[English] 日本語
Yorodumi
- PDB-9f84: Structure of Choline O-acetyltransferase in complex with 1-Methyl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9f84
TitleStructure of Choline O-acetyltransferase in complex with 1-Methyl-4-[2-(1-naphthyl)-2-(propylthio)ethyl]pyridinium at 1.9 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 / cytosol / cytoplasm
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: 1.9 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)-2-(propylthio)ethyl]pyridinium at 1.9 Angstrom resultion.
Authors: Forsgren, N. / Ekstrom, F.
History
DepositionMay 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Choline O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4603
Polymers68,1131
Non-polymers3462
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-14 kcal/mol
Surface area23300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.660, 76.766, 164.324
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

-
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
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-A1IAP / 1-methyl-4-[(2S)-2-naphthalen-1-yl-2-propylsulfanyl-ethyl]-4H-pyridine / CHITOTRIOSE


Mass: 323.495 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25NS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris-HCl pH 8.5 10 %(w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.9→82.16 Å / Num. obs: 55320 / % possible obs: 99.8 % / Redundancy: 8.7 % / Biso Wilson estimate: 25.05 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.3
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 3496 / CC1/2: 0.719

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→34.78 Å / SU ML: 0.177 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.1016
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.197 1135 2.06 %
Rwork0.168 54095 -
obs0.1686 55230 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.55 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4488 0 24 434 4946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00924702
X-RAY DIFFRACTIONf_angle_d0.91036387
X-RAY DIFFRACTIONf_chiral_restr0.0603718
X-RAY DIFFRACTIONf_plane_restr0.0091827
X-RAY DIFFRACTIONf_dihedral_angle_d14.90861738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.990.29621440.236626X-RAY DIFFRACTION99.25
1.99-2.090.20871370.18446669X-RAY DIFFRACTION99.44
2.09-2.220.20061350.16076660X-RAY DIFFRACTION99.52
2.22-2.390.19581550.15826691X-RAY DIFFRACTION99.69
2.39-2.630.21191300.16476736X-RAY DIFFRACTION99.77
2.63-3.020.2031450.17886771X-RAY DIFFRACTION99.94
3.02-3.80.21361400.16736845X-RAY DIFFRACTION99.97
3.8-34.780.16091490.15667097X-RAY DIFFRACTION99.9
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)
10.9199912759320.0889542404214-0.3090560205241.1522451696-0.1661077378781.788701289830.0300690928948-0.0345795638058-0.102907698561-0.1358387054780.001666095831750.03874688047720.1221980724640.116139071963-0.02034569471690.1196955911220.00171346122282-0.0349726706020.158287369662-0.0002748641769450.1767536691114.09344368957-5.4106980498367.9240187751
21.13546203486-0.1069043864040.07336500452511.228999920220.2326354272891.549679213980.02952751922090.271967053837-0.00421420341425-0.502035428109-0.01522978608930.107771239414-0.12741259433-0.0931865274138-0.02260281628690.3571328197410.0331718224155-0.04806956201940.2397693302690.01456546798310.1705932621242.671844437697.3942414245847.3878543462
30.7955640261350.1855831188080.3369990598130.7162118344880.01897621890370.5420625634030.0457603999735-0.0358442903136-0.04000181576160.0437282360789-0.0248513006712-0.029514101974-0.01385266590210.00451985743069-0.01767956059110.1603837270680.00731937345525-0.001025024435750.157164912498-0.002538712868080.1606851170112.71035907144.7907862955577.3258070976
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 152 )8 - 1521 - 142
22chain 'A' and (resid 153 through 398 )153 - 398143 - 370
33chain 'A' and (resid 399 through 606 )399 - 606371 - 578

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more