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- PDB-5cfb: Crystal Structure of Human Glycine Receptor alpha-3 Bound to Stry... -

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Basic information

Entry
Database: PDB / ID: 5cfb
TitleCrystal Structure of Human Glycine Receptor alpha-3 Bound to Strychnine
ComponentsGlycine receptor subunit alpha-3,Glycine receptor subunit alpha-3
KeywordsTRANSPORT PROTEIN / ligand-gated Ion Channel / Neurotransmitter receptor / Membrane Protein / cys-loop receptor
Function / homology
Function and homology information


glycine-gated chloride ion channel activity / glycine-gated chloride channel complex / Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated chloride channel activity / neurotransmitter receptor activity / glycine binding / transmembrane transporter complex / response to amino acid / chloride transmembrane transport / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential ...glycine-gated chloride ion channel activity / glycine-gated chloride channel complex / Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated chloride channel activity / neurotransmitter receptor activity / glycine binding / transmembrane transporter complex / response to amino acid / chloride transmembrane transport / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / protein homooligomerization / transmembrane signaling receptor activity / postsynaptic membrane / perikaryon / neuron projection / intracellular membrane-bounded organelle / synapse / dendrite / metal ion binding / plasma membrane
Similarity search - Function
Glycine receptor alpha3 / Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / 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 ...Glycine receptor alpha3 / Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Distorted Sandwich / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
STRYCHNINE / Glycine receptor subunit alpha-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsShaffer, P.L. / Huang, X. / Chen, H.
CitationJournal: Nature / Year: 2015
Title: Crystal structure of human glycine receptor-alpha 3 bound to antagonist strychnine.
Authors: Huang, X. / Chen, H. / Michelsen, K. / Schneider, S. / Shaffer, P.L.
History
DepositionJul 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Jul 20, 2016Group: Data collection
Revision 1.4Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
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.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Glycine receptor subunit alpha-3,Glycine receptor subunit alpha-3
B: Glycine receptor subunit alpha-3,Glycine receptor subunit alpha-3
C: Glycine receptor subunit alpha-3,Glycine receptor subunit alpha-3
D: Glycine receptor subunit alpha-3,Glycine receptor subunit alpha-3
E: Glycine receptor subunit alpha-3,Glycine receptor subunit alpha-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,47115
Polymers209,2875
Non-polymers3,18410
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25360 Å2
ΔGint-133 kcal/mol
Surface area66830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.242, 143.198, 180.054
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glycine receptor subunit alpha-3,Glycine receptor subunit alpha-3


Mass: 41857.402 Da / Num. of mol.: 5 / Fragment: UNP residues 34-460, with 343-418 deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLRA3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75311
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SY9 / STRYCHNINE


Mass: 334.412 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H22N2O2 / Comment: alkaloid*YM
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 4.32 Å3/Da / Density % sol: 71.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 30-33% PEG-400, 200 mM magnesium chloride, 100 mM potassium chloride, 25 mM sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 68041 / % possible obs: 97.8 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.064 / Rrim(I) all: 0.211 / Χ2: 1.273 / Net I/av σ(I): 12.906 / Net I/σ(I): 5.3 / Num. measured all: 684083
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3-3.115.858640.560.4530.74885.4
3.11-3.237.364280.6580.4240.76893.8
3.23-3.38967900.8310.2920.856990.8980.947
3.38-3.5610.569160.9190.2090.9781000.6750.708
3.56-3.7811.268960.9570.1461.131000.4820.505
3.78-4.0711.369030.980.0961.3471000.3230.337
4.07-4.4811.369420.9840.0671.5031000.2260.236
4.48-5.1311.369640.9890.0521.5451000.1740.182
5.13-6.4611.370590.990.0461.3571000.1540.161
6.46-5010.772790.9830.051.83499.70.1650.173

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
SCALEPACK0.98data scaling
PDB_EXTRACT3.15data extraction
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TNV

4tnv


Resolution: 3.04→50 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.884 / SU B: 53.59 / SU ML: 0.401 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.93 / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2826 3426 5 %RANDOM
Rwork0.2603 ---
obs0.2615 64544 96.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 255.17 Å2 / Biso mean: 120.798 Å2 / Biso min: 34.31 Å2
Baniso -1Baniso -2Baniso -3
1-12.93 Å20 Å2-0 Å2
2---10.89 Å2-0 Å2
3----2.03 Å2
Refinement stepCycle: final / Resolution: 3.04→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13317 0 223 0 13540
Biso mean--123.87 --
Num. residues----1684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213932
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212879
X-RAY DIFFRACTIONr_angle_refined_deg1.061.97419061
X-RAY DIFFRACTIONr_angle_other_deg0.7083.00129320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86951677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3323.813598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.136152146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9811566
X-RAY DIFFRACTIONr_chiral_restr0.060.22207
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02115536
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023255
X-RAY DIFFRACTIONr_mcbond_it2.6659.0276729
X-RAY DIFFRACTIONr_mcbond_other2.6629.0276728
X-RAY DIFFRACTIONr_mcangle_it4.46913.5398399
LS refinement shellResolution: 3.042→3.121 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 184 -
Rwork0.376 3585 -
all-3769 -
obs--73.92 %
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)
11.3262-0.7454-1.18183.15150.61742.24650.20140.142-0.0976-0.5854-0.17410.7284-0.1959-0.3856-0.02740.13470.0163-0.18480.63630.05820.3229120.193150.21519.342
24.8834-0.4829-2.00692.04811.8863.1130.53890.65240.155-0.5858-0.1826-0.2675-0.5228-0.099-0.35630.48360.16630.10230.48030.09970.0724161.999145.868-15.57
31.52980.1511-0.3031.6602-0.28991.0407-0.09350.2329-0.2855-0.16920.07280.47040.191-0.19330.02070.0623-0.1141-0.03580.35830.00750.2248129.013125.22226.206
44.95040.7559-2.040.8717-0.77922.5017-0.21540.1430.1472-0.2556-0.0487-0.08930.09350.24920.26410.2439-0.00830.120.33480.04830.159172.732130.975-5.261
50.28540.18890.06562.1482-0.12690.9113-0.11560.0627-0.06330.34380.0842-0.09520.29760.00790.03140.27780.03280.04040.33740.03720.0379147.753127.85145.944
63.43632.5612-2.76252.5302-2.94145.1169-0.7064-0.1323-0.6681-0.77740.0786-1.02170.3557-0.11990.62780.45810.0040.58140.2689-0.10820.8345186.42139.3479.672
71.0756-0.0969-1.93833.514-0.20283.9535-0.07860.13480.04371.09310.1858-0.22330.01050.1769-0.10720.3460.0351-0.09130.5022-0.02430.1456150.607154.57651.241
81.68151.272-1.74111.7226-1.74375.8126-0.06980.10770.1108-0.3584-0.2011-0.43310.62691.02910.27080.21080.08850.2610.68490.0980.411183.567160.459.38
90.6146-0.29030.07351.93580.36351.21130.0428-0.0420.0275-0.10370.09010.2511-0.241-0.0897-0.13290.06010.06240.03830.35720.08930.0858133.82168.39134.802
102.5297-0.4369-1.70561.25940.0884.47770.0811-0.12930.1808-0.62290.2645-0.3554-0.42680.4294-0.34560.5456-0.150.3050.2861-0.04810.1872169.337164.932-6.678
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 219
2X-RAY DIFFRACTION2A220 - 347
3X-RAY DIFFRACTION3B1 - 219
4X-RAY DIFFRACTION4B220 - 347
5X-RAY DIFFRACTION5C1 - 219
6X-RAY DIFFRACTION6C220 - 347
7X-RAY DIFFRACTION7D1 - 219
8X-RAY DIFFRACTION8D220 - 347
9X-RAY DIFFRACTION9E1 - 219
10X-RAY DIFFRACTION10E220 - 347

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