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- PDB-4tk4: GephE in complex with a GABA receptor alpha3 subunit derived doub... -

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Basic information

Entry
Database: PDB / ID: 4tk4
TitleGephE in complex with a GABA receptor alpha3 subunit derived double mutant peptide in space group P61
Components
  • Gamma-aminobutyric acid receptor subunit alpha-3
  • Gephyrin
KeywordsBIOSYNTHETIC PROTEIN / Structural Protein / Scaffolding protein / Neurotransmitter receptor anchoring / Molybdenum co factor bio synthesis
Function / homology
Function and homology information


GABA receptor activation / Molybdenum cofactor biosynthesis / glycine receptor clustering / molybdopterin cofactor biosynthetic process / establishment of synaptic specificity at neuromuscular junction / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / molybdopterin molybdotransferase / nitrate reductase activity / molybdopterin molybdotransferase activity ...GABA receptor activation / Molybdenum cofactor biosynthesis / glycine receptor clustering / molybdopterin cofactor biosynthetic process / establishment of synaptic specificity at neuromuscular junction / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / molybdopterin molybdotransferase / nitrate reductase activity / molybdopterin molybdotransferase activity / gamma-aminobutyric acid receptor clustering / postsynaptic specialization / inhibitory synapse / Mo-molybdopterin cofactor biosynthetic process / auditory behavior / glycinergic synapse / molybdopterin cofactor binding / inhibitory synapse assembly / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / response to metal ion / postsynaptic specialization, intracellular component / postsynaptic specialization membrane / neurotransmitter receptor localization to postsynaptic specialization membrane / gamma-aminobutyric acid signaling pathway / synaptic transmission, GABAergic / chloride channel complex / protein targeting / synapse assembly / presynaptic active zone membrane / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / tubulin binding / chloride transmembrane transport / synaptic membrane / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / establishment of protein localization / GABA-ergic synapse / response to lead ion / cytoplasmic side of plasma membrane / protein-macromolecule adaptor activity / molecular adaptor activity / chemical synaptic transmission / dendritic spine / postsynaptic membrane / cytoskeleton / postsynapse / postsynaptic density / signaling receptor binding / neuronal cell body / dendrite / synapse / ATP binding / metal ion binding / identical protein binding / 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 / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis proteins signature 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 / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis proteins signature 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
Gamma-aminobutyric acid receptor subunit alpha-3 / Gephyrin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.601 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 / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
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_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)93,7524
Polymers93,7524
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9250 Å2
ΔGint-56 kcal/mol
Surface area35410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.180, 160.180, 127.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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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: 1223.418 Da / Num. of mol.: 2 / Fragment: UNP residues 396-406 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P20236
Has protein modificationY

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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: 5.05 Å3/Da / Density % sol: 75.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.15 M Calcium acetate, 0.1 M sodium cacodylate pH 6.0, 6-10 % Isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 3.6→67.89 Å / Num. obs: 21728 / % possible obs: 100 % / Redundancy: 5.6 % / Rsym value: 0.15 / Net I/σ(I): 7.6

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FU3

2fu3


Resolution: 3.601→67.88 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.06 / Phase error: 22.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2168 2217 5.24 %
Rwork0.1762 --
obs0.1784 42271 99.45 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.601→67.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6398 0 0 0 6398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036522
X-RAY DIFFRACTIONf_angle_d0.7078869
X-RAY DIFFRACTIONf_dihedral_angle_d11.5742465
X-RAY DIFFRACTIONf_chiral_restr0.0261039
X-RAY DIFFRACTIONf_plane_restr0.0031162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.601-3.72930.38681890.31634078X-RAY DIFFRACTION100
3.7293-3.87860.30472260.27443991X-RAY DIFFRACTION100
3.8786-4.05520.27312250.23233976X-RAY DIFFRACTION100
4.0552-4.26890.24672410.19914026X-RAY DIFFRACTION99
4.2689-4.53630.20522060.15923991X-RAY DIFFRACTION100
4.5363-4.88650.16012430.13134002X-RAY DIFFRACTION99
4.8865-5.37810.18292320.14124002X-RAY DIFFRACTION100
5.3781-6.15580.21042550.15693987X-RAY DIFFRACTION100
6.1558-7.75390.21292000.16354010X-RAY DIFFRACTION100
7.7539-67.89330.20042000.16293991X-RAY DIFFRACTION98
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)
17.07096.43671.02317.18380.65754.94990.4818-0.8449-0.54910.772-0.5806-0.86530.13620.43420.13470.98670.2134-0.04560.8088-0.02090.8798-60.5041-13.45625.9966
22.47183.98323.43864.83385.95546.9261-0.16490.21210.02570.04220.1797-0.0721-0.0506-0.1043-0.04510.73620.00050.01950.74070.0690.7554-83.0484-50.0241-22.184
30.690.18090.25068.6913-0.87290.4321-0.1846-0.19340.07721.96920.28540.0535-0.2160.0026-0.13291.02630.0970.03030.75540.02210.6357-73.9201-6.88984.7251
44.00650.0541-0.8217.97482.44187.12170.002-0.55960.24051.01850.1716-1.1918-0.58270.6005-0.16050.8363-0.0006-0.1960.75940.01940.8517-60.683-2.83413.5553
52.60170.79931.9414.4851-3.5545.7041-1.20110.247-0.1774-0.57980.6983-0.3907-0.53270.19660.50041.2487-0.13290.21841.1642-0.10321.0692-59.28891.9845-14.7863
61.8171.73140.82357.00592.80591.4436-0.32160.13930.5599-0.46930.29910.1121-0.15230.51820.00130.97490.0194-0.0380.9340.08570.7404-70.777813.3979-2.7004
72.54340.5476-0.32852.30572.02134.90160.0543-0.27830.15720.0738-0.87481.3949-0.0152-0.56050.91910.93190.0456-0.01050.9326-0.07110.9718-87.2869-31.0138-9.0944
88.51623.1647-0.33996.72910.47564.1029-0.24480.831-0.2996-1.35620.11250.6269-0.1118-0.20860.12761.07790.0366-0.1870.74890.01470.5615-83.656-21.8915-22.124
96.141-5.49351.15035.58450.18295.83-0.63761.1919-1.6178-0.15281.1698-0.4634-0.5020.3404-0.37270.87-0.08410.21721.1618-0.16651.0705-65.7834-28.1064-16.7999
109.619-2.4170.17833.4213.17913.35771.52020.85370.3798-0.57990.9377-1.6345-0.63350.3667-2.27971.37-0.13860.28481.0698-0.07590.9995-64.1178-23.1652-29.4246
111.0315-0.1301-2.05890.01970.29524.09680.1553-0.60170.493-1.0252-0.2538-0.57460.19322.00410.38251.8808-0.0905-0.1232.03660.34181.2094-67.5703-16.6775-32.8868
128.87271.9847-1.54277.16444.9865.3825-0.7273-0.8419-0.6658-0.5810.1876-1.10750.0762.13130.78661.2909-0.0040.02931.5231-0.08011.7281-48.5395-6.2924-12.2891
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 320:349 )A320 - 349
2X-RAY DIFFRACTION2( CHAIN A AND RESID 350:472 )A350 - 472
3X-RAY DIFFRACTION3( CHAIN A AND RESID 473:550 )A473 - 550
4X-RAY DIFFRACTION4( CHAIN A AND RESID 551:686 )A551 - 686
5X-RAY DIFFRACTION5( CHAIN A AND RESID 687:736 )A687 - 736
6X-RAY DIFFRACTION6( CHAIN B AND RESID 320:506 )B320 - 506
7X-RAY DIFFRACTION7( CHAIN B AND RESID 507:550 )B507 - 550
8X-RAY DIFFRACTION8( CHAIN B AND RESID 551:686 )B551 - 686
9X-RAY DIFFRACTION9( CHAIN B AND RESID 687:712 )B687 - 712
10X-RAY DIFFRACTION10( CHAIN B AND RESID 713:736 )B713 - 736
11X-RAY DIFFRACTION11( CHAIN C AND RESID 370:376 )C370 - 376
12X-RAY DIFFRACTION12( CHAIN D AND RESID 370:376 )D370 - 376

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