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- PDB-5tio: Crystal Structure of Human Glycine Receptor alpha-3 Bound to AM-3607 -

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Basic information

Entry
Database: PDB / ID: 5tio
TitleCrystal Structure of Human Glycine Receptor alpha-3 Bound to AM-3607
ComponentsGlycine 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 / glycine binding / 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 ...glycine-gated chloride ion channel activity / glycine-gated chloride channel complex / Neurotransmitter receptors and postsynaptic signal transmission / extracellularly glycine-gated chloride channel activity / glycine binding / 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 / perikaryon / postsynaptic membrane / neuron projection / intracellular membrane-bounded organelle / dendrite / synapse / 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
Chem-7C6 / GLYCINE / Glycine receptor subunit alpha-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsShaffer, P.L. / Huang, X. / Chen, H.
CitationJournal: To Be Published
Title: Crystal Structures of Human GlyRa3 Bound to a Novel Class of Potentiators with Efficacy in a Mouse Model of Neuropathic Pain
Authors: Huang, X. / Shaffer, P.L. / Ayube, S. / Bregman, H. / Chen, H. / Lehto, S.G. / Luther, J.A. / Matson, D.J. / McDonough, S.I. / Michelsen, K. / Plant, M.M. / Schneider, S. / Simard, J.R. / ...Authors: Huang, X. / Shaffer, P.L. / Ayube, S. / Bregman, H. / Chen, H. / Lehto, S.G. / Luther, J.A. / Matson, D.J. / McDonough, S.I. / Michelsen, K. / Plant, M.M. / Schneider, S. / Simard, J.R. / Teffera, Y. / Yi, S. / Zhang, M. / DiMauro, E.F. / Gingras, J.
History
DepositionOct 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 4, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Glycine receptor subunit alpha-3
A: Glycine receptor subunit alpha-3
B: Glycine receptor subunit alpha-3
D: Glycine receptor subunit alpha-3
E: Glycine receptor subunit alpha-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,21821
Polymers209,2875
Non-polymers2,93116
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25730 Å2
ΔGint-274 kcal/mol
Surface area64760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.120, 119.120, 429.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A
12C
22B
13C
23D
14C
24E
15A
25B
16A
26D
17A
27E
18B
28D
19B
29E
110D
210E

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTYRTYRCA8 - 3458 - 345
21METMETTYRTYRAB8 - 3458 - 345
12METMETILEILECA8 - 3448 - 344
22METMETILEILEBC8 - 3448 - 344
13METMETILEILECA8 - 3448 - 344
23METMETILEILEDD8 - 3448 - 344
14METMETTYRTYRCA8 - 3458 - 345
24METMETTYRTYREE8 - 3458 - 345
15METMETILEILEAB8 - 3448 - 344
25METMETILEILEBC8 - 3448 - 344
16METMETILEILEAB8 - 3448 - 344
26METMETILEILEDD8 - 3448 - 344
17METMETTYRTYRAB8 - 3458 - 345
27METMETTYRTYREE8 - 3458 - 345
18ALAALAILEILEBC6 - 3446 - 344
28ALAALAILEILEDD6 - 3446 - 344
19METMETILEILEBC8 - 3448 - 344
29METMETILEILEEE8 - 3448 - 344
110METMETILEILEDD8 - 3448 - 344
210METMETILEILEEE8 - 3448 - 344

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
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: Chemical
ChemComp-7C6 / (3S,3aS,9bS)-2-[(2H-1,3-benzodioxol-5-yl)sulfonyl]-3,5-dimethyl-1,2,3,3a,5,9b-hexahydro-4H-pyrrolo[3,4-c][1,6]naphthyridin-4-one


Mass: 401.436 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C19H19N3O5S
#3: Chemical
ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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: 3.87 Å3/Da / Density % sol: 68.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM Calcium Chloride, 22.5-27.5% PEG-350MME, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 47335 / % possible obs: 99.8 % / Redundancy: 13.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.131 / Net I/σ(I): 16.2
Reflection shellResolution: 3.25→3.37 Å / Redundancy: 10.4 % / Rmerge(I) obs: 1.061 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.74 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-20002.3.8data scaling
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RIF

4rif


Resolution: 3.25→50 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc free: 0.842 / SU B: 44.182 / SU ML: 0.327 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.453 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2490 5 %RANDOM
Rwork0.233 ---
obs0.234 47335 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 117.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.49 Å20 Å20 Å2
2--4.49 Å20 Å2
3----8.98 Å2
Refinement stepCycle: LAST / Resolution: 3.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13543 0 184 0 13727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0214105
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213163
X-RAY DIFFRACTIONr_angle_refined_deg1.0481.96719240
X-RAY DIFFRACTIONr_angle_other_deg0.7473.00130054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57451695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22323.702605
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.233152251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6921568
X-RAY DIFFRACTIONr_chiral_restr0.0580.22170
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02115718
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023315
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_it2.15.6236810
X-RAY DIFFRACTIONr_mcbond_other2.15.6236806
X-RAY DIFFRACTIONr_mcangle_it3.4778.4398495
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11C207290.02
12A207290.02
21C206560.02
22B206560.02
31C205810.02
32D205810.02
41C207390.02
42E207390.02
51A206570.02
52B206570.02
61A206580.02
62D206580.02
71A208130.02
72E208130.02
81B206570.02
82D206570.02
91B206580.02
92E206580.02
101D206940.01
102E206940.01
LS refinement shellResolution: 3.25→3.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 174 -
Rwork0.298 3334 -
obs--97.85 %
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)
11.9094-0.21050.56232.61450.62651.84740.3646-0.1911-0.83660.7126-0.0053-0.33660.99720.0034-0.35930.8253-0.0352-0.2260.03380.02860.7641503.479102.909479.812
21.34810.49490.11073.54710.97952.12930.08270.3031-0.3724-0.4145-0.13770.05580.2855-0.30730.05510.33350.035-0.00080.1576-0.16950.4156489.767114.109442.933
31.1537-0.10970.17443.23290.80312.06430.2473-0.0477-0.51050.3881-0.26830.21430.7033-0.44140.0210.3635-0.17950.0570.1402-0.12620.6701482.645107.327466.084
41.40890.24190.13212.55030.97512.14930.21780.1856-0.66320.40270.2364-0.83480.84570.6843-0.45410.42430.2913-0.33810.2738-0.32581.1202523.499107.547465.263
51.3716-0.01630.25922.88480.9072.32360.19890.5246-0.5279-0.50480.1554-0.50590.24320.5333-0.35430.2280.09120.14190.2999-0.33640.7742515.01114.089442.078
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C8 - 345
2X-RAY DIFFRACTION1C401 - 403
3X-RAY DIFFRACTION2A8 - 345
4X-RAY DIFFRACTION2A401 - 402
5X-RAY DIFFRACTION3B6 - 348
6X-RAY DIFFRACTION3B401 - 403
7X-RAY DIFFRACTION4D3 - 345
8X-RAY DIFFRACTION4E401
9X-RAY DIFFRACTION5E8 - 345
10X-RAY DIFFRACTION5E402 - 403

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