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- PDB-7br3: Crystal structure of the protein 1 -

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Basic information

Entry
Database: PDB / ID: 7br3
TitleCrystal structure of the protein 1
ComponentsGonadotropin-releasing hormone receptor,GlgA glycogen synthase,Gonadotropin-releasing hormone receptor
KeywordsSIGNALING PROTEIN / GPCR / helix / transmembrane
Function / homology
Function and homology information


gonadotropin-releasing hormone receptor activity / Hormone ligand-binding receptors / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / multicellular organism development / glycogen biosynthetic process / plasma membrane => GO:0005886 / G protein-coupled receptor activity / peptide binding / G alpha (q) signalling events / G protein-coupled receptor signaling pathway ...gonadotropin-releasing hormone receptor activity / Hormone ligand-binding receptors / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / multicellular organism development / glycogen biosynthetic process / plasma membrane => GO:0005886 / G protein-coupled receptor activity / peptide binding / G alpha (q) signalling events / G protein-coupled receptor signaling pathway / membrane / plasma membrane / cytosol
Similarity search - Function
Gonadotrophin-releasing hormone receptor family / Glycosyl transferases group 1 / Bacterial/plant glycogen synthase / Starch synthase, catalytic domain / Starch synthase catalytic domain / Glycosyl transferases group 1 / 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
(2R)-2,3-dihydroxypropyl dodecanoate / Chem-F5O / FORMIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / Gonadotropin-releasing hormone receptor / Glycogen synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Pyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsCheng, L. / Shao, Z.
CitationJournal: Nat Commun / Year: 2020
Title: Structure of the human gonadotropin-releasing hormone receptor GnRH1R reveals an unusual ligand binding mode.
Authors: Yan, W. / Cheng, L. / Wang, W. / Wu, C. / Yang, X. / Du, X. / Ma, L. / Qi, S. / Wei, Y. / Lu, Z. / Yang, S. / Shao, Z.
History
DepositionMar 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gonadotropin-releasing hormone receptor,GlgA glycogen synthase,Gonadotropin-releasing hormone receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,58512
Polymers60,2831
Non-polymers2,30211
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-0 kcal/mol
Surface area21880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.964, 73.964, 231.156
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Gonadotropin-releasing hormone receptor,GlgA glycogen synthase,Gonadotropin-releasing hormone receptor / GnRH-R / Glycogen synthase / GnRH-R


Mass: 60283.402 Da / Num. of mol.: 1 / Mutation: P128K
Source method: isolated from a genetically manipulated source
Details: The fusion protein of Gonadotropin-releasing hormone receptor (UNP residues 1-242), GlgA glycogen synthase (UNP residues 218-413), Gonadotropin-releasing hormone receptor (UNP residues 257-328)
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea)
Gene: GNRHR, GRHR, PAB2292 / Strain: GE5 / Orsay / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P30968, UniProt: Q9V2J8

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Non-polymers , 5 types, 11 molecules

#2: Chemical ChemComp-1QW / (2R)-2,3-dihydroxypropyl dodecanoate / 1-Lauroyl-rac-glycerol


Mass: 274.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H30O4
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-F5O / 4-[[(1R)-2-[5-(2-fluoranyl-3-methoxy-phenyl)-3-[[2-fluoranyl-6-(trifluoromethyl)phenyl]methyl]-4-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]-1-phenyl-ethyl]amino]butanoic acid


Mass: 631.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H30F5N3O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antagonist, hormone*YM

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Details

Has ligand of interestY

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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: 3.1 Å3/Da / Density % sol: 60.31 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: 100 mM Na cacodyalte pH 6.0-6.5, 30%-38% PEG400, 150-350 mM NH4NO3
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 17136 / % possible obs: 89.9 % / Redundancy: 3.6 % / CC1/2: 0.992 / CC star: 0.998 / Net I/σ(I): 6.5
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 3.5 % / Num. unique obs: 878 / CC1/2: 0.53 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S0V

4s0v


Resolution: 2.79→31.15 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.98
RfactorNum. reflection% reflection
Rfree0.284 1319 9.96 %
Rwork0.243 11930 -
obs0.247 13249 69.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.45 Å2 / Biso mean: 51.29 Å2 / Biso min: 33.3 Å2
Refinement stepCycle: final / Resolution: 2.79→31.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3638 0 132 0 3770
Biso mean--46.99 --
Num. residues----470
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.79-2.89830.3978490.348440222
2.8983-3.03010.3584790.297663234
3.0301-3.18970.3416880.32296450
3.1897-3.38930.32811420.2864139273
3.3893-3.65060.28771790.2682166488
3.6506-4.01730.29472210.2386167790
4.0173-4.5970.25152010.2206162385
4.597-5.78570.27761870.2219177991
5.7857-31.150.26111730.2265179786
Refinement TLS params.Method: refined / Origin x: -36.9156 Å / Origin y: 16.2136 Å / Origin z: 16.1147 Å
111213212223313233
T0.4181 Å2-0.0931 Å2-0.0395 Å2-0.3337 Å2-0.0818 Å2--0.275 Å2
L1.3993 °20.2362 °2-1.2769 °2-0.3844 °2-0.4053 °2--2.4101 °2
S-0.0848 Å °-0.0748 Å °-0.0738 Å °-0.063 Å °-0.1263 Å °0.0726 Å °0.0457 Å °-0.1724 Å °0.2091 Å °
Refinement TLS groupSelection details: ALL

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