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- PDB-6hsn: Crystal structure of the ternary complex of GephE-ADP-GABA(A) rec... -

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Basic information

Entry
Database: PDB / ID: 6hsn
TitleCrystal structure of the ternary complex of GephE-ADP-GABA(A) receptor derived peptide
Components
  • Gamma-aminobutyric acid receptor subunit alpha-3
  • Gephyrin
KeywordsSTRUCTURAL PROTEIN / Gephyrin / GABAA receptor / moonlighting protein / Scaffolding protein
Function / homology
Function and homology information


GABA receptor activation / Molybdenum cofactor biosynthesis / molybdopterin cofactor biosynthetic process / glycine receptor clustering / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / establishment of synaptic specificity at neuromuscular junction / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / postsynaptic specialization ...GABA receptor activation / Molybdenum cofactor biosynthesis / molybdopterin cofactor biosynthetic process / glycine receptor clustering / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / establishment of synaptic specificity at neuromuscular junction / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / postsynaptic specialization / gamma-aminobutyric acid receptor clustering / nitrate reductase activity / inhibitory synapse / inhibitory extracellular ligand-gated monoatomic ion channel activity / benzodiazepine receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor activity / GABA-A receptor complex / inhibitory synapse assembly / Mo-molybdopterin cofactor biosynthetic process / glycinergic synapse / postsynaptic neurotransmitter receptor diffusion trapping / synaptic transmission, GABAergic / response to metal ion / postsynaptic specialization membrane / gamma-aminobutyric acid signaling pathway / molybdopterin cofactor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic specialization, intracellular component / chloride channel complex / GABA-ergic synapse / transmembrane transporter complex / regulation of postsynaptic membrane potential / protein targeting / presynaptic active zone membrane / chloride transmembrane transport / dendrite membrane / synapse assembly / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / tubulin binding / synaptic membrane / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / establishment of protein localization / cytoplasmic side of plasma membrane / protein-macromolecule adaptor activity / postsynapse / chemical synaptic transmission / postsynaptic membrane / molecular adaptor activity / postsynaptic density / cytoskeleton / neuron projection / signaling receptor binding / neuronal cell body / synapse / dendrite / ATP binding / identical protein binding / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Gamma-aminobutyric-acid A receptor, alpha 3 subunit / 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 ...Gamma-aminobutyric-acid A receptor, alpha 3 subunit / 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 / : / Gamma-aminobutyric-acid A receptor, alpha subunit / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Beta Complex / Alpha-Beta Complex / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-3F8 / ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Gamma-aminobutyric acid receptor subunit alpha-3 / Gephyrin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsKasaragod, V.B. / Schindelin, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSCHI 425/ 8-2 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
DepositionOct 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Revision 1.2Feb 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 1.3Mar 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 1.4Jan 24, 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 / struct_conn_type
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gephyrin
D: Gamma-aminobutyric acid receptor subunit alpha-3
E: Gamma-aminobutyric acid receptor subunit alpha-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,61020
Polymers47,8813
Non-polymers1,72917
Water8,647480
1
A: Gephyrin
D: Gamma-aminobutyric acid receptor subunit alpha-3
E: Gamma-aminobutyric acid receptor subunit alpha-3
hetero molecules

A: Gephyrin
D: Gamma-aminobutyric acid receptor subunit alpha-3
E: Gamma-aminobutyric acid receptor subunit alpha-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,22040
Polymers95,7626
Non-polymers3,45834
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1
MethodPISA
Unit cell
Length a, b, c (Å)86.962, 99.217, 111.608
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-811-

ACT

21A-901-

HOH

31A-1259-

HOH

41A-1368-

HOH

51A-1370-

HOH

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ADE

#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
#2: Protein/peptide Gamma-aminobutyric acid receptor subunit alpha-3 / GABA(A) receptor subunit alpha-3


Mass: 1114.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P20236

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Non-polymers , 8 types, 497 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-3F8 / 1,1'-[ethane-1,2-diylbis(oxyethane-2,1-diyl)]bis(1H-pyrrole-2,5-dione)


Mass: 308.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N2O6
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate pH 4.5 18-36 % MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.55→43.48 Å / Num. obs: 69059 / % possible obs: 98.7 % / Redundancy: 4.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.06 / Rrim(I) all: 0.095 / Net I/σ(I): 9.6
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3337 / CC1/2: 0.655 / Rpim(I) all: 0.592 / Rrim(I) all: 0.974 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U90

4u90


Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.653 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19575 3466 5 %RANDOM
Rwork0.15903 ---
obs0.16083 65584 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.037 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å2-0 Å20 Å2
2---0.16 Å20 Å2
3----0.6 Å2
Refinement stepCycle: 1 / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3291 0 113 480 3884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133742
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173602
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.6635150
X-RAY DIFFRACTIONr_angle_other_deg1.4881.5798408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0295508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69522.471174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39215642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2611524
X-RAY DIFFRACTIONr_chiral_restr0.1280.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024209
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02702
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6142.7791834
X-RAY DIFFRACTIONr_mcbond_other2.5662.7641825
X-RAY DIFFRACTIONr_mcangle_it3.6834.1342303
X-RAY DIFFRACTIONr_mcangle_other3.6844.142304
X-RAY DIFFRACTIONr_scbond_it3.5633.2471907
X-RAY DIFFRACTIONr_scbond_other3.5153.241904
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2464.7132808
X-RAY DIFFRACTIONr_long_range_B_refined7.69651.89415201
X-RAY DIFFRACTIONr_long_range_B_other7.69551.89615202
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 254 -
Rwork0.262 4723 -
obs--97.47 %

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