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- PDB-4u91: GephE in complex with Para-Phenyl crosslinked Glycine receptor be... -

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Basic information

Entry
Database: PDB / ID: 4u91
TitleGephE in complex with Para-Phenyl crosslinked Glycine receptor beta subunit derived dimeric peptide
Components
  • Gephyrin
  • Glycine receptor subunit beta
KeywordsTRANSFER PROTEIN / STRUCTURAL PROTEIN / Transferase / Scaffolding protein / Inhibitory synapse / GABA type A receptor / transfer protein - structural protein complex
Function / homology
Function and homology information


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 ...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 / Mo-molybdopterin cofactor biosynthetic process / glycinergic synapse / postsynaptic neurotransmitter receptor diffusion trapping / response to metal ion / postsynaptic specialization membrane / molybdopterin cofactor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic specialization, intracellular component / GABA-ergic synapse / protein targeting / synapse assembly / tubulin binding / synaptic membrane / establishment of protein localization / cytoplasmic side of plasma membrane / protein-macromolecule adaptor activity / postsynapse / postsynaptic membrane / molecular adaptor activity / postsynaptic density / cytoskeleton / signaling receptor binding / neuronal cell body / dendrite / ATP binding / identical protein binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
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 ...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 / Beta Complex / Alpha-Beta Complex / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
1,1'-benzene-1,4-diylbis(1H-pyrrole-2,5-dione) / ACETATE ION / 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 / pdbx_validate_symm_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 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_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
B: Glycine receptor subunit beta
E: Glycine receptor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4717
Polymers48,0413
Non-polymers4294
Water5,188288
1
A: Gephyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8144
Polymers45,6521
Non-polymers1613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycine receptor subunit beta
E: Glycine receptor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,6573
Polymers2,3892
Non-polymers2681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.440, 99.210, 112.490
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-950-

HOH

21A-1105-

HOH

31A-1125-

HOH

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Components

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

#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 Glycine receptor subunit beta / Glycine receptor 58 kDa subunit


Mass: 1194.382 Da / Num. of mol.: 2 / Mutation: Additional Cysteine at the C terminus / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat)

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Non-polymers , 5 types, 292 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-3F7 / 1,1'-benzene-1,4-diylbis(1H-pyrrole-2,5-dione)


Mass: 268.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H8N2O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2 M calcium acetate, 0.1M 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: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→56.2 Å / Num. obs: 33407 / % possible obs: 100 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 2.5 / % 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: 0.967 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.705 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22563 1688 5.1 %RANDOM
Rwork0.16851 ---
obs0.17145 31672 99.81 %-
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: 48.437 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å2-0 Å2
2---0.29 Å20 Å2
3----0.22 Å2
Refinement stepCycle: 1 / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 29 288 3647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193471
X-RAY DIFFRACTIONr_bond_other_d0.0020.023398
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.9964722
X-RAY DIFFRACTIONr_angle_other_deg0.8563.0017839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7785447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71524.043141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.43515590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8991527
X-RAY DIFFRACTIONr_chiral_restr0.0980.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213899
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02718
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_it3.4283.8571765
X-RAY DIFFRACTIONr_mcbond_other3.4293.8531763
X-RAY DIFFRACTIONr_mcangle_it5.0895.7392204
X-RAY DIFFRACTIONr_mcangle_other5.0885.7412205
X-RAY DIFFRACTIONr_scbond_it4.0074.4261706
X-RAY DIFFRACTIONr_scbond_other4.0074.4261706
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.046.452514
X-RAY DIFFRACTIONr_long_range_B_refined9.4736.35314156
X-RAY DIFFRACTIONr_long_range_B_other9.4736.35514157
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
Rfree0.286 132 -
Rwork0.268 2281 -
obs--99.96 %
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)
10.14880.1040.14470.09870.04260.34210.006-0.0220.0241-0.0102-0.01690.0169-0.0171-0.03970.01080.05240.0180.00260.0704-0.01760.064537.89620.024227.7484
28.31723.7515-3.95699.1096-1.87061.88360.49630.11450.55510.6237-0.2348-0.1203-0.2436-0.053-0.26150.22430.0551-0.05280.04230.01360.121731.795341.0266215.704
32.29373.15951.58947.79282.26881.10520.1690.1172-0.01440.406-0.16360.15160.1360.0801-0.00540.14240.03840.04230.0576-0.01880.084355.644658.2363215.5575
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A319 - 736
2X-RAY DIFFRACTION2B398 - 408
3X-RAY DIFFRACTION3E398 - 408

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