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- PDB-5unf: XFEL structure of human angiotensin II type 2 receptor (Monoclini... -

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Basic information

Entry
Database: PDB / ID: 5unf
TitleXFEL structure of human angiotensin II type 2 receptor (Monoclinic form) in complex with compound 1 (N-benzyl-N-(2-ethyl-4-oxo-3-{[2'-(2H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl])
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 / monoclinic 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 / electron transport chain / negative regulation of cell growth / 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 / 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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)94,2614
Polymers93,0132
Non-polymers1,2472
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-30 kcal/mol
Surface area37220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.390, 69.110, 90.070
Angle α, β, γ (deg.)90.00, 104.33, 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 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.: 2
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 / Plasmid: pFastBac / 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.: 2 / Source method: obtained synthetically / Formula: C36H29N7O2S
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: 2.51 Å3/Da / Density % sol: 50.98 %
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: 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→30 Å / Num. obs: 22934 / % possible obs: 100 % / Redundancy: 61.6 % / Biso Wilson estimate: 90.78 Å2 / Rmerge(I) obs: 0.164 / Net I/σ(I): 4.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 61.6 % / Rmerge(I) obs: 1.72 / Mean I/σ(I) obs: 0.8 / % possible all: 100
Serial crystallography measurementFocal spot size: 1.5 µm2 / Photons per pulse: 1011 Tphotons/pulse / Pulse duration: 40 fsec. / Pulse photon energy: 1.8 keV / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography data reductionCrystal hits: 175241 / Frames indexed: 22774 / Frames total: 2701530

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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: 2.8→29.57 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.9 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.359
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1118 4.88 %RANDOM
Rwork0.227 ---
obs0.228 22906 99.9 %-
Displacement parametersBiso mean: 111.9 Å2
Baniso -1Baniso -2Baniso -3
1-7.1036 Å20 Å2-1.5875 Å2
2---10.1802 Å20 Å2
3---3.0766 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: 1 / Resolution: 2.8→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6151 0 92 0 6243
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_angle_deg0.98739HARMONIC2.5
X-RAY DIFFRACTIONt_dihedral_angle_d2836SINUSOIDAL15
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes117HARMONIC2
X-RAY DIFFRACTIONt_gen_planes925HARMONIC5
X-RAY DIFFRACTIONt_it6414HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.54
X-RAY DIFFRACTIONt_other_torsion1.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion850SEMIHARMONIC5
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_contact7691SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.92 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.249 149 5.39 %
Rwork0.224 2613 -
all0.225 2762 -
obs--99.78 %
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)
14.82390.4122-3.73274.063-2.07036.34580.1144-0.2944-0.28360.2874-0.11440.2193-0.0306-0.06150-0.192-0.0324-0.03250.04450.0221-0.1112102.584519.775341.697
20.6346-1.3278-0.51262.2799-0.28022.8729-0.2198-0.662-0.23990.40530.32530.40660.21410.3926-0.1055-0.33720.10960.06090.3040.1849-0.270768.9021-1.949634.3486
39.2243-1.7595-1.66285.7082-1.11697.40660.0113-0.0034-0.0337-0.25320.0186-0.38550.0050.0802-0.0299-0.3009-0.0056-0.0345-0.2209-0.01270.067638.797630.94614.3458
42.2431-0.8457-0.39222.0458-0.28561.3565-0.0445-0.25170.15850.07370.1-0.12670.04730.0532-0.0555-0.2139-0.0067-0.0348-0.2136-0.01390.01975.027811.93596.0131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A| 1001 - 1100 }
2X-RAY DIFFRACTION2{ A| 43 - 334 }
3X-RAY DIFFRACTION3{ B| 1001 - 1110 }
4X-RAY DIFFRACTION4{ B| 35 - 334 }

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