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- PDB-5obh: Crystal structure of glycine binding protein in complex with bicu... -

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Basic information

Entry
Database: PDB / ID: 5obh
TitleCrystal structure of glycine binding protein in complex with bicuculline
ComponentsSoluble acetylcholine receptor
KeywordsSIGNALING PROTEIN / receptor / acetylcholine binding
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / metal ion binding / identical protein binding / membrane
Similarity search - Function
Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / 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 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
triacetyl-beta-chitotriose / Chem-J94 / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDawson, A. / Hunter, W.N. / Jones, M.
CitationJournal: Chembiochem / Year: 2020
Title: A Structural Rationale for N-Methylbicuculline Acting as a Promiscuous Competitive Antagonist of Inhibitory Pentameric Ligand-Gated Ion Channels.
Authors: Jones, M.J. / Dawson, A. / Hales, T.G. / Hunter, W.N.
History
DepositionJun 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
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 / entity_name_com / 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_molecule_features / 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 2.1Jun 30, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Jan 17, 2024Group: 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 2.3Oct 16, 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: Soluble acetylcholine receptor
B: Soluble acetylcholine receptor
C: Soluble acetylcholine receptor
D: Soluble acetylcholine receptor
E: Soluble acetylcholine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,70818
Polymers141,5485
Non-polymers3,15913
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15110 Å2
ΔGint-120 kcal/mol
Surface area43620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.243, 132.236, 132.631
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: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA20 - 22520 - 225
21ARGARGBB20 - 22520 - 225
12ALAALAAA20 - 22620 - 226
22ALAALACC20 - 22620 - 226
13ARGARGAA20 - 22520 - 225
23ARGARGDD20 - 22520 - 225
14ALAALAAA20 - 22620 - 226
24ALAALAEE20 - 22620 - 226
15ARGARGBB20 - 22420 - 224
25ARGARGCC20 - 22420 - 224
16ARGARGBB20 - 22520 - 225
26ARGARGDD20 - 22520 - 225
17ARGARGBB20 - 22420 - 224
27ARGARGEE20 - 22420 - 224
18ARGARGCC20 - 22420 - 224
28ARGARGDD20 - 22420 - 224
19ALAALACC20 - 22620 - 226
29ALAALAEE20 - 22620 - 226
110ARGARGDD20 - 22420 - 224
210ARGARGEE20 - 22420 - 224

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
Soluble acetylcholine receptor / Glycine binding protein


Mass: 28309.680 Da / Num. of mol.: 5
Mutation: T53F, Q74R, Y110A, I135S, G162E, S206K, C207G, C208T, P209G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WSF8

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Sugars , 2 types, 3 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: isolated from a natural 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 , 3 types, 414 molecules

#3: Chemical
ChemComp-J94 / (5S)-6,6-dimethyl-5-[(6R)-8-oxo-6,8-dihydrofuro[3,4-e][1,3]benzodioxol-6-yl]-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-g]isoquinolin-6-ium


Mass: 382.387 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H20NO6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.21 Å3/Da / Density % sol: 44.26 % / Description: block
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Reservoir buffer: 0.2 M ammonium formate, 20 % PEG 3350 Protein buffer: 50 mM tris, 250 mM NaCl, pH 7.5. 2 mM bicuculline

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54157 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 16, 2016
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54157 Å / Relative weight: 1
ReflectionResolution: 2.4→46.82 Å / Num. obs: 49817 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 48.1 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.9
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.776 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4510 / CC1/2: 0.826 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5oan

5oan


Resolution: 2.4→46.82 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.923 / SU B: 10.024 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.479 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24944 2447 4.9 %RANDOM
Rwork0.22955 ---
obs0.23054 47302 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.177 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20 Å2
2--0.27 Å20 Å2
3----1.38 Å2
Refinement stepCycle: 1 / Resolution: 2.4→46.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8192 0 215 404 8811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0198636
X-RAY DIFFRACTIONr_bond_other_d0.0060.027629
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.94711811
X-RAY DIFFRACTIONr_angle_other_deg0.919317742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64651020
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70324.212406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.774151370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4111555
X-RAY DIFFRACTIONr_chiral_restr0.080.21302
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219975
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021773
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_it2.7554.3474100
X-RAY DIFFRACTIONr_mcbond_other2.7554.3494101
X-RAY DIFFRACTIONr_mcangle_it4.6346.495109
X-RAY DIFFRACTIONr_mcangle_other4.6296.495109
X-RAY DIFFRACTIONr_scbond_it2.7734.9544536
X-RAY DIFFRACTIONr_scbond_other2.7734.9564537
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6377.3156696
X-RAY DIFFRACTIONr_long_range_B_refined7.74650.5349092
X-RAY DIFFRACTIONr_long_range_B_other7.73950.5169046
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)
11A127240.06
12B127240.06
21A128480.06
22C128480.06
31A128520.05
32D128520.05
41A127740.05
42E127740.05
51B126000.06
52C126000.06
61B127620.05
62D127620.05
71B126340.06
72E126340.06
81C126960.06
82D126960.06
91C126840.07
92E126840.07
101D126840.05
102E126840.05
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 211 -
Rwork0.283 3411 -
obs--99.94 %

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