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- PDB-4tk1: Geph E in complex with a GABA receptor alpha3 subunit derived pep... -

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Basic information

Entry
Database: PDB / ID: 4tk1
TitleGeph E in complex with a GABA receptor alpha3 subunit derived peptide in space group P21212
Components
  • Gamma-aminobutyric acid receptor subunit alpha-3
  • Gephyrin
KeywordsBIOSYNTHETIC PROTEIN / Structural protein / Scaffolding protein / Neurotransmitter receptor anchoring / Molybdenum co factor biosynthesis
Function / homology
Function and homology information


GABA receptor activation / Molybdenum cofactor biosynthesis / molybdopterin cofactor biosynthetic process / glycine receptor clustering / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / chemical synaptic transmission, postsynaptic / establishment of synaptic specificity at neuromuscular junction / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity ...GABA receptor activation / Molybdenum cofactor biosynthesis / molybdopterin cofactor biosynthetic process / glycine receptor clustering / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / chemical synaptic transmission, postsynaptic / 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 / GABA-gated chloride ion channel activity / GABA-A receptor activity / GABA-A receptor complex / Mo-molybdopterin cofactor biosynthetic process / glycinergic synapse / postsynaptic neurotransmitter receptor diffusion trapping / synaptic transmission, GABAergic / postsynaptic specialization membrane / gamma-aminobutyric acid signaling pathway / response to metal ion / molybdopterin cofactor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic specialization, intracellular component / chloride channel complex / GABA-ergic synapse / regulation of postsynaptic membrane potential / protein targeting / presynaptic active zone membrane / monoatomic ion transmembrane transport / chloride transmembrane transport / synapse assembly / dendrite membrane / 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 / postsynaptic density / molecular adaptor activity / cytoskeleton / neuron projection / signaling receptor binding / neuronal cell body / synapse / dendrite / ATP binding / identical protein binding / metal ion binding / cytosol / cytoplasm
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
BETA-MERCAPTOETHANOL / Gamma-aminobutyric acid receptor subunit alpha-3 / Gephyrin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKasaragod, V.B. / Maric, H.M. / Schindelin, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)Schi 425/ 8-1 Germany
CitationJournal: Nat Commun / Year: 2014
Title: Molecular basis of the alternative recruitment of GABAA versus glycine receptors through gephyrin.
Authors: Maric, H.M. / Kasaragod, V.B. / Hausrat, T.J. / Kneussel, M. / Tretter, V. / Strmgaard, K. / Schindelin, H.
History
DepositionMay 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)94,0447
Polymers93,7824
Non-polymers2623
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-57 kcal/mol
Surface area34760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.439, 157.695, 51.018
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 320 - 736 / Label seq-ID: 3 - 419

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 45652.395 Da / Num. of mol.: 2 / Fragment: domain E (UNP residues 344-762)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gphn, Gph / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q03555, molybdopterin adenylyltransferase, molybdopterin molybdotransferase
#2: Protein/peptide Gamma-aminobutyric acid receptor subunit alpha-3 / GABA(A) receptor subunit alpha-3


Mass: 1238.389 Da / Num. of mol.: 2 / Fragment: UNP residues 396-406 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P20236
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Tris pH 7.5, 21-27% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.7→48.6 Å / Num. obs: 25198 / % possible obs: 99 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.212 / Net I/σ(I): 7.8

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FU3

2fu3


Resolution: 2.7→48.54 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.892 / SU B: 31.279 / SU ML: 0.303 / Cross valid method: THROUGHOUT / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26441 1255 5 %RANDOM
Rwork0.21518 ---
obs0.21759 23902 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.596 Å2
Baniso -1Baniso -2Baniso -3
1-4.53 Å2-0 Å2-0 Å2
2---1.18 Å20 Å2
3----3.35 Å2
Refinement stepCycle: 1 / Resolution: 2.7→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6368 0 16 116 6500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196503
X-RAY DIFFRACTIONr_bond_other_d0.0030.026388
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.9888839
X-RAY DIFFRACTIONr_angle_other_deg0.877314729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115827
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56924.415265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.675151097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9751544
X-RAY DIFFRACTIONr_chiral_restr0.0740.21036
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217269
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021327
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 23928 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 94 -
Rwork0.386 1713 -
obs--99.72 %
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)
12.5103-3.0967-0.64676.4830.83230.78440.159-0.16230.3769-0.4958-0.0394-0.1087-0.3298-0.0185-0.11960.2502-0.0293-0.02670.1111-0.03160.1124-53.168544.1739-23.7996
21.5551-1.3929-0.05924.0474-0.28170.96590.0852-0.0884-0.0896-0.2708-0.11660.2872-0.0715-0.02970.03140.0311-0.0021-0.01830.0915-0.04150.0371-48.597821.0354-18.8673
33.270.88680.35573.88461.35221.51440.1568-0.1911-0.3696-0.1888-0.1008-0.26810.26580.0163-0.05590.15210.00360.05080.03060.0210.1295-31.02156.0873-20.7486
43.7444-1.3218-0.20193.79480.64343.7266-0.1293-0.9165-0.06430.54920.2252-0.11570.18510.0642-0.09590.1091-0.02550.03230.3018-0.0440.2757-22.925619.6907-7.8698
51.8244-1.9690.46864.1266-0.7810.83260.0046-0.1267-0.2476-0.14760.0272-0.05560.22830.1283-0.03180.07930.02540.02280.18980.02270.0984-38.46369.4166-4.8421
64.6425-0.5274-1.27023.0790.40892.26950.03650.13620.4931-0.35690.1112-0.1354-0.3659-0.0699-0.14770.11440.0303-0.0160.0876-0.05230.1067-45.95740.0879-8.6695
77.7227.42295.76447.35154.375310.62620.2083-0.6195-0.59060.3667-0.6316-0.7323-0.9296-0.01780.42340.2643-0.0905-0.04360.2563-0.03530.4129-13.498521.214-18.5617
81.92212.93071.313911.3721-7.370213.66360.20810.3529-0.1931.0580.0096-0.0981-1.15960.9915-0.21770.37220.00040.06830.3468-0.3480.497-29.658243.7292-6.303
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A320 - 434
2X-RAY DIFFRACTION2A435 - 572
3X-RAY DIFFRACTION3A573 - 679
4X-RAY DIFFRACTION4A680 - 736
5X-RAY DIFFRACTION5B320 - 550
6X-RAY DIFFRACTION6B551 - 736
7X-RAY DIFFRACTION7C370 - 378
8X-RAY DIFFRACTION8D370 - 376

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