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- PDB-4u90: GephE in complex with PEG crosslinked GABA receptor alpha3 subuni... -

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Basic information

Entry
Database: PDB / ID: 4u90
TitleGephE in complex with PEG crosslinked GABA receptor alpha3 subunit derived dimeric peptide
Components
  • Gamma-aminobutyric acid receptor subunit alpha-3
  • Gephyrin
KeywordsTRANSFER PROTEIN / STRUCTURAL PROTEIN / Inhibitory synapse / Scaffolding protein / GABA type A receptor / transferase / transfer protein - structural protein complex
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 / 1,4-BUTANEDIOL / Gamma-aminobutyric acid receptor subunit alpha-3 / Gephyrin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKasaragod, V.B. / Maric, H.M. / Schindelin, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSchi 425/ 8-1 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Design and Synthesis of High-Affinity Dimeric Inhibitors Targeting the Interactions between Gephyrin and Inhibitory Neurotransmitter Receptors.
Authors: Maric, H.M. / Kasaragod, V.B. / Haugaard-Kedstrom, L. / Hausrat, T.J. / Kneussel, M. / Schindelin, H. / Strmgaard, K.
History
DepositionAug 5, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 2.0Dec 20, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_struct_special_symmetry / pdbx_validate_close_contact
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2

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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)48,2795
Polymers47,8813
Non-polymers3982
Water4,594255
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)96,55910
Polymers95,7626
Non-polymers7974
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_577x,-y+2,-z+21
Unit cell
Length a, b, c (Å)88.538, 99.240, 114.406
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-1100-

HOH

21A-1103-

HOH

31A-1104-

HOH

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Components

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


Mass: 45652.395 Da / Num. of mol.: 1 / Fragment: Gephyrin E domain, 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)
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 / Mutation: Addition of Cysteine at the C terminus / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P20236
#3: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium acetate pH 4.5, 20-30 % 2-Methyl-2,4-pentanediol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.91 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2→44.2 Å / Num. obs: 34354 / % possible obs: 99 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FU3

2fu3


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 8.411 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21103 1694 4.9 %RANDOM
Rwork0.16655 ---
obs0.16878 32616 99.67 %-
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: 53.214 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å2-0 Å2
2---1.5 Å20 Å2
3---1.63 Å2
Refinement stepCycle: 1 / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3293 0 28 255 3576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193433
X-RAY DIFFRACTIONr_bond_other_d0.0020.023345
X-RAY DIFFRACTIONr_angle_refined_deg1.9071.9914676
X-RAY DIFFRACTIONr_angle_other_deg0.9333.0027716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.635440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.85424.406143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24115569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5211524
X-RAY DIFFRACTIONr_chiral_restr0.1110.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213861
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02713
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_it3.1733.371739
X-RAY DIFFRACTIONr_mcbond_other3.1723.3681738
X-RAY DIFFRACTIONr_mcangle_it4.445.0242171
X-RAY DIFFRACTIONr_mcangle_other4.445.0272172
X-RAY DIFFRACTIONr_scbond_it4.2963.9181693
X-RAY DIFFRACTIONr_scbond_other4.2863.9181693
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1995.6772501
X-RAY DIFFRACTIONr_long_range_B_refined8.99932.73513691
X-RAY DIFFRACTIONr_long_range_B_other8.99932.73613692
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 107 -
Rwork0.267 2392 -
obs--99.92 %
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)
10.14240.034-0.05080.0643-0.07930.4607-0.0173-0.0125-0.0107-0.0139-0.06640.0350.0330.13180.08380.20090.0111-0.00330.11030.04880.22575.5557128.7595117.6979
22.50212.4633-0.06254.0018-2.0752.57460.120.02990.0303-0.0582-0.2556-0.07570.24530.34740.13560.27040.07010.03240.07830.0040.217512.0804109.3488106.3605
310.5619-12.25251.402616.80730.05922.85470.1614-0.24030.6064-0.69860.0589-1.4144-0.41030.1-0.22020.3686-0.14180.04240.17430.13490.282312.195489.1361122.4718
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A319 - 736
2X-RAY DIFFRACTION2D368 - 377
3X-RAY DIFFRACTION3E368 - 377

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