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- PDB-7zpb: Structure of hemiacetylated human butyrylcholinesterase upon reac... -

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Basic information

Entry
Database: PDB / ID: 7zpb
TitleStructure of hemiacetylated human butyrylcholinesterase upon reaction with 8-(3-(4-(prop-2-yn-1-yl)piperazin-1-yl)propoxy)quinoline-2-carbaldehyde
ComponentsCholinesterase
KeywordsHYDROLASE / Butyrylcholinesterase / Inhibitor / Complex
Function / homology
Function and homology information


cholinesterase / : / neuroblast differentiation / response to folic acid / choline binding / Neurotransmitter clearance / cholinesterase activity / choline metabolic process / response to alkaloid / acetylcholine catabolic process ...cholinesterase / : / neuroblast differentiation / response to folic acid / choline binding / Neurotransmitter clearance / cholinesterase activity / choline metabolic process / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission / peptide hormone processing / hydrolase activity, acting on ester bonds / acetylcholinesterase activity / Aspirin ADME / Synthesis of PC / nuclear envelope lumen / catalytic activity / Synthesis, secretion, and deacylation of Ghrelin / xenobiotic metabolic process / response to glucocorticoid / learning / amyloid-beta binding / blood microparticle / endoplasmic reticulum lumen / negative regulation of cell population proliferation / enzyme binding / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family ...Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-JS0 / PROPANOIC ACID / N-acetyl-alpha-neuraminic acid / Cholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsDenic, M. / Chioua, M. / Knez, D. / Gobec, S. / Nachon, F. / Marco-Contelles, J.L. / Brazzolotto, X.
Funding support France, 1items
OrganizationGrant numberCountry
French Ministry of Armed ForcesNBC-5-C-4210 France
CitationJournal: Acta Pharm Sin B / Year: 2023
Title: 8-Hydroxyquinolylnitrones as multifunctional ligands for the therapy of neurodegenerative diseases.
Authors: Knez, D. / Diez-Iriepa, D. / Chioua, M. / Gottinger, A. / Denic, M. / Chantegreil, F. / Nachon, F. / Brazzolotto, X. / Skrzypczak-Wiercioch, A. / Meden, A. / Pislar, A. / Kos, J. / Zakelj, S. ...Authors: Knez, D. / Diez-Iriepa, D. / Chioua, M. / Gottinger, A. / Denic, M. / Chantegreil, F. / Nachon, F. / Brazzolotto, X. / Skrzypczak-Wiercioch, A. / Meden, A. / Pislar, A. / Kos, J. / Zakelj, S. / Stojan, J. / Salat, K. / Serrano, J. / Fernandez, A.P. / Sanchez-Garcia, A. / Martinez-Murillo, R. / Binda, C. / Lopez-Munoz, F. / Gobec, S. / Marco-Contelles, J.
History
DepositionApr 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,85219
Polymers59,7141
Non-polymers4,13918
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-8 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.244, 154.244, 128.113
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cholinesterase / Acylcholine acylhydrolase / Butyrylcholine esterase / Choline esterase II / Pseudocholinesterase


Mass: 59713.512 Da / Num. of mol.: 1
Mutation: N17Q, N455Q, N481Q, N486Q mutations compared to mature wild type sequence to avoid too much N-glycozylation. Numeration on the maturated enzyme (devoid of the signal peptide)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCHE, CHE1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06276, cholinesterase

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Sugars , 4 types, 7 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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.: 1 / Source method: obtained synthetically / 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
#7: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 123 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-JS0 / [8-[3-(4-prop-2-ynylpiperazin-1-yl)propoxy]quinolin-2-yl]methanol / 8-(3-(4-(prop-2-yn-1-yl)piperazin-1-yl)propoxy)quinoline-2-carbaldehyde


Mass: 339.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N3O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#9: Chemical ChemComp-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2
#10: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.19 Å3/Da / Density % sol: 61.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976253 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976253 Å / Relative weight: 1
ReflectionResolution: 2.31→109.1 Å / Num. obs: 34171 / % possible obs: 99.76 % / Redundancy: 8.6 % / Biso Wilson estimate: 49.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07855 / Rpim(I) all: 0.02818 / Rrim(I) all: 0.0837 / Net I/σ(I): 15.78
Reflection shellResolution: 2.31→2.393 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.8594 / Mean I/σ(I) obs: 2.37 / Num. unique obs: 3358 / CC1/2: 0.752 / Rpim(I) all: 0.3066 / Rrim(I) all: 0.9146 / % possible all: 99.94

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Processing

Software
NameVersionClassification
MxCuBEdata collection
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QAA

6qaa


Resolution: 2.31→109.07 Å / SU ML: 0.2492 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.127
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2172 1714 5.02 %
Rwork0.1771 32457 -
obs0.1791 34171 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.16 Å2
Refinement stepCycle: LAST / Resolution: 2.31→109.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4191 0 268 112 4571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084623
X-RAY DIFFRACTIONf_angle_d0.97086285
X-RAY DIFFRACTIONf_chiral_restr0.0583699
X-RAY DIFFRACTIONf_plane_restr0.0073781
X-RAY DIFFRACTIONf_dihedral_angle_d13.0688701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.370.29811390.24172675X-RAY DIFFRACTION99.93
2.37-2.450.26811320.23722684X-RAY DIFFRACTION100
2.45-2.540.30371350.22592679X-RAY DIFFRACTION100
2.54-2.640.23891580.21732646X-RAY DIFFRACTION100
2.64-2.760.26121270.19832700X-RAY DIFFRACTION99.96
2.76-2.910.24281410.19652688X-RAY DIFFRACTION99.96
2.91-3.090.24791510.20622688X-RAY DIFFRACTION100
3.09-3.330.24471400.19732691X-RAY DIFFRACTION99.96
3.33-3.660.23131390.17272712X-RAY DIFFRACTION99.89
3.66-4.190.19541420.15272722X-RAY DIFFRACTION99.76
4.19-5.280.16551540.13922739X-RAY DIFFRACTION99.42
5.28-109.070.21251560.17682833X-RAY DIFFRACTION98.39
Refinement TLS params.Method: refined / Origin x: 16.641344389 Å / Origin y: 32.0111963813 Å / Origin z: 39.07867261 Å
111213212223313233
T0.41249356733 Å2-0.0203919997651 Å20.0195664020904 Å2-0.38350910152 Å20.0349919923827 Å2--0.415022400209 Å2
L0.682181643062 °20.251997282616 °2-0.271106106521 °2-0.893397140252 °2-0.178221897177 °2--1.03551545531 °2
S-2.83413130484E-5 Å °-0.0428535150841 Å °0.090572219808 Å °-0.072484757456 Å °0.0450346586086 Å °0.0163801436985 Å °-0.0528640029152 Å °0.028379199115 Å °1.3590113945E-5 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 4 through 529)

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