[English] 日本語
Yorodumi
- PDB-4pqe: Crystal Structure of Human Acetylcholinesterase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pqe
TitleCrystal Structure of Human Acetylcholinesterase
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Structural Genomics / Israel Structural Proteomics Center / ISPC / alpha/beta hydrolase
Function / homology
Function and homology information


negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / acetylcholine catabolic process / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholinesterase / cholinesterase activity / acetylcholine receptor signaling pathway ...negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / acetylcholine catabolic process / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholinesterase / cholinesterase activity / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / Synthesis of PC / basement membrane / regulation of receptor recycling / Synthesis, secretion, and deacylation of Ghrelin / laminin binding / side of membrane / synaptic cleft / synapse assembly / collagen binding / positive regulation of protein secretion / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / nervous system development / positive regulation of cold-induced thermogenesis / amyloid-beta binding / hydrolase activity / cell adhesion / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / extracellular region / membrane / nucleus / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain ...Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / 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
Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsDym, O. / Unger, T. / Toker, L. / Silman, I. / Sussman, J.L. / Israel Structural Proteomics Center (ISPC)
CitationJournal: To be Published
Title: Crystal Structure of Human Acetylcholinesterase
Authors: Dym, O. / Unger, T. / Toker, L. / Silman, I. / Sussman, J.L. / Israel Structural Proteomics Center (ISPC)
History
DepositionMar 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetylcholinesterase


Theoretical massNumber of molelcules
Total (without water)59,5761
Polymers59,5761
Non-polymers00
Water21612
1
A: Acetylcholinesterase

A: Acetylcholinesterase


Theoretical massNumber of molelcules
Total (without water)119,1522
Polymers119,1522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,x-y+1,-z1
Buried area1890 Å2
ΔGint-15 kcal/mol
Surface area37900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.307, 125.307, 131.396
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

-
Components

#1: Protein Acetylcholinesterase / / AChE


Mass: 59576.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE
Cell line (production host): Human Embryonic Kidney 293 cells
Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: UniProt: P22303, acetylcholinesterase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5 Å3/Da / Density % sol: 75.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Imidazol pH=7, 12% PEG 20000, 0.5% Ethyl Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 23, 2012
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 26326 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 17.7
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.043 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LII

3lii


Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.911 / SU B: 8.932 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.377 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21811 1288 4.9 %RANDOM
Rwork0.18525 ---
obs0.18684 25021 99.92 %-
all-24993 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.226 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å2-0 Å2
3----1.76 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4087 0 0 12 4099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194215
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1791.9535764
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7645525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07422.526190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.6115594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1221536
X-RAY DIFFRACTIONr_chiral_restr0.1360.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0223325
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.76632109
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.4014.4882631
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5343.052106
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.901→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 80 -
Rwork0.223 1865 -
obs--99.85 %

+
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