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- PDB-6os2: Structure of synthetic nanobody-stabilized angiotensin II type 1 ... -

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Basic information

Entry
Database: PDB / ID: 6os2
TitleStructure of synthetic nanobody-stabilized angiotensin II type 1 receptor bound to TRV026
Components
  • Nanobody Nb.AT110i1_le
  • TRV026 peptide
  • Type-1 angiotensin II receptor,Soluble cytochrome b562 BRIL fusion protein
KeywordsMEMBRANE PROTEIN / GPCR
Function / homology
Function and homology information


angiotensin type I receptor 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 cholesterol metabolic process / low-density lipoprotein particle remodeling ...angiotensin type I receptor 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 cholesterol metabolic process / low-density lipoprotein particle remodeling / positive regulation of macrophage derived foam cell differentiation / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of vasoconstriction / Rho protein signal transduction / Peptide ligand-binding receptors / blood vessel diameter maintenance / angiotensin-activated signaling pathway / cell chemotaxis / kidney development / regulation of cell growth / calcium-mediated signaling / electron transport chain / positive regulation of reactive oxygen species metabolic process / positive regulation of inflammatory response / Cargo recognition for clathrin-mediated endocytosis / regulation of cell population proliferation / Clathrin-mediated endocytosis / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / periplasmic space / electron transfer activity / G protein-coupled receptor signaling pathway / iron ion binding / inflammatory response / protein heterodimerization activity / heme binding / symbiont entry into host cell / membrane / plasma membrane
Similarity search - Function
Angiotensin II receptor type 1 / Angiotensin II receptor family / Cytochrome c/b562 / : / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / Four Helix Bundle (Hemerythrin (Met), subunit A) / G-protein coupled receptors family 1 signature. ...Angiotensin II receptor type 1 / Angiotensin II receptor family / Cytochrome c/b562 / : / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / 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
CHOLESTEROL / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Soluble cytochrome b562 / Type-1 angiotensin II receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsWingler, L.M. / Staus, D.P. / Skiba, M.A. / McMahon, C. / Kleinhenz, A.L.W. / Lefkowitz, R.J. / Kruse, A.C.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL16037 United States
National Institutes of Health/Office of the Director5DP5OD021345 United States
Other private United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2020
Title: Angiotensin and biased analogs induce structurally distinct active conformations within a GPCR.
Authors: Wingler, L.M. / Skiba, M.A. / McMahon, C. / Staus, D.P. / Kleinhenz, A.L.W. / Suomivuori, C.M. / Latorraca, N.R. / Dror, R.O. / Lefkowitz, R.J. / Kruse, A.C.
History
DepositionMay 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type-1 angiotensin II receptor,Soluble cytochrome b562 BRIL fusion protein
D: Nanobody Nb.AT110i1_le
B: TRV026 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,96311
Polymers63,2163
Non-polymers2,7478
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-24 kcal/mol
Surface area23950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.960, 101.350, 225.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein / Antibody / Protein/peptide / Sugars , 4 types, 4 molecules ADB

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


Mass: 48514.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: AGTR1, AGTR1A, AGTR1B, AT2R1, AT2R1B, cybC / Plasmid: pcDNA-Zeo-tetO / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P30556, UniProt: P0ABE7
#2: Antibody Nanobody Nb.AT110i1_le


Mass: 13796.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#3: Protein/peptide TRV026 peptide


Mass: 905.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 28 molecules

#5: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8
Details: Protein complex was reconstituted with a 10:1 (w/w) mixture of monoolein and cholesterol. Crystals were grown in 100 mM Tris pH 8, 65 mM MgCl2, 26-28% PEG 300, 4.5% 1,3-butanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2018
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.7→46.91 Å / Num. obs: 19466 / % possible obs: 99.7 % / Redundancy: 7.433 % / Biso Wilson estimate: 70.546 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.202 / Rrim(I) all: 0.217 / Χ2: 0.989 / Net I/σ(I): 6.87 / Num. measured all: 144683 / Scaling rejects: 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.776.9132.0530.669609142213900.4532.21497.7
2.77-2.847.7481.590.9610731138513850.6071.701100
2.84-2.927.7831.4941.0610289132213220.6311.598100
2.92-3.017.7391.151.4210309133213320.7471.23100
3.01-3.117.7531.031.79761126012590.7241.10299.9
3.11-3.227.5230.8162.179186122112210.7910.875100
3.22-3.347.0710.6462.758563121112110.8830.696100
3.34-3.487.5650.5423.578662114611450.8950.58199.9
3.48-3.647.2860.3824.927891108410830.9510.41199.9
3.64-3.817.7140.2826.598208106410640.9830.302100
3.81-4.027.6020.2138.727632100410040.9840.228100
4.02-4.267.5470.16610.7172009559540.9910.17899.9
4.26-4.567.3660.1313.1766669059050.9910.14100
4.56-4.927.0920.10215.2860008478460.9960.1199.9
4.92-5.397.1780.11214.0554987687660.9950.1299.7
5.39-6.037.5220.13313.1553787157150.9930.142100
6.03-6.967.510.11814.8447096276270.9940.127100
6.96-8.537.1420.07221.3339355535510.9960.07899.6
8.53-12.066.5410.04926.5128194314310.9970.053100
12.06-46.916.420.04427.9516372632550.9990.04897

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DO1

6do1


Resolution: 2.7→46.91 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.72
RfactorNum. reflection% reflection
Rfree0.2852 1811 9.32 %
Rwork0.2327 --
obs0.2376 19379 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 209.26 Å2 / Biso mean: 83.797 Å2 / Biso min: 24.26 Å2
Refinement stepCycle: final / Resolution: 2.7→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3939 0 109 21 4069
Biso mean--91.49 60.29 -
Num. residues----514
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.770.3981340.35941303143798
2.77-2.850.32651370.321113331470100
2.85-2.940.36131380.318813421480100
2.94-3.050.36351360.321513281464100
3.05-3.170.39521390.308313541493100
3.17-3.310.34941360.288113251461100
3.31-3.490.31011390.263913541493100
3.49-3.710.32921380.239213451483100
3.71-3.990.28491400.2313581498100
3.99-4.390.25651400.198713601500100
4.39-5.030.25061400.186813671507100
5.03-6.330.271440.234913881532100
6.34-46.910.24281500.198814641614100
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)
11.5758-0.0940.00521.57020.04343.08590.05210.26490.2287-0.0502-0.0935-0.083-0.24750.05440.10660.45590.04090.03070.66550.00640.4304-19.7611-11.4328-57.6442
21.81120.2144-0.75272.251-1.37053.91270.0268-0.1145-0.2150.6101-0.2586-0.4933-0.54020.90180.25870.5902-0.1296-0.1090.7841-0.01070.4602-5.864-9.9476-43.029
31.1763-0.074-0.31492.4638-1.89084.0576-0.18840.019-0.1216-0.2735-0.0382-0.16720.7554-0.46790.21650.5112-0.0664-0.00730.7283-0.08920.4414-11.99-30.0708-44.5482
45.7983-1.95110.70471.21221.35448.91720.08750.29570.28291.0428-0.9346-0.38782.77662.32330.76771.56610.2702-0.20831.58250.17141.0058-7.4322-50.6531-12.5445
54.56220.4381-0.68644.4203-3.53414.0568-0.1195-0.7452-0.83581.00910.4183-0.69461.6123-1.28960.25881.7378-0.2721-0.10981.24280.18190.8648-18.7114-44.1604-13.5037
62.2305-0.8106-0.86752.0257-0.45753.2457-0.1861-0.21510.06010.12920.1410.070.42330.15590.05740.4308-0.0401-0.01840.7367-0.00920.3965-19.3037-22.3053-54.8352
74.65463.43975.7856.53914.90558.1270.2666-1.38210.47510.5063-0.48830.35040.277-0.69890.18990.85880.01830.01911.0084-0.06060.5046-8.2071-13.0808-12.8766
85.7741.47575.47815.20182.12646.92660.1809-0.0872-0.3911-0.1861-0.0861-0.20940.06940.2141-0.19530.66670.02610.03580.8821-0.00910.4557-2.041-17.6485-13.0713
94.38454.29325.57915.59965.57596.649-0.3284-0.15350.5150.604-0.24880.4823-0.8038-0.77831.02480.77240.0485-0.09170.924-0.02350.4655-13.4662-14.4527-22.2471
103.43973.8387-3.61364.7366-4.77245.0049-0.70540.5359-0.8766-0.39451.14430.1151.71150.8365-0.42540.52140.0907-0.08910.8774-0.08950.3927-14.5863-16.6015-72.7843
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 131 )A11 - 131
2X-RAY DIFFRACTION2chain 'A' and (resid 132 through 165 )A132 - 165
3X-RAY DIFFRACTION3chain 'A' and (resid 166 through 266 )A166 - 266
4X-RAY DIFFRACTION4chain 'A' and (resid 267 through 305 )A267 - 305
5X-RAY DIFFRACTION5chain 'A' and (resid 306 through 1237 )A306 - 1237
6X-RAY DIFFRACTION6chain 'A' and (resid 1238 through 1318 )A0
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 44 )D1 - 44
8X-RAY DIFFRACTION8chain 'D' and (resid 45 through 98 )D45 - 98
9X-RAY DIFFRACTION9chain 'D' and (resid 99 through 126 )D99 - 126
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 7 )B2 - 7

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