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- PDB-5unh: Synchrotron structure of human angiotensin II type 2 receptor in ... -

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Entry
Database: PDB / ID: 5unh
TitleSynchrotron structure of human angiotensin II type 2 receptor in complex with compound 2 (N-[(furan-2-yl)methyl]-N-(4-oxo-2-propyl-3-{[2'-(2H-tetrazol-5-yl)[1,1'- biphenyl]-4-yl]methyl}-3,4-dihydroquinazolin-6-yl)benzamide)
ComponentsSoluble cytochrome b562,Type-2 angiotensin II receptor
KeywordsSIGNALING PROTEIN / human Angiotensin II receptor complex / GPCR signaling / GPCR / BRIL / membrane protein / LCP / Synchrotron / blood pressure regulation / compound 2 (cpd 2)
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 / 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-mediated vasodilation involved in regulation of systemic arterial blood pressure / angiotensin type II receptor activity / 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 / exploration behavior / negative regulation of heart rate / negative regulation of blood vessel endothelial cell migration / blood vessel remodeling / nitric oxide-cGMP-mediated signaling / Peptide ligand-binding receptors / electron transport chain / negative regulation of cell growth / brain development / regulation of blood pressure / vasodilation / G alpha (i) signalling events / neuron apoptotic process / periplasmic space / electron transfer activity / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / inflammatory response / iron ion binding / 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-8EM / Soluble cytochrome b562 / Type-2 angiotensin II receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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: Database references
Revision 1.2Oct 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 1.3Nov 20, 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: Soluble cytochrome b562,Type-2 angiotensin II receptor
B: Soluble cytochrome b562,Type-2 angiotensin II receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2564
Polymers93,0132
Non-polymers1,2432
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-24 kcal/mol
Surface area37860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.420, 68.200, 89.060
Angle α, β, γ (deg.)90.00, 104.32, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

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


Mass: 46506.535 Da / Num. of mol.: 2
Fragment: UNP P0ABE7 residues 23-128 and UNP P50052 35-335 linked via LINKER resdiues GSGS,UNP P0ABE7 residues 23-128 and UNP P50052 35-335 linked via LINKER resdiues GSGS
Mutation: M1007W, H1102I, R1106L,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 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P0ABE7, UniProt: P50052
#2: Chemical ChemComp-8EM / N-[(furan-2-yl)methyl]-N-(4-oxo-2-propyl-3-{[2'-(2H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl]methyl}-3,4-dihydroquinazolin-6-yl)benzamide


Mass: 621.687 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H31N7O3
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: 2.48 Å3/Da / Density % sol: 50.42 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 18479 / % possible obs: 91 % / Redundancy: 3.5 % / Biso Wilson estimate: 79.1 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.8
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.8 / % possible all: 83.2

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Processing

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

4yay

4zud


Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.861 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.421
RfactorNum. reflection% reflectionSelection details
Rfree0.259 906 4.91 %RANDOM
Rwork0.216 ---
obs0.218 18462 90.3 %-
Displacement parametersBiso mean: 100.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.3299 Å20 Å2-2.0241 Å2
2---4.875 Å20 Å2
3---4.5451 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: 1 / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5783 0 94 0 5877
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096020HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.978214HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2659SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes106HARMONIC2
X-RAY DIFFRACTIONt_gen_planes971HARMONIC5
X-RAY DIFFRACTIONt_it6020HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.13
X-RAY DIFFRACTIONt_other_torsion3.18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion822SEMIHARMONIC5
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_contact6972SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.246 130 4.79 %
Rwork0.216 2584 -
all0.217 2714 -
obs--82.73 %
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)
13.4674-0.8538-0.57011.8742-0.5121.0939-0.0473-0.24280.2591-0.00880.0117-0.08960.00070.06230.0357-0.2559-0.0214-0.0392-0.2318-0.02050.1474114.6504-74.20665.9264
24.1142-1.566-0.60462.85090.09021.8774-0.4839-1.2601-0.23590.61750.57840.31130.15460.5355-0.0944-0.39330.2710.05120.27110.1672-0.3425109.7739-88.178434.4947
312.4995-2.3005-3.55786.61140.18538.6577-0.0993-0.06420.1867-0.35350.1118-0.31150.08570.044-0.0125-0.41290.0408-0.034-0.33650.05060.157878.238-55.01684.2674
44.1985-0.995-3.44137.5969-0.37957.63220.0253-0.0181-0.4040.6468-0.07170.3650.0636-0.40270.0463-0.3997-0.16130.03050.0844-0.1066-0.2247142.7703-66.781641.3025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A| 39 - 333 }
2X-RAY DIFFRACTION2{ B| 44 - 332 }
3X-RAY DIFFRACTION3{ A| 1001 - 1106 }
4X-RAY DIFFRACTION4{ B| 1002 - 1101 }

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