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- PDB-5vdh: Crystal Structure of Human Glycine Receptor alpha-3 Bound to AM-3... -

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Basic information

Entry
Database: PDB / ID: 5vdh
TitleCrystal Structure of Human Glycine Receptor alpha-3 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 / 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 / Chem-IVM / Glycine receptor subunit alpha-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 1.2Jul 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
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
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)216,62927
Polymers209,2875
Non-polymers7,34222
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28080 Å2
ΔGint-297 kcal/mol
Surface area64980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.065, 119.065, 429.934
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
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: 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
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
16ALAALAILEILEBB6 - 3446 - 344
26ALAALAILEILEDD6 - 3446 - 344
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 / Sugars , 2 types, 6 molecules ABCDE

#1: Protein
Glycine receptor subunit alpha-3 /


Mass: 41857.402 Da / Num. of mol.: 5
Fragment: UNP residues 34-342, ATG linker, UNP residues 419-460
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
#7: 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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Non-polymers , 6 types, 77 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: isolated from a genetically manipulated source
Formula: C19H19N3O5S
#3: Chemical
ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
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 / Ivermectin


Mass: 875.093 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
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: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.86 Å3/Da / Density % sol: 68.16 %
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: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 11, 2014
RadiationMonochromator: Rosenbaum-Rock double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 73411 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.5
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.904 / % possible all: 100

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Processing

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

5tio


Resolution: 2.85→50 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.916 / SU B: 28.1 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.673 / ESU R Free: 0.308 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3666 5 %RANDOM
Rwork0.226 ---
obs0.227 69660 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 90.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20 Å20 Å2
2---1.25 Å20 Å2
3---2.49 Å2
Refinement stepCycle: LAST / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13513 0 495 56 14064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0214415
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213468
X-RAY DIFFRACTIONr_angle_refined_deg0.962.00719715
X-RAY DIFFRACTIONr_angle_other_deg0.7243.00430299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.98351695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09623.817600
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.384152236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4271563
X-RAY DIFFRACTIONr_chiral_restr0.0530.22270
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02115798
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023295
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)
11A202870.02
12B202870.02
21A203660.03
22C203660.03
31A202840.03
32D202840.03
41A204590.03
42E204590.03
51B202820.02
52C202820.02
61B202880.02
62D202880.02
71B203020.02
72E203020.02
81C202100.03
82D202100.03
91C203760.02
92E203760.02
101D203280.01
102E203280.01
LS refinement shellResolution: 2.85→2.92 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 262 -
Rwork0.3 5004 -
obs--98.6 %
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)
10.95570.05730.0243.31670.82151.57030.03510.2444-0.3186-0.4538-0.08180.07040.186-0.19870.04670.43850.01250.00760.2912-0.14360.128489.261112.7442.721
21.0262-0.20870.04882.91620.83141.61890.1523-0.0439-0.4060.4561-0.25240.3050.5913-0.32660.10010.542-0.12240.06050.2713-0.08630.2229483.507106.104466.029
31.31940.06170.34012.34640.74421.46680.2302-0.143-0.61020.85470.0098-0.35120.82010.0206-0.240.9107-0.027-0.20080.17950.02140.3386502.516101.592479.41
41.12180.44290.2342.29720.79821.53730.14340.1551-0.60540.30620.2749-0.99990.62770.5301-0.41830.53120.1909-0.2520.3645-0.27290.7216523.359106.053464.315
51.08640.01970.0532.60580.85091.67610.04430.372-0.4593-0.44310.2419-0.69630.15910.3553-0.28610.42190.03240.16350.396-0.26720.4047514.538112.911441.496
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 345
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION2B6 - 348
4X-RAY DIFFRACTION2B401 - 405
5X-RAY DIFFRACTION3C8 - 345
6X-RAY DIFFRACTION3C401 - 405
7X-RAY DIFFRACTION4D3 - 345
8X-RAY DIFFRACTION4D401 - 404
9X-RAY DIFFRACTION5E8 - 345
10X-RAY DIFFRACTION5E401 - 406

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