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- PDB-5tin: Crystal Structure of Human Glycine Receptor alpha-3 Mutant N38Q B... -

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Basic information

Entry
Database: PDB / ID: 5tin
TitleCrystal Structure of Human Glycine Receptor alpha-3 Mutant N38Q 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 / neurotransmitter receptor activity / glycine binding / transmembrane transporter complex / chloride transmembrane transport / 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 / neurotransmitter receptor activity / glycine binding / transmembrane transporter complex / chloride transmembrane transport / 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: 2.61 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 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Oct 4, 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 / struct_ncs_dom_lim
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.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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: Glycine receptor subunit alpha-3
C: 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)212,10221
Polymers209,3575
Non-polymers2,74516
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25290 Å2
ΔGint-310 kcal/mol
Surface area64710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.301, 136.787, 192.495
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETILEILEAA8 - 3448 - 344
21METMETILEILEBB8 - 3448 - 344
12METMETTYRTYRAA8 - 3458 - 345
22METMETTYRTYRCC8 - 3458 - 345
13METMETILEILEAA8 - 3448 - 344
23METMETILEILEDD8 - 3448 - 344
14METMETTYRTYRAA8 - 3458 - 345
24METMETTYRTYREE8 - 3458 - 345
15METMETILEILEBB8 - 3448 - 344
25METMETILEILECC8 - 3448 - 344
16ALAALALYSLYSBB6 - 3466 - 346
26ALAALALYSLYSDD6 - 3466 - 346
17METMETILEILEBB8 - 3448 - 344
27METMETILEILEEE8 - 3448 - 344
18METMETILEILECC8 - 3448 - 344
28METMETILEILEDD8 - 3448 - 344
19METMETTYRTYRCC8 - 3458 - 345
29METMETTYRTYREE8 - 3458 - 345
110METMETILEILEDD8 - 3448 - 344
210METMETILEILEEE8 - 3448 - 344

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

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Glycine receptor subunit alpha-3


Mass: 41871.426 Da / Num. of mol.: 5 / Fragment: UNP residues 34-460, with 343-418 deleted / Mutation: N38Q
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

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Non-polymers , 5 types, 416 molecules

#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


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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 4.53 Å3/Da / Density % sol: 72.84 %
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: Dec 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. obs: 105901 / % possible obs: 98.4 % / Redundancy: 7.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.138 / Net I/σ(I): 11.42
Reflection shellResolution: 2.61→2.7 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.7 / CC1/2: 0.749 / % possible all: 86.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-20002.3.8data collection
HKL-20002.3.8data scaling
PDB_EXTRACT3.2data extraction
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RIF

3rif


Resolution: 2.61→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.927 / SU B: 15.475 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.207 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2006 1.9 %RANDOM
Rwork0.204 ---
obs0.205 105901 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.86 Å2
Baniso -1Baniso -2Baniso -3
1--4.26 Å20 Å20 Å2
2--6.32 Å20 Å2
3----2.05 Å2
Refinement stepCycle: LAST / Resolution: 2.61→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13562 0 171 400 14133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214109
X-RAY DIFFRACTIONr_bond_other_d0.0030.0213198
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.96619239
X-RAY DIFFRACTIONr_angle_other_deg0.793.00130131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66351695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13623.581606
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.496152264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5191572
X-RAY DIFFRACTIONr_chiral_restr0.0610.22165
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02115718
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023331
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_it1.8634.0536810
X-RAY DIFFRACTIONr_mcbond_other1.8624.0526806
X-RAY DIFFRACTIONr_mcangle_it2.9916.0768495
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)
11A205550.04
12B205550.04
21A207040.03
22C207040.03
31A206580.03
32D206580.03
41A206760.03
42E206760.03
51B205980.04
52C205980.04
61B207490.03
62D207490.03
71B205590.03
72E205590.03
81C206440.03
82D206440.03
91C207110.03
92E207110.03
101D206130.02
102E206130.02
LS refinement shellResolution: 2.61→2.68 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 132 -
Rwork0.307 6679 -
obs--84.6 %
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)
10.2670.05350.1360.63090.57420.60440.0347-0.1641-0.00170.0443-0.10060.03310.0393-0.20240.06590.1927-0.02610.00320.216-0.07270.0475-55.607-24.82229.59
20.36690.12460.15060.47690.59810.89960.01740.0230.1158-0.0499-0.05750.0605-0.1235-0.11620.04010.21020.05210.00810.0789-0.01950.066-44.071-9.29913.613
30.2382-0.0103-0.08530.30980.52070.99310.0619-0.02250.0457-0.06150.0286-0.0722-0.1470.0027-0.09050.22090.01120.01290.094-0.06660.0615-19.187-12.14416.622
40.26060.0003-0.05960.63710.6980.83250.0624-0.1332-0.01120.04440.0772-0.12080.05080.1157-0.13960.21480.0505-0.05270.1493-0.05510.0559-15.365-29.80134.136
50.36710.01820.07380.90420.74040.72130.0539-0.2836-0.06540.1409-0.0284-0.03340.1846-0.0672-0.02550.2686-0.0212-0.02140.22170.04970.015-37.979-37.80242.191
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 401
2X-RAY DIFFRACTION2B6 - 401
3X-RAY DIFFRACTION3C8 - 401
4X-RAY DIFFRACTION4D5 - 401
5X-RAY DIFFRACTION5E8 - 401

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