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- PDB-4pd1: Structure of gephyrin E domain with Glycine-beta receptor peptide -

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Basic information

Entry
Database: PDB / ID: 4pd1
TitleStructure of gephyrin E domain with Glycine-beta receptor peptide
Components
  • Gephyrin
  • Glycine receptor subunit beta
KeywordsSTRUCTURAL PROTEIN/TRANSPORT PROTEIN / Scaffolding protein / Neurotransmitter receptor anchoring protein / Molybdenum cofactor biosynthesis / STRUCTURAL PROTEIN-SIGNALING PROTEIN complex / STRUCTURAL PROTEIN-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


Neurotransmitter receptors and postsynaptic signal transmission / Molybdenum cofactor biosynthesis / glycine receptor clustering / glycine-gated chloride channel complex / molybdopterin cofactor biosynthetic process / establishment of synaptic specificity at neuromuscular junction / acrosome reaction / synaptic transmission, glycinergic / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity ...Neurotransmitter receptors and postsynaptic signal transmission / Molybdenum cofactor biosynthesis / glycine receptor clustering / glycine-gated chloride channel complex / molybdopterin cofactor biosynthetic process / establishment of synaptic specificity at neuromuscular junction / acrosome reaction / synaptic transmission, glycinergic / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / gamma-aminobutyric acid receptor clustering / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / nitrate reductase activity / postsynaptic specialization / chemical synaptic transmission, postsynaptic / inhibitory synapse / extracellularly glycine-gated ion channel activity / righting reflex / extracellularly glycine-gated chloride channel activity / Mo-molybdopterin cofactor biosynthetic process / glycinergic synapse / postsynaptic neurotransmitter receptor diffusion trapping / response to metal ion / adult walking behavior / molybdopterin cofactor binding / postsynaptic specialization membrane / neuromuscular process / neurotransmitter receptor activity / neurotransmitter receptor localization to postsynaptic specialization membrane / glycine binding / postsynaptic specialization, intracellular component / startle response / neuropeptide signaling pathway / transmembrane transporter complex / GABA-ergic synapse / regulation of postsynaptic membrane potential / protein targeting / monoatomic ion transport / chloride transmembrane transport / monoatomic ion transmembrane transport / synapse assembly / visual perception / tubulin binding / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / establishment of protein localization / cytoplasmic side of plasma membrane / transmembrane signaling receptor activity / nervous system development / protein-macromolecule adaptor activity / chemical synaptic transmission / postsynaptic membrane / perikaryon / postsynapse / molecular adaptor activity / postsynaptic density / cytoskeleton / neuron projection / signaling receptor binding / neuronal cell body / synapse / dendrite / protein-containing complex binding / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / : / Glycine receptor beta / 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. ...: / : / Glycine receptor beta / 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 / 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
ACETATE ION / Glycine receptor subunit beta / Gephyrin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.975 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: Acs Chem.Biol. / Year: 2014
Title: Modulation of gephyrin-glycine receptor affinity by multivalency.
Authors: Maric, H.M. / Kasaragod, V.B. / Schindelin, H.
History
DepositionApr 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Sep 17, 2014Group: Database references
Revision 1.3Dec 3, 2014Group: Database references
Revision 1.4Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / 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_oper_list / pdbx_validate_symm_contact / 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_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 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
C: Glycine receptor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,13111
Polymers47,3352
Non-polymers7969
Water3,135174
1
A: Gephyrin
C: Glycine receptor subunit beta
hetero molecules

A: Gephyrin
C: Glycine receptor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,26222
Polymers94,6704
Non-polymers1,59218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z1
Buried area12370 Å2
ΔGint-54 kcal/mol
Surface area35290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.660, 100.060, 117.500
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-923-

HOH

21A-958-

HOH

31A-973-

HOH

41A-975-

HOH

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Components

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


Mass: 45652.395 Da / Num. of mol.: 1 / Fragment: E-domain (UNP residues 350-768)
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 Glycine receptor subunit beta / Glycine receptor 58 kDa subunit


Mass: 1682.850 Da / Num. of mol.: 1 / Fragment: UNP residues 419-433 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P20781
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium citrate, pH 4.5, 28-34 % 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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.975→36.472 Å / Num. obs: 35783 / % possible obs: 100 % / Redundancy: 14.7 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 17.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FU3

2fu3


Resolution: 1.975→36.472 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1955 1792 5.01 %
Rwork0.1586 --
obs0.1605 35777 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.975→36.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 52 174 3386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113282
X-RAY DIFFRACTIONf_angle_d1.2974451
X-RAY DIFFRACTIONf_dihedral_angle_d13.3181241
X-RAY DIFFRACTIONf_chiral_restr0.08518
X-RAY DIFFRACTIONf_plane_restr0.008580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.975-2.02840.23821510.20652571X-RAY DIFFRACTION100
2.0284-2.08810.23761460.18282590X-RAY DIFFRACTION100
2.0881-2.15550.21121200.16342591X-RAY DIFFRACTION100
2.1555-2.23250.20261360.15712570X-RAY DIFFRACTION100
2.2325-2.32190.19491250.14992618X-RAY DIFFRACTION100
2.3219-2.42760.20011250.13932583X-RAY DIFFRACTION100
2.4276-2.55550.19371340.14532600X-RAY DIFFRACTION100
2.5555-2.71560.2161240.15672607X-RAY DIFFRACTION100
2.7156-2.92520.18271320.15062620X-RAY DIFFRACTION100
2.9252-3.21940.19731640.14892587X-RAY DIFFRACTION100
3.2194-3.68490.1961340.14592652X-RAY DIFFRACTION100
3.6849-4.6410.17831580.1432639X-RAY DIFFRACTION100
4.641-36.47830.19051430.19242757X-RAY DIFFRACTION100
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)
11.96210.05751.11063.1672.29096.28980.11590.00050.3370.46720.1071-0.3198-0.02090.5405-0.14090.2027-0.09180.04040.20080.05020.2995-23.9386-31.05434.5403
22.6212-1.62373.57941.239-1.53176.45470.39830.45930.0777-0.3456-0.34570.01350.18780.2405-0.07380.3060.07930.02770.34010.08620.2734-44.1086-32.4905-36.0893
31.3729-0.07421.81512.4804-0.72472.63460.35110.49180.0814-0.5789-0.49-0.02310.49020.48620.15440.48370.23260.00130.55340.08190.3247-52.2262-30.1213-46.5433
44.8895-2.40484.65921.3868-2.0655.36840.34410.49930.1847-0.195-0.48830.06970.38440.37320.08940.38790.0732-0.01960.36590.07470.3884-48.6242-28.555-41.0027
50.63270.0911-0.6350.6288-0.63416.67570.0498-0.11280.07510.0884-0.0781-0.03220.01820.07870.04320.1997-0.0258-0.01370.2114-0.00380.2686-36.141-39.64168.3215
63.2113-0.067-0.28893.7713-0.8961.6485-0.0641-0.5413-0.01070.4530.0049-0.4609-0.12690.46990.03540.2374-0.0521-0.06960.35830.01820.2812-22.1401-37.308518.1403
71.2025-1.3374-0.78311.7041.36192.0730.0406-0.02260.3019-0.1273-0.0927-0.0631-0.39930.10990.02530.2723-0.0628-0.00910.1891-0.0090.3289-32.1479-25.40196.8423
85.16060.66922.13873.13011.0723.8267-0.3112-0.42240.20780.67270.26450.3042-0.6394-0.38620.08270.55580.04780.0450.2403-0.02640.4349-42.5618-13.209812.9777
90.28551.3803-0.17276.8241-0.13792.8963-0.0517-0.3821-0.18020.5210.00211.32110.0364-0.47090.06120.62860.01720.06770.4172-0.05760.7877-48.5327-19.138111.8492
102.83960.1874-0.54011.19491.62563.79580.0449-0.38820.85050.34550.0443-0.7717-1.02680.1824-0.06230.7215-0.0591-0.11410.2823-0.09090.5795-35.9881-8.9814.3935
115.1945-3.8571-4.37752.973.22153.69550.94210.46181.4602-0.7562-0.2531-0.9937-0.8235-0.2853-0.81131.03-0.0179-0.04670.51980.02781.0352-29.0334-11.6468.6219
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 321 through 349 )
2X-RAY DIFFRACTION2chain 'A' and (resid 350 through 398 )
3X-RAY DIFFRACTION3chain 'A' and (resid 399 through 434 )
4X-RAY DIFFRACTION4chain 'A' and (resid 435 through 472 )
5X-RAY DIFFRACTION5chain 'A' and (resid 473 through 550 )
6X-RAY DIFFRACTION6chain 'A' and (resid 551 through 627 )
7X-RAY DIFFRACTION7chain 'A' and (resid 628 through 661 )
8X-RAY DIFFRACTION8chain 'A' and (resid 662 through 686 )
9X-RAY DIFFRACTION9chain 'A' and (resid 687 through 712 )
10X-RAY DIFFRACTION10chain 'A' and (resid 713 through 736 )
11X-RAY DIFFRACTION11chain 'C' and (resid 397 through 406 )

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