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- PDB-4yay: XFEL structure of human Angiotensin Receptor -

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Basic information

Entry
Database: PDB / ID: 4yay
TitleXFEL structure of human Angiotensin Receptor
ComponentsSoluble cytochrome b562,Type-1 angiotensin II receptor
KeywordsMEMBRANE PROTEIN / XFEL / Serial Femtosecond Crystallography / human Angiotensin Receptor AT1R / BRIL / G Protein-Coupled Receptor / GPCR / GPCR network / Lipidic Cubic Phase / LCP / structural genomics / ZD7155 / angiotensin receptor blocker / room temperature / PSI-Biology
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 / 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 / cell chemotaxis / kidney development / angiotensin-activated signaling pathway / regulation of cell growth / calcium-mediated signaling / electron transport chain / positive regulation of inflammatory response / positive regulation of reactive oxygen species metabolic process / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / regulation of cell population proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / regulation of inflammatory response / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / periplasmic space / electron transfer activity / inflammatory response / iron ion binding / symbiont entry into host cell / protein heterodimerization activity / G protein-coupled receptor signaling pathway / 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 ...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
Chem-ZD7 / Soluble cytochrome b562 / Type-1 angiotensin II receptor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZhang, H. / Unal, H. / Gati, C. / Han, G.W. / Zatsepin, N.A. / James, D. / Wang, D. / Nelson, G. / Weierstall, U. / Messerschmidt, M. ...Zhang, H. / Unal, H. / Gati, C. / Han, G.W. / Zatsepin, N.A. / James, D. / Wang, D. / Nelson, G. / Weierstall, U. / Messerschmidt, M. / Williams, G.J. / Boutet, S. / Yefanov, O.M. / White, T.A. / Liu, W. / Ishchenko, A. / Tirupula, K.C. / Desnoyer, R. / Sawaya, M.C. / Xu, Q. / Coe, J. / Cornrad, C.E. / Fromme, P. / Stevens, R.C. / Katritch, V. / Karnik, S.S. / Cherezov, V. / 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: Cell / Year: 2015
Title: Structure of the Angiotensin receptor revealed by serial femtosecond crystallography.
Authors: Zhang, H. / Unal, H. / Gati, C. / Han, G.W. / Liu, W. / Zatsepin, N.A. / James, D. / Wang, D. / Nelson, G. / Weierstall, U. / Sawaya, M.R. / Xu, Q. / Messerschmidt, M. / Williams, G.J. / ...Authors: Zhang, H. / Unal, H. / Gati, C. / Han, G.W. / Liu, W. / Zatsepin, N.A. / James, D. / Wang, D. / Nelson, G. / Weierstall, U. / Sawaya, M.R. / Xu, Q. / Messerschmidt, M. / Williams, G.J. / Boutet, S. / Yefanov, O.M. / White, T.A. / Wang, C. / Ishchenko, A. / Tirupula, K.C. / Desnoyer, R. / Coe, J. / Conrad, C.E. / Fromme, P. / Stevens, R.C. / Katritch, V. / Karnik, S.S. / Cherezov, V.
History
DepositionFeb 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Structure summary
Revision 1.2May 13, 2015Group: Database references
Revision 1.3May 27, 2015Group: Database references
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Nov 22, 2017Group: Refinement description / Category: software
Revision 1.6Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.7Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.8Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.9Oct 23, 2024Group: Refinement description / Structure summary
Category: pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Soluble cytochrome b562,Type-1 angiotensin II receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6792
Polymers47,2411
Non-polymers4391
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.800, 41.000, 167.700
Angle α, β, γ (deg.)90.00, 99.40, 90.00
Int Tables number5
Space group name H-MC121
DetailsAuthors state that the biological unit is unknown

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Components

#1: Protein Soluble cytochrome b562,Type-1 angiotensin II receptor / Cytochrome b-562 / AT1AR / AT1BR / Angiotensin II type-1 receptor / AT1


Mass: 47240.707 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-ZD7 / 5,7-diethyl-1-{[2'-(1H-tetrazol-5-yl)biphenyl-4-yl]methyl}-3,4-dihydro-1,6-naphthyridin-2(1H)-one


Mass: 438.524 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H26N6O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 457275

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 294 K / Method: lipidic cubic phase / pH: 5
Details: 100 mM sodium citrate, pH 5.0, 450 mM NH4H2PO4, 28% (v/v) PEG400 and 4% (v/v) DMSO

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.56 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Feb 1, 2014
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.56 Å / Relative weight: 1
ReflectionResolution: 2.9→32.629 Å / Num. obs: 11190 / % possible obs: 100 % / Redundancy: 1288 % / Biso Wilson estimate: 76.13 Å2 / Net I/σ(I): 8.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 215 % / Mean I/σ(I) obs: 0.84 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
PHASERphasing
CrystFELdata scaling
CrystFELdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GPCR hybrid model

Resolution: 2.9→32.91 Å / Cor.coef. Fo:Fc: 0.9017 / Cor.coef. Fo:Fc free: 0.8509 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.406
RfactorNum. reflection% reflectionSelection details
Rfree0.2742 576 5.16 %RANDOM
Rwork0.2283 ---
obs0.2306 11167 99.99 %-
Displacement parametersBiso mean: 95.45 Å2
Baniso -1Baniso -2Baniso -3
1--11.8521 Å20 Å2-6.6407 Å2
2---4.0788 Å20 Å2
3---15.9309 Å2
Refine analyzeLuzzati coordinate error obs: 0.612 Å
Refinement stepCycle: LAST / Resolution: 2.9→32.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3077 0 33 0 3110
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013187HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.954336HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1448SINUSOIDAL4
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes54HARMONIC2
X-RAY DIFFRACTIONt_gen_planes460HARMONIC5
X-RAY DIFFRACTIONt_it3187HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.99
X-RAY DIFFRACTIONt_other_torsion2.46
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion436SEMIHARMONIC5
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_contact3683SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.18 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3131 150 5.66 %
Rwork0.2539 2500 -
all0.2573 2650 -
obs--99.99 %
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)
10.3611-1.357-0.45471.13732.72544.5097-0.0370.2550.20960.1181-0.0836-0.1595-0.04810.230.12060.2884-0.02560.03010.1755-0.0776-0.31022.94997.994814.071
21.0532-0.7640.40850.7978-0.48.24750.0292-0.12430.0783-0.49310.1735-0.35380.027-0.1706-0.20260.2481-0.12550.1705-0.304-0.0425-0.2207-15.38511.08252.2432
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1002-1106 }
2X-RAY DIFFRACTION2{ A| 12- 317 }

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