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- PDB-6do1: Structure of nanobody-stabilized angiotensin II type 1 receptor b... -

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Basic information

Entry
Database: PDB / ID: 6do1
TitleStructure of nanobody-stabilized angiotensin II type 1 receptor bound to S1I8
Components
  • Angiotensin-like peptide S1I8
  • Nanobody Nb.AT110i1
  • Type-1 angiotensin II receptor,Soluble cytochrome b562 BRIL fusion protein
KeywordsMEMBRANE PROTEIN / nanobody / GPCR / synthetic antibody
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 / electron transport chain / calcium-mediated signaling / 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 / G protein-coupled receptor signaling pathway / protein heterodimerization activity / heme binding / membrane / plasma membrane
Similarity search - Function
Angiotensin II receptor type 1 / Angiotensin II receptor family / : / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. ...Angiotensin II receptor type 1 / Angiotensin II receptor family / : / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 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) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
(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 / Resolution: 2.901 Å
AuthorsWingler, L.M. / McMahon, C. / Staus, D.P. / Lefkowitz, R.J. / Kruse, A.C.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director5DP5OD021345 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL16037 United States
Other privateThe Vallee Foundation United States
Other privateThe Smith Family Foundation United States
Other privateMandel Center for Hypertension and Atherosclerosis United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2019
Title: Distinctive Activation Mechanism for Angiotensin Receptor Revealed by a Synthetic Nanobody.
Authors: Wingler, L.M. / McMahon, C. / Staus, D.P. / Lefkowitz, R.J. / Kruse, A.C.
History
DepositionJun 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 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

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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
B: Type-1 angiotensin II receptor,Soluble cytochrome b562 BRIL fusion protein
C: Nanobody Nb.AT110i1
D: Nanobody Nb.AT110i1
E: Nanobody Nb.AT110i1
F: Nanobody Nb.AT110i1
G: Angiotensin-like peptide S1I8
H: Angiotensin-like peptide S1I8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,22020
Polymers153,8188
Non-polymers2,40212
Water1,36976
1
A: Type-1 angiotensin II receptor,Soluble cytochrome b562 BRIL fusion protein
C: Nanobody Nb.AT110i1
E: Nanobody Nb.AT110i1
H: Angiotensin-like peptide S1I8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,95010
Polymers76,9094
Non-polymers1,0416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type-1 angiotensin II receptor,Soluble cytochrome b562 BRIL fusion protein
D: Nanobody Nb.AT110i1
F: Nanobody Nb.AT110i1
G: Angiotensin-like peptide S1I8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,27110
Polymers76,9094
Non-polymers1,3626
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.682, 227.796, 41.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Antibody / Protein/peptide / Sugars , 4 types, 10 molecules ABCDEFGH

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


Mass: 48514.918 Da / Num. of mol.: 2
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 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P30556, UniProt: P0ABE7
#2: Antibody
Nanobody Nb.AT110i1


Mass: 13711.979 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide Angiotensin-like peptide S1I8


Mass: 970.169 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / 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, 86 molecules

#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C21H40O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 8
Details: Protein was reconstituted with a 10:1 (w:w) mix of monoolein and cholesterol. Crystals were grown in cubic phase sandwich plates with using 100 mM Tris pH 8.0, 15-25 mM MgCl2, and 28-29% PEG 300

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.9→45.6 Å / Num. obs: 29111 / % possible obs: 98.5 % / Redundancy: 3.6 % / CC1/2: 0.962 / Rrim(I) all: 0.41 / Χ2: 0.96 / Net I/σ(I): 2.1
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.457 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4662 / CC1/2: 0.562 / Rrim(I) all: 1.697 / Χ2: 0.98 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
JBluIce-EPICSdata collection
Cootmodel building
PHASERphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YAY, 3P0G

4yay

3p0g


Resolution: 2.901→43.618 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 41.04 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflection
Rfree0.3593 1942 6.74 %
Rwork0.3045 --
obs0.3082 28820 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.901→43.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7744 0 110 76 7930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038032
X-RAY DIFFRACTIONf_angle_d0.91210919
X-RAY DIFFRACTIONf_dihedral_angle_d13.6814646
X-RAY DIFFRACTIONf_chiral_restr0.0441277
X-RAY DIFFRACTIONf_plane_restr0.0041339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9006-2.97310.38231230.36711935X-RAY DIFFRACTION98
2.9731-3.05350.38391300.36341889X-RAY DIFFRACTION98
3.0535-3.14330.40161330.34631885X-RAY DIFFRACTION98
3.1433-3.24480.39621410.33711925X-RAY DIFFRACTION99
3.2448-3.36070.3611440.33531891X-RAY DIFFRACTION98
3.3607-3.49520.38731350.31421926X-RAY DIFFRACTION98
3.4952-3.65420.35531300.30521909X-RAY DIFFRACTION99
3.6542-3.84670.38131370.28811934X-RAY DIFFRACTION98
3.8467-4.08760.31141490.28041922X-RAY DIFFRACTION98
4.0876-4.40290.31451560.25691896X-RAY DIFFRACTION98
4.4029-4.84550.36051290.25741922X-RAY DIFFRACTION97
4.8455-5.54540.36161470.29451943X-RAY DIFFRACTION97
5.5454-6.9820.34651520.33181946X-RAY DIFFRACTION95
6.982-43.62290.36941360.31921955X-RAY DIFFRACTION91

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