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- PDB-6fgc: Crystal structure of Gephyrin E domain in complex with Artesunate -

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Basic information

Entry
Database: PDB / ID: 6fgc
TitleCrystal structure of Gephyrin E domain in complex with Artesunate
ComponentsGephyrin
KeywordsSTRUCTURAL PROTEIN / Antimalarial compound / artemisinins and its derivatives / Inhibitory neurotransmission / Moco biosynthesis
Function / homology
Function and homology information


Molybdenum cofactor biosynthesis / glycine receptor clustering / molybdopterin cofactor biosynthetic process / establishment of synaptic specificity at neuromuscular junction / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / gamma-aminobutyric acid receptor clustering / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / postsynaptic specialization ...Molybdenum cofactor biosynthesis / glycine receptor clustering / molybdopterin cofactor biosynthetic process / establishment of synaptic specificity at neuromuscular junction / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / gamma-aminobutyric acid receptor clustering / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / postsynaptic specialization / nitrate reductase activity / inhibitory synapse / Mo-molybdopterin cofactor biosynthetic process / glycinergic synapse / postsynaptic neurotransmitter receptor diffusion trapping / postsynaptic specialization membrane / response to metal ion / molybdopterin cofactor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic specialization, intracellular component / GABA-ergic synapse / protein targeting / synapse assembly / tubulin binding / synaptic membrane / establishment of protein localization / cytoplasmic side of plasma membrane / protein-macromolecule adaptor activity / postsynaptic membrane / postsynapse / postsynaptic density / molecular adaptor activity / cytoskeleton / signaling receptor binding / dendrite / neuronal cell body / ATP binding / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Molybdopterin biosynthesis moeA protein; domain 3 / Molybdopterin biosynthesis moea protein, domain 3. / Beta-clip / MoeA, C-terminal, domain IV / Molybdenum cofactor biosynthesis proteins signature 2. / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis proteins signature 1. / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily ...Molybdopterin biosynthesis moeA protein; domain 3 / Molybdopterin biosynthesis moea protein, domain 3. / Beta-clip / MoeA, C-terminal, domain IV / Molybdenum cofactor biosynthesis proteins signature 2. / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis proteins signature 1. / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily / Molybdopterin biosynthesis protein MoeA-like / MoeA N-terminal region (domain I and II) / MoeA C-terminal region (domain IV) / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis, conserved site / MoaB/Mog-like domain / Molybdenum Cofactor Biosythetic Enzyme; Chain A / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain / Beta Complex / Alpha-Beta Complex / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / Artesunate / PHOSPHATE ION / Gephyrin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKasaragod, V.B. / Schindelin, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSchi425/8-1 Germany
CitationJournal: Neuron / Year: 2019
Title: Elucidating the Molecular Basis for Inhibitory Neurotransmission Regulation by Artemisinins.
Authors: Kasaragod, V.B. / Hausrat, T.J. / Schaefer, N. / Kuhn, M. / Christensen, N.R. / Tessmer, I. / Maric, H.M. / Madsen, K.L. / Sotriffer, C. / Villmann, C. / Kneussel, M. / Schindelin, H.
History
DepositionJan 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 6, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gephyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,46118
Polymers45,6521
Non-polymers1,80917
Water7,062392
1
A: Gephyrin
hetero molecules

A: Gephyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,92336
Polymers91,3052
Non-polymers3,61834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area13200 Å2
ΔGint-149 kcal/mol
Surface area34280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.100, 99.220, 113.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1055-

HOH

21A-1226-

HOH

31A-1290-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Gephyrin / / Putative glycine receptor-tubulin linker protein


Mass: 45652.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gphn, Gph / Production host: Escherichia coli (E. coli)
References: UniProt: Q03555, molybdopterin adenylyltransferase, molybdopterin molybdotransferase

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Non-polymers , 9 types, 409 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-D95 / Artesunate / Artesunate


Mass: 384.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28O8 / Comment: medication*YM
#9: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M sodium acetate 20-36 % MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.5→43.55 Å / Num. obs: 78437 / % possible obs: 99.9 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 23.2
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 1.464

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ERR

5err


Resolution: 1.5→43.55 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.162 3917 4.99 %
Rwork0.143 --
obs0.144 78431 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 117 392 3648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093570
X-RAY DIFFRACTIONf_angle_d1.1864913
X-RAY DIFFRACTIONf_dihedral_angle_d16.9082233
X-RAY DIFFRACTIONf_chiral_restr0.064571
X-RAY DIFFRACTIONf_plane_restr0.008640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51830.23651320.21542609X-RAY DIFFRACTION100
1.5183-1.53750.23181420.19232634X-RAY DIFFRACTION100
1.5375-1.55770.22731500.18262645X-RAY DIFFRACTION100
1.5577-1.57910.22261400.17832620X-RAY DIFFRACTION100
1.5791-1.60160.21951340.16572624X-RAY DIFFRACTION100
1.6016-1.62560.22131460.16082630X-RAY DIFFRACTION100
1.6256-1.6510.15721210.1462656X-RAY DIFFRACTION100
1.651-1.6780.20341380.14132648X-RAY DIFFRACTION100
1.678-1.7070.19061320.13772667X-RAY DIFFRACTION100
1.707-1.7380.16161300.1342648X-RAY DIFFRACTION100
1.738-1.77140.15981300.12962671X-RAY DIFFRACTION100
1.7714-1.80760.16881340.12822625X-RAY DIFFRACTION100
1.8076-1.84690.1431450.1292621X-RAY DIFFRACTION100
1.8469-1.88990.15511410.13252671X-RAY DIFFRACTION100
1.8899-1.93710.16761750.12452611X-RAY DIFFRACTION100
1.9371-1.98950.15671230.12732645X-RAY DIFFRACTION100
1.9895-2.0480.14681310.12962645X-RAY DIFFRACTION100
2.048-2.11410.15851460.12422675X-RAY DIFFRACTION100
2.1141-2.18970.15361380.12312648X-RAY DIFFRACTION100
2.1897-2.27740.15131570.12292659X-RAY DIFFRACTION100
2.2774-2.3810.14951170.12262668X-RAY DIFFRACTION100
2.381-2.50650.14911370.13062680X-RAY DIFFRACTION99
2.5065-2.66360.17281410.13842662X-RAY DIFFRACTION100
2.6636-2.86920.15871390.13682683X-RAY DIFFRACTION100
2.8692-3.15780.16861550.13882691X-RAY DIFFRACTION100
3.1578-3.61460.14711430.14072708X-RAY DIFFRACTION100
3.6146-4.55320.13811530.13262734X-RAY DIFFRACTION100
4.5532-43.56830.18941470.18522836X-RAY DIFFRACTION100

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