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- PDB-1mah: FASCICULIN2-MOUSE ACETYLCHOLINESTERASE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1mah
TitleFASCICULIN2-MOUSE ACETYLCHOLINESTERASE COMPLEX
Components
  • ACETYLCHOLINESTERASE
  • FASCICULIN 2
KeywordsCOMPLEX (HYDROLASE/TOXIN) / HYDROLASE / SERINE ESTERASE / SYNAPSE / VENOM / TOXIN / COMPLEX (HYDROLASE-TOXIN) COMPLEX
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity ...acetylcholine metabolic process / serine hydrolase activity / choline binding / acetylcholine catabolic process / acetylcholine binding / acetylcholinesterase / acetylcholine receptor signaling pathway / positive regulation of dendrite morphogenesis / osteoblast development / acetylcholinesterase activity / choline metabolic process / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / laminin binding / side of membrane / synaptic cleft / synapse assembly / collagen binding / response to insulin / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / presynaptic membrane / nuclear envelope / positive regulation of cold-induced thermogenesis / toxin activity / postsynaptic membrane / cell adhesion / endoplasmic reticulum lumen / axon / neuronal cell body / synapse / dendrite / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / Snake toxin-like superfamily / Cholinesterase / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. ...Snake toxins signature. / Snake toxin, conserved site / CD59 / CD59 / Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / Snake toxin-like superfamily / 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 / 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-1 / Fasciculin-2 / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
Dendroaspis angusticeps (eastern green mamba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsBourne, Y. / Taylor, P. / Marchot, P.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1995
Title: Acetylcholinesterase inhibition by fasciculin: crystal structure of the complex.
Authors: Bourne, Y. / Taylor, P. / Marchot, P.
History
DepositionNov 21, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 31, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYLCHOLINESTERASE
F: FASCICULIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7543
Polymers66,5332
Non-polymers2211
Water0
1
A: ACETYLCHOLINESTERASE
F: FASCICULIN 2
hetero molecules

A: ACETYLCHOLINESTERASE
F: FASCICULIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,5096
Polymers133,0674
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Unit cell
Length a, b, c (Å)75.500, 75.500, 556.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Atom site foot note1: CIS PROLINE - PRO A 106
2: ARG A 107 - PRO A 108 OMEGA = 243.30 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: LEU A 161 - PRO A 162 OMEGA = 222.75 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: SER A 497 - PRO A 498 OMEGA = 139.38 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: CIS PROLINE - PRO F 31 / 6: CIS PROLINE - PRO F 56
DetailsSYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: A 4 .. 61 GENERATE A DIMER OF THE MACHE-FAS2 COMPLEX ACROSS A TWO-FOLD CRYSTALLOGRAPHIC AXIS SYMMETRY1 1 -1.000000 0.000000 0.000000 75.46878 SYMMETRY2 1 0.000000 1.000000 0.000000 -0.07648 SYMMETRY3 1 0.000000 0.000000 -1.000000 278.07110

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Components

#1: Protein ACETYLCHOLINESTERASE / / MACHE


Mass: 59764.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BLACK6-CBA CROSS F1 / Cell line: 293 / Gene: MOUSE ACHE / Organ: BRAIN (CDNA) / Plasmid: LAMBDA-ZAP AND LAMBDA-FIX CDNA AND GENOMIC DNA / Cell line (production host): HEK 293 / Gene (production host): MOUSE ACHE / Production host: Homo sapiens (human) / References: UniProt: P21836, acetylcholinesterase
#2: Protein FASCICULIN 2 / / TOXIN F-VII / FAS2 / TOXIN TAI


Mass: 6768.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Dendroaspis angusticeps (eastern green mamba)
Cell line: 293 / Organ: BRAIN (CDNA) / Tissue: VENOM / References: UniProt: P01403, UniProt: P0C1Z0*PLUS
#3: 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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.21 %
Crystal growDetails: DATA SETS FROM FOUR CRYSTALS HAVE BEEN MERGED
Crystal
*PLUS
Density % sol: 60 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 7.5 / PH range high: 6.5
Components of the solutions
*PLUS
Conc.: 0.1 M / Chemical formula: NaAc

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.0, 1.5
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 25, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.51
ReflectionResolution: 3.2→37 Å / Num. obs: 14488 / % possible obs: 85 % / Redundancy: 4 % / Rmerge(I) obs: 0.089
Reflection
*PLUS
Num. measured all: 62214 / Rmerge(I) obs: 0.089

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 3.2→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.294 -5 %
Rwork0.184 --
obs0.184 13823 85 %
Displacement parametersBiso mean: 35 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 3.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4576 0 14 0 4590
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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