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- PDB-4tk2: Geph E in complex with a GABA receptor alpha3 subunit derived pep... -

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Basic information

Entry
Database: PDB / ID: 4tk2
TitleGeph E in complex with a GABA receptor alpha3 subunit derived 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 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 / 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 / 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) ...Gamma-aminobutyric-acid A receptor, alpha 3 subunit / 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) / Molybdenum cofactor biosynthesis, conserved site / 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
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: 4.1 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

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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)93,7824
Polymers93,7824
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-46 kcal/mol
Surface area37300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.510, 164.510, 129.429
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: 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

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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: 5.39 Å3/Da / Density % sol: 77.18 %
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: 4.1→49.72 Å / Num. obs: 15728 / % possible obs: 99 % / Redundancy: 4.1 % / Rsym value: 0.2 / Net I/σ(I): 6
Reflection shellMean I/σ(I) obs: 1.6

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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: 4.1→47.9 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 0.97 / Phase error: 22.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2364 1614 5.27 %
Rwork0.1832 --
obs0.186 30619 99.79 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.1→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6411 0 0 0 6411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026533
X-RAY DIFFRACTIONf_angle_d0.5848883
X-RAY DIFFRACTIONf_dihedral_angle_d11.4412465
X-RAY DIFFRACTIONf_chiral_restr0.0221040
X-RAY DIFFRACTIONf_plane_restr0.0031166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1-4.24660.32671490.28542889X-RAY DIFFRACTION100
4.2466-4.41650.30261860.27492884X-RAY DIFFRACTION100
4.4165-4.61730.27941290.22352906X-RAY DIFFRACTION100
4.6173-4.86050.26581910.20242934X-RAY DIFFRACTION100
4.8605-5.16470.23891480.19092884X-RAY DIFFRACTION100
5.1647-5.5630.26141760.19562881X-RAY DIFFRACTION100
5.563-6.12180.2281840.19892909X-RAY DIFFRACTION100
6.1218-7.00520.23371610.18122882X-RAY DIFFRACTION100
7.0052-8.81690.23661340.14362924X-RAY DIFFRACTION100
8.8169-47.9030.16591560.12862912X-RAY DIFFRACTION99
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)
12.29223.48620.71895.1788-0.05920.21930.48640.0977-0.40681.0689-0.2858-0.88230.39640.3419-0.28981.3452-0.0709-0.07241.1654-0.08111.3756-67.5776-23.26971.9065
25.88161.63631.22438.78245.35993.36650.5507-0.11530.31530.3175-0.58740.2235-0.25830.3063-0.0771.0676-0.1055-0.02461.10340.10441.2151-88.9616-55.678-27.3973
38.49751.13114.37535.48875.34636.03690.3545-0.39320.47670.0019-0.6770.5782-0.2609-0.34090.37061.1956-0.04910.10691.0042-0.0761.0398-89.2159-55.8159-28.0581
43.0664.36534.0725.05646.69079.63520.41280.01240.10010.42660.1614-0.56980.2049-0.6947-0.74771.14070.0759-0.0041.25020.11491.2293-83.9729-51.645-24.7104
54.43634.36933.26485.58276.38556.94950.76350.044-0.61150.5175-0.7693-0.6772-0.0856-0.9548-0.06461.12530.0865-0.04671.09680.0371.0172-74.7415-23.5931.3065
66.0278-2.4710.2914.6386-2.83044.9994-0.1631-0.53980.05762.94820.46380.0888-0.4518-0.2555-0.3731.5472-0.0867-01.21620.00011.0873-76.564.81786.6633
78.44310.1841.37037.80222.13553.05151.5197-1.3752-0.09222.8178-1.7559-0.8521-0.3872-0.63750.08892.0599-0.2086-0.251.32640.15141.0587-69.5488-0.532516.996
83.8478-1.8687-0.2569.0166-0.06473.8978-0.0672-0.86140.95372.5332-0.1883-2.3208-0.75640.99590.12521.7475-0.2214-0.54991.3374-0.11211.9425-57.34291.656813.0934
91.97240.5136-2.57696.5176-2.83297.9565-0.0874-0.1163-0.02490.55320.1894-0.9135-0.6460.7104-0.06431.09630.0296-0.17631.01470.03081.2238-61.4582-5.0753-1.6999
103.708-1.1323-2.07372.7336-0.83663.1156-0.0693-0.8074-0.0239-0.72950.6523-0.481-0.4294-0.5383-0.54531.38770.20210.03991.53730.07851.5005-68.1209-0.0323-20.1919
114.20911.37014.99534.2825-1.22336.8645-0.39540.2108-0.4637-0.4927-0.1526-0.1683-0.59670.81620.54891.20210.07590.41541.37430.07571.6506-54.7384-0.7472-15.3683
123.41173.49514.30069.2237.60294.5479-0.90280.76620.4551-1.9311-0.29752.2849-1.19661.11391.05411.93350.17-0.34961.20520.12221.2335-89.4026-12.1237-22.503
133.82895.96493.2728.57536.83175.1960.5878-0.18140.19160.5363-0.46190.20840.66130.3363-0.01371.43080.0916-0.12121.22-0.11491.6092-67.627124.60754.3134
149.20345.22894.60846.32975.40144.45750.35240.0223-1.1489-0.15470.9911-1.21580.34761.7641-1.46511.4406-0.0709-0.16391.87610.04442.4787-54.496328.0947.4941
151.57220.1709-0.09282.91630.230.77230.3587-0.0470.2129-0.0003-0.91991.1754-0.1686-0.15190.55881.25070.07110.01661.2313-0.00381.3709-87.1352-15.5334-9.4347
167.95376.41012.13827.9883.84467.2165-0.1668-0.24630.1941-0.4130.4421.56921.00890.32320.01921.20870.0718-0.39911.36440.08461.4467-100.7527-27.7333-18.8963
176.00221.1604-1.50598.31580.81623.6839-0.47350.7229-0.3997-1.33250.01481.75840.6966-0.16940.44721.87840.1096-0.41191.12450.06651.1689-91.3069-22.1082-24.3059
189.5536-2.5461-3.57886.9595-1.13043.2923-0.61780.72070.1487-1.49470.3781-0.3474-0.64810.2850.11911.40780.0369-0.00451.0336-0.12671.0511-71.1625-21.046-25.3075
195.27684.4572-5.94686.017-4.14986.0720.1804-0.0241-0.45750.93890.1891-0.8620.01331.0904-0.28691.26140.066-0.05111.6133-0.04061.4488-62.8182-25.192-16.3139
205.8683-0.6896-1.55586.59075.56359.88480.34380.9666-0.3766-0.79560.2381-1.10740.681-1.1788-0.72181.8833-0.11860.3631.3554-0.00661.3878-66.976-23.2624-29.646
215.1088-6.9632-4.33321.95024.57957.64571.5012-1.6781-2.0022-3.1783-1.7643-0.23730.53010.9653-0.04572.10490.35290.10152.23-0.24082.5651-69.4637-16.6895-33.9167
228.27162.77433.77181.92882.75515.31911.13830.7661-1.939-0.07410.34054.104-2.23981.8927-1.20261.6111-0.1591-0.06041.77790.14781.6354-50.2871-7.7561-12.0563
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 320:369 )A320 - 369
2X-RAY DIFFRACTION2( CHAIN A AND RESID 370:398 )A370 - 398
3X-RAY DIFFRACTION3( CHAIN A AND RESID 399:434 )A399 - 434
4X-RAY DIFFRACTION4( CHAIN A AND RESID 435:472 )A435 - 472
5X-RAY DIFFRACTION5( CHAIN A AND RESID 473:506 )A473 - 506
6X-RAY DIFFRACTION6( CHAIN A AND RESID 507:550 )A507 - 550
7X-RAY DIFFRACTION7( CHAIN A AND RESID 551:579 )A551 - 579
8X-RAY DIFFRACTION8( CHAIN A AND RESID 580:607 )A580 - 607
9X-RAY DIFFRACTION9( CHAIN A AND RESID 608:679 )A608 - 679
10X-RAY DIFFRACTION10( CHAIN A AND RESID 680:707 )A680 - 707
11X-RAY DIFFRACTION11( CHAIN A AND RESID 708:736 )A708 - 736
12X-RAY DIFFRACTION12( CHAIN B AND RESID 320:349 )B320 - 349
13X-RAY DIFFRACTION13( CHAIN B AND RESID 350:422 )B350 - 422
14X-RAY DIFFRACTION14( CHAIN B AND RESID 423:462 )B423 - 462
15X-RAY DIFFRACTION15( CHAIN B AND RESID 463:550 )B463 - 550
16X-RAY DIFFRACTION16( CHAIN B AND RESID 551:587 )B551 - 587
17X-RAY DIFFRACTION17( CHAIN B AND RESID 588:646 )B588 - 646
18X-RAY DIFFRACTION18( CHAIN B AND RESID 647:679 )B647 - 679
19X-RAY DIFFRACTION19( CHAIN B AND RESID 680:707 )B680 - 707
20X-RAY DIFFRACTION20( CHAIN B AND RESID 708:736 )B708 - 736
21X-RAY DIFFRACTION21( CHAIN C AND RESID 370:376 )C370 - 376
22X-RAY DIFFRACTION22( CHAIN D AND RESID 370:375 )D370 - 375

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