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- PDB-6rnk: Crystal structure of a humanized (K18E, K269N) rat succinate rece... -

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Basic information

Entry
Database: PDB / ID: 6rnk
TitleCrystal structure of a humanized (K18E, K269N) rat succinate receptor SUCNR1 (GPR91) in complex with a nanobody and antagonist NF-56-EJ40.
Components
  • Nanobody6
  • Succinate receptor 1
KeywordsMEMBRANE PROTEIN / SUCNR1 / GPR91 / GPCR / G-Protein coupled receptor / Nanobody / Antagonist / 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 / positive regulation of inflammatory response / response to calcium ion / 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 / positive regulation of inflammatory response / response to calcium ion / 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
Chem-KAZ / (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 / Resolution: 1.94 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
DepositionMay 8, 2019Deposition 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 / citation_author
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 / refine / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _software.name

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,62118
Polymers55,3552
Non-polymers5,26716
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-11 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.830, 150.930, 68.230
Angle α, β, γ (deg.)90.000, 112.420, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-416-

SO4

21B-209-

HOH

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Components

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Protein / Antibody , 2 types, 2 molecules AB

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


Mass: 39827.676 Da / Num. of mol.: 1 / Mutation: K18E, K269N
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.: 1
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, 258 molecules

#3: Chemical ChemComp-KAZ / 2-[2-[[3-[4-[(4-methylpiperazin-1-yl)methyl]phenyl]phenyl]carbonylamino]phenyl]ethanoic acid


Mass: 443.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29N3O3
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 3.36 Å3/Da / Density % sol: 63.5 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 7
Details: 50 mM ADA, pH 7.0, 28% PEG MME 550, 0.55 M (NH4)2SO4, 100-400 microM compound 3, 1-4 % (v/v) DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.43→75.47 Å / Num. obs: 88565 / % possible obs: 67 % / Redundancy: 6.5 % / Biso Wilson estimate: 34.46 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.213 / Rpim(I) all: 0.091 / Rrim(I) all: 0.232 / Net I/σ(I): 4.8 / Num. measured all: 575822 / Scaling rejects: 8
Reflection shellResolution: 1.43→1.51 Å / Redundancy: 3.4 % / Rmerge(I) obs: 8.756 / Num. measured all: 5597 / Num. unique obs: 1652 / Rpim(I) all: 5.465 / Rrim(I) all: 10.378 / Net I/σ(I) obs: 0.2 / % possible all: 8.6

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Processing

Software
NameVersionClassification
BUSTERrefinement
XDSBUILT 20190315data reduction
autoPROC20190301data scaling
PHASER2.8.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IBB

6ibb


Resolution: 1.94→75.47 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.144 / SU Rfree Blow DPI: 0.128 / SU Rfree Cruickshank DPI: 0.129
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1980 4.88 %RANDOM
Rwork0.177 ---
obs0.178 40585 76.6 %-
Displacement parametersBiso max: 154.62 Å2 / Biso mean: 45.42 Å2 / Biso min: 21.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.1815 Å20 Å23.5761 Å2
2---1.6138 Å20 Å2
3---1.4323 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 1.94→75.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3281 0 286 242 3809
Biso mean--69.52 61.94 -
Num. residues----414
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1309SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes572HARMONIC5
X-RAY DIFFRACTIONt_it3638HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion449SEMIHARMONIC5
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_contact4359SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3638HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4869HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion16.97
LS refinement shellResolution: 1.94→2.03 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2212 39 4.8 %
Rwork0.205 773 -
all0.2058 812 -
obs--11.92 %
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)
10.6328-0.2005-0.1682.35970.35120.7668-0.00280.06170.044-0.26740.0041-0.0691-0.02660.0444-0.0013-0.0367-0.00320.0481-0.04620.0033-0.0452-3.197423.230918.53
22.44040.1628-0.39265.83521.71612.232-0.02090.05480.0519-0.43020.0823-0.2496-0.14510.0769-0.0613-0.0481-0.05920.0561-0.15270.0341-0.02482.606963.833525.0224
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A7 - 305
2X-RAY DIFFRACTION2{ B|* }B9 - 137

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