[English] 日本語
Yorodumi
- PDB-4ey6: Crystal Structure of Recombinant Human Acetylcholinesterase in Co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ey6
TitleCrystal Structure of Recombinant Human Acetylcholinesterase in Complex with (-)-galantamine
ComponentsAcetylcholinesterase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / acetylcholinesterase / hydrolase / galantamine / inhibitor / galanthamine / HYDROLASE-HYDROLASE INHIBITOR complex
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
(-)-GALANTHAMINE / NITRATE ION / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3983 Å
AuthorsCheung, J. / Rudolph, M. / Burshteyn, F. / Cassidy, M. / Gary, E. / Love, J. / Height, J. / Franklin, M.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Structures of human acetylcholinesterase in complex with pharmacologically important ligands.
Authors: Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M.S. / Gary, E.N. / Love, J. / Franklin, M.C. / Height, J.J.
History
DepositionMay 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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 2.1Sep 13, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,51213
Polymers118,8942
Non-polymers2,61811
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint30 kcal/mol
Surface area37590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.975, 104.975, 323.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Acetylcholinesterase / / AChE


Mass: 59447.105 Da / Num. of mol.: 2 / Fragment: UNP Residues 33-574
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Cell line (production host): HEK-293 / Production host: Homo sapiens (human) / References: UniProt: P22303, acetylcholinesterase

-
Sugars , 2 types, 3 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
#5: 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.: 1
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

-
Non-polymers , 5 types, 393 molecules

#3: Chemical ChemComp-GNT / (-)-GALANTHAMINE / Galantamine


Mass: 287.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21NO3 / Comment: inhibitor, alkaloid*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#7: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Polyethylene glycol


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 4.33 Å3/Da / Density % sol: 71.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 12 to 18% PEG 3350, 0.2M potassium nitrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.398→50 Å / Num. all: 82061 / Num. obs: 81569 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.398-2.443.80.505199.3
2.44-2.493.70.436199.2
2.49-2.533.70.364199.4
2.53-2.593.70.327199.3
2.59-2.643.70.298199.5
2.64-2.73.70.246199.5
2.7-2.773.70.219199.6
2.77-2.853.70.186199.6
2.85-2.933.70.154199.6
2.93-3.023.70.122199.9
3.02-3.133.70.102199.9
3.13-3.263.70.0861100
3.26-3.413.70.069199.9
3.41-3.583.70.058199.9
3.58-3.813.60.05199.8
3.81-4.13.60.049199.7
4.1-4.523.60.049199.5
4.52-5.173.60.044199.3
5.17-6.513.40.037199.3
6.51-503.60.026195.5

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EY7

4ey7


Resolution: 2.3983→47.191 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.25 / σ(F): 0 / Phase error: 21.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2059 4062 4.99 %
Rwork0.1671 --
obs0.1691 81467 99.27 %
all-86150 -
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.7748 Å20 Å2-0 Å2
2--7.7748 Å2-0 Å2
3----15.5496 Å2
Refinement stepCycle: LAST / Resolution: 2.3983→47.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8284 0 177 385 8846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078824
X-RAY DIFFRACTIONf_angle_d1.13312060
X-RAY DIFFRACTIONf_dihedral_angle_d16.3623226
X-RAY DIFFRACTIONf_chiral_restr0.0761293
X-RAY DIFFRACTIONf_plane_restr0.0051581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3983-2.42650.28561310.22862600X-RAY DIFFRACTION97
2.4265-2.45610.2541370.22052635X-RAY DIFFRACTION99
2.4561-2.48720.29331710.22222558X-RAY DIFFRACTION99
2.4872-2.51990.30311350.21062638X-RAY DIFFRACTION99
2.5199-2.55440.27721270.21062660X-RAY DIFFRACTION99
2.5544-2.59090.281320.21222625X-RAY DIFFRACTION99
2.5909-2.62960.29511530.20622652X-RAY DIFFRACTION100
2.6296-2.67070.28891420.20022624X-RAY DIFFRACTION99
2.6707-2.71450.22161470.1912609X-RAY DIFFRACTION99
2.7145-2.76130.24421230.19172711X-RAY DIFFRACTION100
2.7613-2.81150.23951520.19012595X-RAY DIFFRACTION100
2.8115-2.86550.25921430.17982650X-RAY DIFFRACTION100
2.8655-2.9240.22241220.18392694X-RAY DIFFRACTION100
2.924-2.98760.22911320.17942650X-RAY DIFFRACTION100
2.9876-3.05710.23221400.17862658X-RAY DIFFRACTION100
3.0571-3.13350.26371420.17812684X-RAY DIFFRACTION100
3.1335-3.21820.23721290.18432636X-RAY DIFFRACTION100
3.2182-3.31290.23341420.18672701X-RAY DIFFRACTION100
3.3129-3.41980.21831520.17632663X-RAY DIFFRACTION100
3.4198-3.5420.21021440.17252667X-RAY DIFFRACTION100
3.542-3.68370.19931340.16832697X-RAY DIFFRACTION100
3.6837-3.85130.18811480.15462688X-RAY DIFFRACTION100
3.8513-4.05430.16731320.14212722X-RAY DIFFRACTION100
4.0543-4.30810.15871390.1392694X-RAY DIFFRACTION100
4.3081-4.64050.16261460.12572697X-RAY DIFFRACTION99
4.6405-5.1070.1321270.12922710X-RAY DIFFRACTION99
5.107-5.84480.1731600.15272755X-RAY DIFFRACTION100
5.8448-7.35930.18721420.16532758X-RAY DIFFRACTION99
7.3593-47.20010.18151380.15822774X-RAY DIFFRACTION94

+
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