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- PDB-4ey8: Crystal structure of recombinant human acetylcholinesterase in co... -

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Basic information

Entry
Database: PDB / ID: 4ey8
TitleCrystal structure of recombinant human acetylcholinesterase in complex with fasciculin-2
Components
  • Acetylcholinesterase
  • Fasciculin-2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / acetylcholinesterase / hydrolase / fasciculin 2 / snake venom toxin / inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / acetylcholine catabolic process in synaptic cleft / Neurotransmitter clearance / cholinesterase activity / acetylcholine catabolic process / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine binding / osteoblast development ...negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / acetylcholine catabolic process in synaptic cleft / Neurotransmitter clearance / cholinesterase activity / acetylcholine catabolic process / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine binding / osteoblast development / acetylcholine receptor signaling pathway / acetylcholinesterase activity / Synthesis of PC / basement membrane / regulation of receptor recycling / Synthesis, secretion, and deacylation of Ghrelin / synaptic cleft / side of membrane / collagen binding / synapse assembly / laminin binding / positive regulation of protein secretion / neuromuscular junction / receptor internalization / nervous system development / positive regulation of cold-induced thermogenesis / amyloid-beta binding / retina development in camera-type eye / toxin activity / hydrolase activity / cell adhesion / synapse / perinuclear region of cytoplasm / cell surface / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / nucleus / membrane / plasma membrane
Similarity search - Function
Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / CD59 / CD59 / Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : ...Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / CD59 / CD59 / Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / Cholinesterase / Snake toxin-like superfamily / 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 / Ribbon / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Fasciculin-2 / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
Dendroaspis angusticeps (eastern green mamba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5958 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: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Fasciculin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5548
Polymers66,2162
Non-polymers1,3386
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-8 kcal/mol
Surface area22300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.705, 151.705, 247.862
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Detailsdimer

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Acetylcholinesterase / AChE


Mass: 59447.105 Da / Num. of mol.: 1 / Fragment: UNP Residues 33-574
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Production host: Homo sapiens (human) / Tissue (production host): HEK-293 / References: UniProt: P22303, acetylcholinesterase
#2: Protein Fasciculin-2 / Fas-2 / Fas2 / Acetylcholinesterase toxin F-VII / Fasciculin-II / FAS-II / Toxin TA1


Mass: 6768.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Dendroaspis angusticeps (eastern green mamba)
Secretion: VENOM / References: UniProt: P0C1Z0

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Sugars , 2 types, 2 molecules

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


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(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


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

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Non-polymers , 2 types, 48 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.14 Å3/Da / Density % sol: 70.32 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 1.6 to 2.0M ammonium sulphate, 0.1M HEPES pH 7.5 - 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 283K
PH range: 7.5 - 7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.99 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.5958→50 Å / Num. all: 34182 / Num. obs: 33704 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.5958-2.643.60.29188.5
2.64-2.693.90.308194.7
2.69-2.744.20.32198.9
2.74-2.84.50.31100
2.8-2.864.60.254199.9
2.86-2.934.70.2181100
2.93-34.70.179199.9
3-3.084.70.158199.9
3.08-3.174.70.134199.9
3.17-3.284.70.106199.6
3.28-3.394.70.095199.9
3.39-3.534.70.086199.5
3.53-3.694.70.071199.5
3.69-3.884.70.062199.2
3.88-4.134.60.056199.3
4.13-4.454.60.049199.2
4.45-4.894.60.045199
4.89-5.65.10.044199.2
5.6-7.059.30.048199.1
7.05-508.20.032197.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1b41

1b41


Resolution: 2.5958→46.381 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.35 / σ(F): 0 / Phase error: 30.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 1681 5.03 %
Rwork0.1939 --
obs0.1964 33413 97.78 %
all-35893 -
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.7066 Å20 Å2-0 Å2
2--15.7066 Å2-0 Å2
3----31.4132 Å2
Refinement stepCycle: LAST / Resolution: 2.5958→46.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4592 0 83 44 4719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084829
X-RAY DIFFRACTIONf_angle_d1.1876590
X-RAY DIFFRACTIONf_dihedral_angle_d17.081765
X-RAY DIFFRACTIONf_chiral_restr0.079713
X-RAY DIFFRACTIONf_plane_restr0.006859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5958-2.67220.38041250.28872431X-RAY DIFFRACTION90
2.6722-2.75840.35391420.26172616X-RAY DIFFRACTION98
2.7584-2.8570.31791430.25812654X-RAY DIFFRACTION99
2.857-2.97140.33741410.25082653X-RAY DIFFRACTION99
2.9714-3.10660.30741340.23492659X-RAY DIFFRACTION99
3.1066-3.27030.3221290.24842667X-RAY DIFFRACTION99
3.2703-3.47520.3021310.24172652X-RAY DIFFRACTION99
3.4752-3.74340.2981610.21442618X-RAY DIFFRACTION98
3.7434-4.11990.2311300.17792646X-RAY DIFFRACTION97
4.1199-4.71550.20961620.15742638X-RAY DIFFRACTION98
4.7155-5.93910.18571470.16312703X-RAY DIFFRACTION99
5.9391-46.3880.18751360.16132795X-RAY DIFFRACTION98

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