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- PDB-4zud: Crystal Structure of Human Angiotensin Receptor in Complex with I... -

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Basic information

Entry
Database: PDB / ID: 4zud
TitleCrystal Structure of Human Angiotensin Receptor in Complex with Inverse Agonist Olmesartan at 2.8A resolution.
ComponentsChimera protein of Soluble cytochrome b562 and Type-1 angiotensin II receptor
KeywordsMEMBRANE PROTEIN / human Angiotensin Receptor AT1R / BRIL / G Protein-Coupled Receptor / GPCR / GPCR network / Lipidic Cubic Phase / LCP / structural genomics / olmesartan / angiotensin receptor blocker / anti-hypertensive drug / PSI-Biology / SIGNALING PROTEIN
Function / homology
Function and homology information


angiotensin type I receptor activity / positive regulation of phospholipase A2 activity / angiotensin type II receptor activity / phospholipase C-activating angiotensin-activated signaling pathway / regulation of renal sodium excretion / maintenance of blood vessel diameter homeostasis by renin-angiotensin / bradykinin receptor binding / renin-angiotensin regulation of aldosterone production / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of macrophage derived foam cell differentiation ...angiotensin type I receptor activity / positive regulation of phospholipase A2 activity / angiotensin type II receptor activity / phospholipase C-activating angiotensin-activated signaling pathway / regulation of renal sodium excretion / maintenance of blood vessel diameter homeostasis by renin-angiotensin / bradykinin receptor binding / renin-angiotensin regulation of aldosterone production / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of macrophage derived foam cell differentiation / C-C chemokine receptor activity / C-C chemokine binding / positive regulation of CoA-transferase activity / low-density lipoprotein particle remodeling / regulation of systemic arterial blood pressure by renin-angiotensin / Rho protein signal transduction / regulation of vasoconstriction / positive regulation of protein metabolic process / blood vessel diameter maintenance / Peptide ligand-binding receptors / neurogenesis / cell chemotaxis / kidney development / angiotensin-activated signaling pathway / regulation of cell growth / calcium-mediated signaling / electron transport chain / brain development / positive regulation of inflammatory response / positive regulation of reactive oxygen species metabolic process / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / phospholipase C-activating G protein-coupled receptor signaling pathway / regulation of cell population proliferation / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / G alpha (q) signalling events / periplasmic space / electron transfer activity / inflammatory response / symbiont entry into host cell / iron ion binding / immune response / G protein-coupled receptor signaling pathway / protein heterodimerization activity / external side of plasma membrane / heme binding / membrane / plasma membrane
Similarity search - Function
Angiotensin II receptor type 1 / Angiotensin II receptor family / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / 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
Olmesartan / Soluble cytochrome b562 / Type-1 angiotensin II receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhang, H. / Unal, H. / Desnoyer, R. / Han, G.W. / Patel, N. / Katritch, V. / Karnik, S.S. / Cherezov, V. / Stevens, R.C. / GPCR Network (GPCR)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM094618 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for Ligand Recognition and Functional Selectivity at Angiotensin Receptor.
Authors: Zhang, H. / Unal, H. / Desnoyer, R. / Han, G.W. / Patel, N. / Katritch, V. / Karnik, S.S. / Cherezov, V. / Stevens, R.C.
History
DepositionMay 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chimera protein of Soluble cytochrome b562 and Type-1 angiotensin II receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1692
Polymers46,7221
Non-polymers4471
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.200, 41.200, 251.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsAuthors state that the biological unit is unknown

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Components

#1: Protein Chimera protein of Soluble cytochrome b562 and Type-1 angiotensin II receptor / Cytochrome b-562 / AT1AR / AT1BR / Angiotensin II type-1 receptor / AT1 / AT1AR / AT1BR / ...Cytochrome b-562 / AT1AR / AT1BR / Angiotensin II type-1 receptor / AT1 / AT1AR / AT1BR / Angiotensin II type-1 receptor / AT1


Mass: 46722.043 Da / Num. of mol.: 1 / 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, AGTR1, AGTR1A, AGTR1B, AT2R1, AT2R1B / Plasmid: pFASTBAC / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P0ABE7, UniProt: P30556
#2: Chemical ChemComp-OLM / Olmesartan


Mass: 446.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26N6O3 / Comment: medication*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.54 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5
Details: 100 mM sodium citrate, pH 5.0, 400 mM KH2PO4, 25% (v/v) PEG400, and 6% (v/v) DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.575
11K, H, -L20.425
ReflectionResolution: 2.8→35.68 Å / Num. obs: 11028 / % possible obs: 94 % / Redundancy: 2.36 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.05
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 2.09 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 1.17 / % possible all: 85.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 4YAY

4yay


Resolution: 2.8→35.68 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.904 / SU B: 20.583 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 555 5 %RANDOM
Rwork0.19383 ---
obs0.19588 10472 93.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.956 Å2
Baniso -1Baniso -2Baniso -3
1-28.35 Å20 Å20 Å2
2--28.35 Å20 Å2
3----56.69 Å2
Refinement stepCycle: LAST / Resolution: 2.8→35.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2918 0 33 0 2951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023021
X-RAY DIFFRACTIONr_bond_other_d0.0020.022941
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.9774123
X-RAY DIFFRACTIONr_angle_other_deg0.9593.0026718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9095372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19324.123114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16515483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.716159
X-RAY DIFFRACTIONr_chiral_restr0.0590.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213342
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02687
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5257.6151500
X-RAY DIFFRACTIONr_mcbond_other1.5257.6161499
X-RAY DIFFRACTIONr_mcangle_it2.65811.4161868
X-RAY DIFFRACTIONr_mcangle_other2.65711.4151869
X-RAY DIFFRACTIONr_scbond_it1.0877.5691521
X-RAY DIFFRACTIONr_scbond_other1.0877.5691522
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.89511.3332256
X-RAY DIFFRACTIONr_long_range_B_refined4.43161.0623512
X-RAY DIFFRACTIONr_long_range_B_other4.4361.0653513
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 32 -
Rwork0.214 699 -
obs--85 %
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)
10.0882-0.24080.322.3768-1.17851.3014-0.04160.0249-0.00360.0387-0.0445-0.1056-0.13490.03660.08610.03220.0020.01220.10810.01470.1438-23.160872.68781.7663
20.58990.0982-0.01890.05010.13411.33070.0267-0.09720.0322-0.0021-0.0328-0.01510.12260.10410.00610.03910.01570.03720.1011-0.03740.1645-40.615263.657136.7014
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A | 1002 - 1106 }A1002 - 1106
2X-RAY DIFFRACTION2{ A | 12 - 304 }A12 - 304

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