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- PDB-6ibb: Crystal structure of the rat isoform of the succinate receptor SU... -

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Basic information

Entry
Database: PDB / ID: 6ibb
TitleCrystal structure of the rat isoform of the succinate receptor SUCNR1 (GPR91) in complex with a nanobody
Components
  • Nanobody6
  • Succinate receptor 1
KeywordsMEMBRANE PROTEIN / SUCNR1 GPR91 GPCR G-Protein coupled receptor Nanobody Succinate Complex
Function / homology
Function and homology information


Class A/1 (Rhodopsin-like receptors) / regulation of angiotensin metabolic process / renin secretion into blood stream / positive regulation of chemotaxis / macrophage activation involved in immune response / G alpha (i) signalling events / G protein-coupled receptor activity / response to calcium ion / positive regulation of inflammatory response / glucose homeostasis ...Class A/1 (Rhodopsin-like receptors) / regulation of angiotensin metabolic process / renin secretion into blood stream / positive regulation of chemotaxis / macrophage activation involved in immune response / G alpha (i) signalling events / G protein-coupled receptor activity / response to calcium ion / positive regulation of inflammatory response / glucose homeostasis / signaling receptor activity / G protein-coupled receptor signaling pathway / plasma membrane
Similarity search - Function
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
CHOLESTEROL / (2~{S},5~{R})-hexane-2,5-diol / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Succinate receptor 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.12 Å
AuthorsHaffke, M. / Jaakola, V.-P.
CitationJournal: Nature / Year: 2019
Title: Structural basis of species-selective antagonist binding to the succinate receptor.
Authors: Haffke, M. / Fehlmann, D. / Rummel, G. / Boivineau, J. / Duckely, M. / Gommermann, N. / Cotesta, S. / Sirockin, F. / Freuler, F. / Littlewood-Evans, A. / Kaupmann, K. / Jaakola, V.P.
History
DepositionNov 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 6, 2019Group: Data collection / 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
Revision 1.3Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Succinate receptor 1
B: Nanobody6
C: Succinate receptor 1
D: Nanobody6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,77723
Polymers110,7404
Non-polymers6,03719
Water5,386299
1
A: Succinate receptor 1
B: Nanobody6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,43312
Polymers55,3702
Non-polymers3,06310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Succinate receptor 1
D: Nanobody6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,34411
Polymers55,3702
Non-polymers2,9759
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.220, 164.000, 63.420
Angle α, β, γ (deg.)90.00, 102.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Antibody , 2 types, 4 molecules ACBD

#1: Protein Succinate receptor 1 / G-protein coupled receptor 91


Mass: 39842.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Sucnr1, Gpr91 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6IYF9
#2: Antibody Nanobody6


Mass: 15527.099 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Spodoptera frugiperda (fall armyworm)

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Non-polymers , 5 types, 318 molecules

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


Mass: 356.540 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-H95 / (2~{S},5~{R})-hexane-2,5-diol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#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.: 299 / 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: 3.07 Å3/Da / Density % sol: 59.95 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: 0.1M Na-Citrate 24-30% PEG400 0.05M NaSCN 2.5% 2,5-Hexanediol 1% DMSO
PH range: 4.8-5.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.42→41.55 Å / Num. obs: 198484 / % possible obs: 88.2 % / Redundancy: 17.88 % / Biso Wilson estimate: 44.21 Å2 / Rmerge(I) obs: 0.763 / Net I/σ(I): 2.92
Reflection shellResolution: 1.42→1.46 Å / Redundancy: 1.59 % / Rmerge(I) obs: 2.119 / Mean I/σ(I) obs: 0.32 / % possible all: 20.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XSCALEBUILT 20160617data scaling
PHASER2.8.0phasing
PDB_EXTRACT3.24data extraction
XDSBUILT 20160617data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XNV

4xnv


Resolution: 2.12→41.55 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.331 / SU Rfree Blow DPI: 0.221 / SU Rfree Cruickshank DPI: 0.227
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1950 4.73 %RANDOM
Rwork0.178 ---
obs0.18 41256 61 %-
Displacement parametersBiso mean: 56.4 Å2
Baniso -1Baniso -2Baniso -3
1-11.4567 Å20 Å22.4984 Å2
2---10.1644 Å20 Å2
3----1.2923 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.12→41.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6643 0 374 299 7316
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017186HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.089677HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2506SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1133HARMONIC5
X-RAY DIFFRACTIONt_it7186HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion19.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion907SEMIHARMONIC5
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_contact8266SEMIHARMONIC4
LS refinement shellResolution: 2.12→2.27 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2466 -4.72 %
Rwork0.2309 787 -
all0.2316 826 -
obs--6.86 %
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)
11.20010.87910.12613.04820.59491.4525-0.0057-0.06550.0260.11220.0035-0.10650.08850.0140.0023-0.07820.01260.0226-0.226-0.0078-0.125776.271210.070830.8709
22.1869-0.66670.40287.84713.52643.8511-0.13650.17640.1376-0.48690.0865-0.2175-0.4940.13180.04990.0834-0.11960.0069-0.34550.0701-0.118587.288749.590634.9085
30.91070.36830.16014.8875-0.03123.043-0.04190.02150.1142-0.35920.1250.2289-0.5902-0.1688-0.08320.01340.00070.0882-0.32120.0146-0.251570.3636.2272-2.1961
43.3629-0.59071.263210.3437-1.61514.76780.12990.237-0.4591-0.39320.23440.76491.022-0.4381-0.36440.2545-0.1837-0.088-0.3994-0.075-0.190165.3738-33.5554-1.2745
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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