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- PDB-6t9r: Aplysia californica AChBP in complex with a cytisine derivative -

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Basic information

Entry
Database: PDB / ID: 6t9r
TitleAplysia californica AChBP in complex with a cytisine derivative
ComponentsAcetylcholine binding protein
KeywordsHYDROLASE / Acetylcholine binding protein / nicotinic receptor surrogate
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / membrane / identical protein binding / metal ion binding
Similarity search - Function
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
Similarity search - Domain/homology
: / Chem-MXQ / PHOSPHATE ION / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsDavis, S. / Hunter, W.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: The thermodynamic profile and molecular interactions of a C(9)-cytisine derivative-binding acetylcholine-binding protein from Aplysia californica.
Authors: Davis, S. / Rego Campello, H. / Gallagher, T. / Hunter, W.N.
History
DepositionOct 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
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 / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 24, 2024Group: 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Acetylcholine binding protein
BBB: Acetylcholine binding protein
CCC: Acetylcholine binding protein
DDD: Acetylcholine binding protein
EEE: Acetylcholine binding protein
FFF: Acetylcholine binding protein
GGG: Acetylcholine binding protein
HHH: Acetylcholine binding protein
III: Acetylcholine binding protein
JJJ: Acetylcholine binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,434101
Polymers283,26810
Non-polymers10,16691
Water52,2252899
1
AAA: Acetylcholine binding protein
BBB: Acetylcholine binding protein
CCC: Acetylcholine binding protein
DDD: Acetylcholine binding protein
EEE: Acetylcholine binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,76351
Polymers141,6345
Non-polymers5,12946
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24090 Å2
ΔGint-145 kcal/mol
Surface area40770 Å2
MethodPISA
2
FFF: Acetylcholine binding protein
GGG: Acetylcholine binding protein
HHH: Acetylcholine binding protein
III: Acetylcholine binding protein
JJJ: Acetylcholine binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,67150
Polymers141,6345
Non-polymers5,03745
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24000 Å2
ΔGint-141 kcal/mol
Surface area39920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.466, 132.874, 131.086
Angle α, β, γ (deg.)90.000, 102.524, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11CCC-613-

HOH

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Components

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Protein / Sugars , 2 types, 20 molecules AAABBBCCCDDDEEEFFFGGGHHHIIIJJJ

#1: Protein
Acetylcholine binding protein


Mass: 28326.750 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Plasmid: pFastBac 1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8WSF8
#3: 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.: 10
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, 2980 molecules

#2: Chemical
ChemComp-MXQ / (1~{R},9~{S})-5-(3-oxidanylpropyl)-7,11-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4-dien-6-one


Mass: 248.321 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C14H20N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2899 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.14 Å3/Da / Density % sol: 60.87 % / Description: Block
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Starting protein concentration 12.5 mg/ml + 6 mM ligand BS82. Crystallised as hanging drops, the drop containing 1.5 ul protein, 0.2 ul reservoir (0.8 M NaH2PO4, 0.8 M KH2PO4, 10% glycerol, ...Details: Starting protein concentration 12.5 mg/ml + 6 mM ligand BS82. Crystallised as hanging drops, the drop containing 1.5 ul protein, 0.2 ul reservoir (0.8 M NaH2PO4, 0.8 M KH2PO4, 10% glycerol, 0.1 M HEPES pH 7.0) and 0.3 ul microseeds from cytisine bound AChBP crystals (grown as sitting drops in 0.8 M NaH2PO4, 0.8 M KH2PO4, 0.1 M HEPES pH 7.5).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.72→127.97 Å / Num. obs: 353432 / % possible obs: 95.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 25.07 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.064 / Rrim(I) all: 0.095 / Χ2: 0.89 / Net I/σ(I): 7.6
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 12162 / CC1/2: 0.435 / Rpim(I) all: 0.787 / Rrim(I) all: 1.138 / Χ2: 0.77 / % possible all: 66.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QKK

6qkk


Resolution: 1.72→111.666 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.192 / WRfactor Rwork: 0.161 / Average fsc free: 0.8746 / Average fsc work: 0.8824 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.085
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1922 17388 4.921 %
Rwork0.1619 335977 -
all0.163 --
obs-353365 95.459 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.393 Å2
Baniso -1Baniso -2Baniso -3
1--2.078 Å20 Å2-0.075 Å2
2--2.651 Å20 Å2
3----0.491 Å2
Refinement stepCycle: LAST / Resolution: 1.72→111.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16425 0 636 2899 19960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01318329
X-RAY DIFFRACTIONr_bond_other_d0.0340.01716456
X-RAY DIFFRACTIONr_angle_refined_deg1.8381.66125208
X-RAY DIFFRACTIONr_angle_other_deg2.4741.59938529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg19.7025.4442412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52822.942938
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.707152894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.45215102
X-RAY DIFFRACTIONr_chiral_restr0.0950.22442
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0222738
X-RAY DIFFRACTIONr_gen_planes_other0.0160.023792
X-RAY DIFFRACTIONr_nbd_refined0.1880.23216
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.215495
X-RAY DIFFRACTIONr_nbtor_refined0.1640.28517
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.27587
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.22404
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0670.23
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.222
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2270.277
X-RAY DIFFRACTIONr_nbd_other0.1890.2125
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.261
X-RAY DIFFRACTIONr_mcbond_it2.6652.8348506
X-RAY DIFFRACTIONr_mcbond_other2.6652.8348505
X-RAY DIFFRACTIONr_mcangle_it3.624.23210682
X-RAY DIFFRACTIONr_mcangle_other3.624.23210683
X-RAY DIFFRACTIONr_scbond_it4.1433.3589823
X-RAY DIFFRACTIONr_scbond_other4.1433.3589824
X-RAY DIFFRACTIONr_scangle_it6.0384.85414383
X-RAY DIFFRACTIONr_scangle_other6.0384.85514384
X-RAY DIFFRACTIONr_lrange_it8.35836.81921401
X-RAY DIFFRACTIONr_lrange_other8.10635.32220441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.7650.3569330.36417640X-RAY DIFFRACTION68.1503
1.765-1.8130.33610170.32620285X-RAY DIFFRACTION79.8665
1.813-1.8660.31311960.29222563X-RAY DIFFRACTION91.9537
1.866-1.9230.27112010.25223750X-RAY DIFFRACTION99.0158
1.923-1.9860.23812000.21323114X-RAY DIFFRACTION99.7784
1.986-2.0560.22611310.18722365X-RAY DIFFRACTION99.8428
2.056-2.1330.21311090.17221650X-RAY DIFFRACTION99.8727
2.133-2.220.20110780.16320786X-RAY DIFFRACTION99.8447
2.22-2.3190.1919850.15619986X-RAY DIFFRACTION99.8476
2.319-2.4320.18710100.14719107X-RAY DIFFRACTION99.861
2.432-2.5640.1859510.14518119X-RAY DIFFRACTION99.8534
2.564-2.7190.1878770.14217175X-RAY DIFFRACTION99.8065
2.719-2.9070.1899000.14416082X-RAY DIFFRACTION99.8824
2.907-3.140.1947690.14715069X-RAY DIFFRACTION99.9684
3.14-3.4390.1816930.14713900X-RAY DIFFRACTION99.9178
3.439-3.8450.166810.14312514X-RAY DIFFRACTION99.9546
3.845-4.4390.1386190.11611087X-RAY DIFFRACTION99.9915
4.439-5.4350.1474710.1179398X-RAY DIFFRACTION99.9595
5.435-7.6790.23540.1827307X-RAY DIFFRACTION99.9609
7.679-111.6660.2152130.194081X-RAY DIFFRACTION99.675

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