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- PDB-2fts: Crystal structure of the glycine receptor-gephyrin complex -

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Basic information

Entry
Database: PDB / ID: 2fts
TitleCrystal structure of the glycine receptor-gephyrin complex
Components
  • Glycine receptor beta chain precursor
  • gephyrin
KeywordsSTRUCTURAL PROTEIN / Glycine receptor / gephyrin / neuroreceptor anchoring
Function / homology
Function and homology information


Neurotransmitter receptors and postsynaptic signal transmission / Molybdenum cofactor biosynthesis / glycine-gated chloride channel complex / molybdopterin cofactor biosynthetic process / glycine receptor clustering / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / chemical synaptic transmission, postsynaptic / establishment of synaptic specificity at neuromuscular junction / molybdopterin molybdotransferase ...Neurotransmitter receptors and postsynaptic signal transmission / Molybdenum cofactor biosynthesis / glycine-gated chloride channel complex / molybdopterin cofactor biosynthetic process / glycine receptor clustering / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / chemical synaptic transmission, postsynaptic / establishment of synaptic specificity at neuromuscular junction / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / postsynaptic specialization / acrosome reaction / gamma-aminobutyric acid receptor clustering / nitrate reductase activity / inhibitory synapse / extracellularly glycine-gated ion channel activity / righting reflex / extracellularly glycine-gated chloride channel activity / synaptic transmission, glycinergic / Mo-molybdopterin cofactor biosynthetic process / glycinergic synapse / postsynaptic neurotransmitter receptor diffusion trapping / response to metal ion / postsynaptic specialization membrane / adult walking behavior / molybdopterin cofactor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / neuromuscular process / neurotransmitter receptor activity / glycine binding / postsynaptic specialization, intracellular component / startle response / GABA-ergic synapse / transmembrane transporter complex / regulation of postsynaptic membrane potential / neuropeptide signaling pathway / protein targeting / monoatomic ion transport / monoatomic ion transmembrane transport / chloride transmembrane transport / synapse assembly / visual perception / tubulin binding / synaptic membrane / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / establishment of protein localization / cytoplasmic side of plasma membrane / transmembrane signaling receptor activity / protein-macromolecule adaptor activity / nervous system development / postsynapse / chemical synaptic transmission / postsynaptic membrane / perikaryon / 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 / cytoplasm / cytosol
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
Glycine receptor subunit beta / Gephyrin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsKim, E.Y. / Schindelin, H.
CitationJournal: Embo J. / Year: 2006
Title: Deciphering the structural framework of glycine receptor anchoring by gephyrin.
Authors: Kim, E.Y. / Schrader, N. / Smolinsky, B. / Bedet, C. / Vannier, C. / Schwarz, G. / Schindelin, H.
History
DepositionJan 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
P: Glycine receptor beta chain precursor


Theoretical massNumber of molelcules
Total (without water)47,1332
Polymers47,1332
Non-polymers00
Water2,702150
1
A: gephyrin
P: Glycine receptor beta chain precursor

A: gephyrin
P: Glycine receptor beta chain precursor


Theoretical massNumber of molelcules
Total (without water)94,2664
Polymers94,2664
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area10430 Å2
ΔGint-60 kcal/mol
Surface area35420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)51.298, 123.541, 155.047
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailsmonomer in an asymmetric unit, dimer as biological assembly

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Components

#1: Protein gephyrin


Mass: 45652.395 Da / Num. of mol.: 1 / Fragment: E domain, Residues 318-736 (NP_074056)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Rattus norvegicus (Norway rat) / Plasmid: pTWIN1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q03555
#2: Protein/peptide Glycine receptor beta chain precursor / Glycine receptor 58 kDa subunit


Mass: 1480.685 Da / Num. of mol.: 1 / Fragment: Residues 420-432 (SWS P20781)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: Rattus norvegicus (Norway rat) / Gene: Glrb / Plasmid: pTYB2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20781
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 311 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris-HCl (pH 7.5), 0.1-0.2 M KSCN, 25-30% PEG 4000, vapor diffusion, hanging drop, temperature 311K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 3, 2005
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 18221 / % possible obs: 89.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.096 / Χ2: 1.774 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID
2.38-2.4775.34.20.56314881.461
2.47-2.5681.34.50.4815971.3941
2.56-2.6884.24.90.42316501.4651
2.68-2.8286.750.34117081.4931
2.82-388.55.10.22617561.5711
3-3.2390.450.15417911.6811
3.23-3.5595.34.90.09719011.8791
3.55-4.0797.94.90.06719582.0121
4.07-5.1398.14.90.04820132.0711
5.13-5097.64.70.04920742.3981

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Phasing

Phasing MRRfactor: 0.374 / Cor.coef. Fo:Fc: 0.653
Highest resolutionLowest resolution
Rotation4.5 Å40.43 Å
Translation4.5 Å40.43 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.883 / SU B: 21.059 / SU ML: 0.243 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.481 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.272 934 5.1 %RANDOM
Rwork0.192 ---
all0.196 ---
obs-18182 93.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--2.46 Å20 Å2
3----2.33 Å2
Refinement stepCycle: LAST / Resolution: 2.41→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3298 0 0 150 3448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223361
X-RAY DIFFRACTIONr_bond_other_d0.0020.023167
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9884569
X-RAY DIFFRACTIONr_angle_other_deg0.83937377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0275430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08524.388139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03715576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2611524
X-RAY DIFFRACTIONr_chiral_restr0.1010.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023717
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02609
X-RAY DIFFRACTIONr_nbd_refined0.2070.2645
X-RAY DIFFRACTIONr_nbd_other0.1870.23333
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21560
X-RAY DIFFRACTIONr_nbtor_other0.0850.22069
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2135
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3010.215
X-RAY DIFFRACTIONr_mcbond_it0.7931.52752
X-RAY DIFFRACTIONr_mcbond_other0.1081.5873
X-RAY DIFFRACTIONr_mcangle_it0.90223505
X-RAY DIFFRACTIONr_scbond_it1.37831331
X-RAY DIFFRACTIONr_scangle_it2.1134.51064
LS refinement shellResolution: 2.41→2.469 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 55 -
Rwork0.272 995 -
obs-1050 74.89 %
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)
11.7925-0.33210.03021.09970.72617.0280.04120.2004-0.0225-0.10710.0843-0.0883-0.10750.4807-0.1254-0.27140.03270.03120.0008-0.0022-0.153715.95911.097-51.673
23.9091.4041-0.87251.781-0.64351.60420.1112-0.5217-0.06090.4938-0.1904-0.0749-0.16040.21630.0792-0.11920.0027-0.0222-0.03670.0179-0.16488.44711.681-18.188
35.3519-1.4412.84247.38692.800410.9681-0.1938-0.33760.0980.3644-0.00980.4638-0.4499-0.69010.20360.08760.0225-0.0133-0.116-0.0057-0.1065-2.30633.795-26.447
43.10931.10910.22596.9854-3.9738.8858-0.22750.27350.0794-0.86060.39280.81950.4495-0.7551-0.16530.0894-0.0993-0.03260.02410.0447-0.05755.89818.579-84.809
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA342 - 36525 - 48
21AA462 - 496145 - 179
32AA318 - 3411 - 24
42AA497 - 653180 - 336
53AA654 - 736337 - 419
63PB398 - 4101 - 13
74AA366 - 46149 - 144

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