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- PDB-5ung: XFEL structure of human angiotensin II type 2 receptor (Orthorhom... -

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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-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-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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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.: 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

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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: 2.78 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

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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→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

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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→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 }

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