshank DPI: 0.363
RfactorNum. reflection% reflectionSelection details
Rfree0.262 691 5.21 %RANDOM
Rwork0.241 ---
obs0.242 13269 99.8 %-
Displacement parametersBiso mean: 82.84 Å2
Baniso -1Baniso -2Baniso -3
1--2.1768 Å20 Å20 Å2
2--4.9374 Å20 Å2
3----2.7606 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: 1 / Resolution: 2.8→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3195 0 70 1 3266
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093351HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.924557HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1105SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes483HARMONIC5
X-RAY DIFFRACTIONt_it3351HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.81
X-RAY DIFFRACTIONt_other_torsion20.37
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion441SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3803SEMIHARMONIC4
LS refinement shellResolution: 2.8→3.02 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.263 149 5.53 %
Rwork0.239 2544 -
all0.24 2693 -
obs--99.89 %
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)
11.34940.76391.74282.9298-0.30123.5237-0.01370.0173-0.0525-0.02950.01970.1097-0.03320.0294-0.0061-0.0262-0.00290.0075-0.1488-0.0382-0.03122.629236.8452-13.5705
21.37170.69110.0633.25870.02191.9040.0973-0.10240.0360.2630.0820.07950.0691-0.1515-0.1793-0.2334-0.0055-0.054-0.21020.0207-0.05459.7938-1.674-19.174
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ B| 1001 - 1110 }
2X-RAY DIFFRACTION2{ B| 35 - 334 }

+
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