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

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Basic information

Entry
Database: PDB / ID: 5vdi
TitleCrystal Structure of Human Glycine Receptor alpha-3 Mutant N38Q Bound to AM-3607, Glycine, and Ivermectin
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 / 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
Chem-7C6 / GLYCINE / Chem-IVM / Glycine receptor subunit alpha-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsShaffer, P.L. / Huang, X. / Chen, H.
CitationJournal: Structure / Year: 2017
Title: Crystal Structures of Human GlyR alpha 3 Bound to Ivermectin.
Authors: Huang, X. / Chen, H. / Shaffer, P.L.
History
DepositionApr 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Refinement description / Category: citation / software
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
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)216,44225
Polymers209,3575
Non-polymers7,08520
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27490 Å2
ΔGint-285 kcal/mol
Surface area63970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.006, 136.000, 191.635
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
16PROPROLYSLYSBB7 - 3467 - 346
26PROPROLYSLYSDD7 - 3467 - 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
1
2
3
4
5
6
7
8
9
10

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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 34-342, ATG linker, UNP residues 419-460
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, 136 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-IVM / (2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside / 22,23-DIHYDROAVERMECTIN B1A / IVERMECTIN


Mass: 875.093 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C48H74O14 / Comment: antiparasitic*YM
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 4.49 Å3/Da / Density % sol: 72.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM calcium chloride, 22.5-27.5% PEG350 MME, 100 mM MES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.2827 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 9, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2827 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 65697 / % possible obs: 99.7 % / Redundancy: 8 % / Rmerge(I) obs: 0.203 / Net I/σ(I): 6
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.896 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5TIN

5tin


Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.811 / SU B: 38.493 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.961 / ESU R Free: 0.373 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1224 1.9 %RANDOM
Rwork0.232 ---
obs0.233 64390 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 61.87 Å2
Baniso -1Baniso -2Baniso -3
1--11.33 Å20 Å20 Å2
2--10.2 Å20 Å2
3---1.13 Å2
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13509 0 480 116 14105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0214396
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213474
X-RAY DIFFRACTIONr_angle_refined_deg1.1242.00619684
X-RAY DIFFRACTIONr_angle_other_deg0.7513.00430310
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.27551693
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2423.74599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.933152242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5321565
X-RAY DIFFRACTIONr_chiral_restr0.0590.22263
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02115773
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023302
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
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)
11A203780.04
12B203780.04
21A206150.02
22C206150.02
31A206990.03
32D206990.03
41A206880.04
42E206880.04
51B205440.03
52C205440.03
61B205530.03
62D205530.03
71B204980.03
72E204980.03
81C205040.03
82D205040.03
91C205880.03
92E205880.03
101D206450.03
102E206450.03
LS refinement shellResolution: 3.08→3.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 77 -
Rwork0.378 3913 -
obs--81.4 %
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)
10.58470.26810.38411.17381.11291.24420.0258-0.31110.0310.068-0.19660.14660.0659-0.34520.17070.5845-0.03850.02260.6076-0.11480.0387-55.613-24.82329.584
20.71750.30560.30930.82360.90071.2908-0.0875-0.02350.154-0.0982-0.07060.1464-0.157-0.13280.15810.64730.1015-0.03720.4437-0.04940.0457-44.07-9.29913.608
30.42940.0391-0.01720.68010.8621.42860.0118-0.02490.0899-0.04280.0272-0.0511-0.11350.0319-0.0390.61330.0078-0.00530.4678-0.0690.0368-19.182-12.14816.618
40.31010.19370.16981.00320.89671.02560.049-0.2348-0.07670.06090.0832-0.09180.09450.1609-0.13220.6340.0666-0.07630.5778-0.03360.0471-15.363-29.80534.139
50.67690.32950.34441.41151.28081.3310.0873-0.5084-0.09950.1391-0.09320.03660.1686-0.14550.00590.736-0.0426-0.02940.57830.08580.023-37.985-37.80742.191
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 345
2X-RAY DIFFRACTION1A401 - 405
3X-RAY DIFFRACTION2B6 - 348
4X-RAY DIFFRACTION2B401 - 404
5X-RAY DIFFRACTION3C8 - 345
6X-RAY DIFFRACTION3C501 - 503
7X-RAY DIFFRACTION4D7 - 347
8X-RAY DIFFRACTION4D401 - 405
9X-RAY DIFFRACTION5E8 - 345
10X-RAY DIFFRACTION5E401 - 403

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