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- PDB-9f85: Structure of Choline O-acetyltransferase in complex with 1-Methyl... -

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Basic information

Entry
Database: PDB / ID: 9f85
TitleStructure of Choline O-acetyltransferase in complex with 1-Methyl-4-[2-(1-naphthyl)ethyl]pyridinium at 1.6 Angstrom resolution
ComponentsCholine O-acetyltransferase
KeywordsTRANSFERASE / ChAT / complex / inhibitor / reversible
Function / homology
Function and homology information


choline O-acetyltransferase / choline O-acetyltransferase activity / acetylcholine biosynthetic process / Acetylcholine Neurotransmitter Release Cycle / phosphatidylcholine biosynthetic process / neuromuscular synaptic transmission / neurotransmitter transport / Synthesis of PC / neuron projection / synapse ...choline O-acetyltransferase / choline O-acetyltransferase activity / acetylcholine biosynthetic process / Acetylcholine Neurotransmitter Release Cycle / phosphatidylcholine biosynthetic process / neuromuscular synaptic transmission / neurotransmitter transport / Synthesis of PC / neuron projection / synapse / nucleus / cytoplasm / cytosol
Similarity search - Function
Acyltransferase ChoActase/COT/CPT / Choline/carnitine acyltransferase domain / Choline/Carnitine o-acyltransferase, domain 2 / Choline/Carnitine o-acyltransferase / Acyltransferases ChoActase / COT / CPT family signature 1. / Acyltransferases ChoActase / COT / CPT family signature 2. / Chloramphenicol acetyltransferase-like domain superfamily
Similarity search - Domain/homology
: / Choline O-acetyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsForsgren, N. / Ekstrom, F.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Other government Sweden
CitationJournal: To Be Published
Title: Structure of choline O-acetyltransferase in complex with 1-Methyl-4-[2-(1-naphthyl)ethyl]pyridinium at 1.6 Angstrom resolution.
Authors: Forsgren, N. / Ekstrom, F.
History
DepositionMay 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Choline O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4094
Polymers68,1131
Non-polymers2953
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-23 kcal/mol
Surface area23080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.760, 76.353, 164.114
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Choline O-acetyltransferase / CHOACTase / ChAT / Choline acetylase


Mass: 68113.352 Da / Num. of mol.: 1 / Mutation: E225A,D226A,E227A,K518A,E519A,K582A,E583A
Source method: isolated from a genetically manipulated source
Details: Engineered mutations: E225A, D226A, E227A, K518A, E519A, K582A, E583A Residues 346-358 from UniProt sequence replaced with PELVRSPMVP,Engineered mutations: E225A, D226A, E227A, K518A, E519A, ...Details: Engineered mutations: E225A, D226A, E227A, K518A, E519A, K582A, E583A Residues 346-358 from UniProt sequence replaced with PELVRSPMVP,Engineered mutations: E225A, D226A, E227A, K518A, E519A, K582A, E583A Residues 346-358 from UniProt sequence replaced with PELVRSPMVP,Engineered mutations: E225A, D226A, E227A, K518A, E519A, K582A, E583A Residues 346-358 from UniProt sequence replaced with PELVRSPMVP,Engineered mutations: E225A, D226A, E227A, K518A, E519A, K582A, E583A Residues 346-358 from UniProt sequence replaced with PELVRSPMVP,Engineered mutations: E225A, D226A, E227A, K518A, E519A, K582A, E583A Residues 346-358 from UniProt sequence replaced with PELVRSPMVP,Engineered mutations: E225A, D226A, E227A, K518A, E519A, K582A, E583A Residues 346-358 from UniProt sequence replaced with PELVRSPMVP,Engineered mutations: E225A, D226A, E227A, K518A, E519A, K582A, E583A Residues 346-358 from UniProt sequence replaced with PELVRSPMVP,Engineered mutations: E225A, D226A, E227A, K518A, E519A, K582A, E583A Residues 346-358 from UniProt sequence replaced with PELVRSPMVP
Source: (gene. exp.) Homo sapiens (human) / Gene: CHAT / Plasmid: pJ301 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P28329, choline O-acetyltransferase
#2: Chemical ChemComp-A1IAO / 1-methyl-4-(2-naphthalen-1-ylethyl)-4H-pyridine


Mass: 249.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19N / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris-HCl pH 8.5 10 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→164.1 Å / Num. obs: 91684 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 23.53 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.5
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 4471 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→34.61 Å / SU ML: 0.164 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.3471
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2 1902 2.08 %
Rwork0.1748 89626 -
obs0.1753 91528 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.25 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4473 0 21 402 4896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01414683
X-RAY DIFFRACTIONf_angle_d1.24956364
X-RAY DIFFRACTIONf_chiral_restr0.0792717
X-RAY DIFFRACTIONf_plane_restr0.0122824
X-RAY DIFFRACTIONf_dihedral_angle_d15.29451731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.19581360.18756298X-RAY DIFFRACTION99.89
1.64-1.680.23991500.18416297X-RAY DIFFRACTION99.88
1.68-1.730.24691420.20376344X-RAY DIFFRACTION99.91
1.73-1.790.20591210.19676312X-RAY DIFFRACTION99.92
1.79-1.850.23061190.18086384X-RAY DIFFRACTION99.97
1.85-1.930.18581500.16796304X-RAY DIFFRACTION99.88
1.93-2.020.20841350.17366387X-RAY DIFFRACTION99.98
2.02-2.120.22041330.18036355X-RAY DIFFRACTION99.83
2.12-2.260.20741340.1666365X-RAY DIFFRACTION99.89
2.26-2.430.17241330.16666402X-RAY DIFFRACTION99.98
2.43-2.670.16591350.1766418X-RAY DIFFRACTION99.97
2.67-3.060.22681360.18526479X-RAY DIFFRACTION100
3.06-3.850.19971360.17896518X-RAY DIFFRACTION99.98
3.85-34.610.1941420.16426763X-RAY DIFFRACTION99.87
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)
10.7370743725920.0756708543302-0.197069143060.907878249193-0.1821156435461.53292620080.02143975821970.120020408688-0.0641696741088-0.289948377854-0.01256763647280.05355661609910.04510633853810.00512505412488-0.006917131733010.2242331190630.0119727408885-0.04290263078120.182140896021-0.02315208804410.1929711099573.528481607350.98295340373754.7933165265
20.8243946223440.03842469320090.3218923715220.6126810213320.055652460710.5442745974950.0561281791572-0.0071131357929-0.01495953310460.0173750762143-0.0458849942056-0.00997072873257-0.0429499164833-0.00235666797325-0.00394744364790.1824467091840.008372206359720.0004156930251520.159818072776-0.004189398292380.18402439517811.32168093816.5133495296174.8203414532
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 8 through 370 )8 - 3701 - 339
22chain 'A' and (resid 371 through 606 )371 - 606340 - 575

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