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- PDB-1t3e: Structural basis of dynamic glycine receptor clustering -

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Basic information

Entry
Database: PDB / ID: 1t3e
TitleStructural basis of dynamic glycine receptor clustering
Components
  • 49-mer fragment of Glycine receptor beta chain
  • Gephyrin
KeywordsSTRUCTURAL PROTEIN/SIGNALING PROTEIN / alfa-beta / STRUCTURAL PROTEIN-SIGNALING PROTEIN COMPLEX
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: 3.25 Å
AuthorsSola, M. / Bavro, V.N. / Timmins, J. / Franz, T. / Ricard-Blum, S. / Schoehn, G. / Ruigrok, R.W.H. / Paarmann, I. / Saiyed, T. / O'Sullivan, G.A.
CitationJournal: Embo J. / Year: 2004
Title: Structural basis of dynamic glycine receptor clustering by gephyrin
Authors: Sola, M. / Bavro, V.N. / Timmins, J. / Franz, T. / Ricard-Blum, S. / Schoehn, G. / Ruigrok, R.W.H. / Paarmann, I. / Saiyed, T. / O'Sullivan, G.A. / Schmitt, B. / Betz, H. / Weissenhorn, W.
History
DepositionApr 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gephyrin
B: Gephyrin
P: 49-mer fragment of Glycine receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,79311
Polymers97,0243
Non-polymers7698
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)161.547, 161.547, 126.252
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Cell settinghexagonal
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHETYRTYRAA321 - 3606 - 45
21PHEPHETYRTYRBB321 - 3606 - 45
32ARGARGASNASNAA466 - 512151 - 197
42ARGARGASNASNBB466 - 512151 - 197
53ASPASPASPASPAA524 - 613209 - 298
63ASPASPASPASPBB524 - 613209 - 298
74ARGARGTRPTRPAA618 - 680303 - 365
84ARGARGTRPTRPBB618 - 680303 - 365
95PROPROALAALAAA685 - 689370 - 374
105PROPROALAALABB685 - 689370 - 374
116LEULEUTHRTHRAA709 - 716394 - 401
126LEULEUTHRTHRBB709 - 716394 - 401
137LEULEULEULEUAA722 - 736407 - 421
147LEULEULEULEUBB722 - 736407 - 421

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Components

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


Mass: 45947.734 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GPHN,GPH / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q03555
#2: Protein/peptide 49-mer fragment of Glycine receptor beta chain / Glycine receptor 58 kDa subunit


Mass: 5128.798 Da / Num. of mol.: 1 / Fragment: Gephyrin binding region (residues 378-426)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Description: modified with a TEV site / Gene: GLRB / Plasmid: pMAL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P20781
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4

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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: 4.9 Å3/Da / Density % sol: 74.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Li2SO4, pH 6., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 27162 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.108 / Net I/σ(I): 7.8
Reflection shellResolution: 3.25→3.33 Å / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 1.6 / Num. unique all: 11074 / % possible all: 97.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Unbound gephyrin (not published)

Resolution: 3.25→50 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.859 / SU B: 27.098 / SU ML: 0.448 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.372 / ESU R Free: 0.484
RfactorNum. reflection% reflectionSelection details
Rfree0.30306 1446 5.1 %RANDOM
Rwork0.24285 ---
all0.2458 28617 --
obs0.2458 27162 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.726 Å2
Baniso -1Baniso -2Baniso -3
1-6.82 Å23.41 Å20 Å2
2--6.82 Å20 Å2
3----10.24 Å2
Refinement stepCycle: LAST / Resolution: 3.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6203 0 40 0 6243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226357
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.9838651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0235816
X-RAY DIFFRACTIONr_chiral_restr0.0780.21003
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024783
X-RAY DIFFRACTIONr_nbd_refined0.2350.23081
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2237
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0090.21
X-RAY DIFFRACTIONr_mcbond_it0.831.54096
X-RAY DIFFRACTIONr_mcangle_it1.50726640
X-RAY DIFFRACTIONr_scbond_it1.10832261
X-RAY DIFFRACTIONr_scangle_it2.1044.52011
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1048tight positional0.040.05
960medium positional0.330.5
1048tight thermal0.060.5
960medium thermal0.372
LS refinement shellResolution: 3.25→3.334 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.406 107
Rwork0.336 1977
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)
1-0.0879-0.02290.32362.66830.14791.5790.0434-0.08340.02010.3340.0023-0.158-0.12270.1016-0.04570.3942-0.01080.02710.19360.00080.3748.0131144.06814.3138
25.48052.53271.02133.66672.37875.3398-0.35690.3170.23550.07590.31910.0375-0.04270.00630.03780.1059-0.02160.07660.20780.01110.4588-3.583186.5205-20.6361
34.6561.17562.18434.7928-0.02322.72470.0287-0.06990.2928-0.18580.0407-0.6496-0.63530.5358-0.06950.3251-0.18310.13290.2681-0.0130.558923.0682143.5286-3.3591
40.7309-0.3410.62092.4798-0.60581.1620.01340.0086-0.2046-0.16450.04820.17180.05710.0067-0.06160.27540.02110.02480.15290.00120.4104-3.0624116.7752-9.5225
55.87147.1408-1.43998.20973.48518.34970.1271-0.3532-0.53871.2379-0.3134-1.0097-0.27351.15940.18630.65130.0689-0.39110.1020.11680.499216.2022171.846320.4616
63.05940.3433-0.15390.99020.14026.5881-0.0909-0.1562-0.2061-0.15630.21-0.57440.6170.5168-0.11910.28530.11810.12830.2336-0.02830.534619.5985119.355-11.7177
7-0.3168-0.6982-0.81354.83731.0393-0.9665-0.4368-0.14570.1411-0.13190.55180.3499-0.16120.2078-0.1150.35150.03720.02610.3046-0.09250.3239-0.5446123.60410.9762
841.3633-66.6882-81.89787.164117.427128.66750.1537-0.2092-0.31754.302-1.9483-2.9421-6.1871.28491.79460.3584-0.0019-0.00340.360.00210.361919.1267124.3745-21.7937
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A318 - 342
2X-RAY DIFFRACTION1B343 - 369
3X-RAY DIFFRACTION1B459 - 495
4X-RAY DIFFRACTION1A496 - 653
5X-RAY DIFFRACTION2A370 - 458
6X-RAY DIFFRACTION3A654 - 697
7X-RAY DIFFRACTION3A700 - 736
8X-RAY DIFFRACTION4B318 - 342
9X-RAY DIFFRACTION4A343 - 369
10X-RAY DIFFRACTION4A459 - 495
11X-RAY DIFFRACTION4B496 - 653
12X-RAY DIFFRACTION5B370 - 430
13X-RAY DIFFRACTION5B445 - 458
14X-RAY DIFFRACTION6B654 - 736
15X-RAY DIFFRACTION7A2 - 8
16X-RAY DIFFRACTION7B1 - 5
17X-RAY DIFFRACTION8P301 - 305

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