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- PDB-1vzj: Structure of the tetramerization domain of acetylcholinesterase: ... -

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Basic information

Entry
Database: PDB / ID: 1vzj
TitleStructure of the tetramerization domain of acetylcholinesterase: four-fold interaction of a WWW motif with a left-handed polyproline helix
Components
  • ACETYLCHOLINESTERASE COLLAGENIC TAIL PEPTIDE
  • ACETYLCHOLINESTERASE
KeywordsHYDROLASE / ACETYLCHOLINESTERASE / SYNAPSE / NEUROTRANSMITTER DEGRADATION / ALTERNATIVE SPLICING / DISEASE MUTATION.
Function / homology
Function and homology information


negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / collagen trimer / acetylcholine catabolic process / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholinesterase / cholinesterase activity ...negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / collagen trimer / acetylcholine catabolic process / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholinesterase / cholinesterase activity / acetylcholine receptor signaling pathway / osteoblast development / extracellular matrix structural constituent / 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 / extracellular matrix organization / extracellular matrix / positive regulation of protein secretion / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / cell junction / heparin binding / nervous system development / positive regulation of cold-induced thermogenesis / amyloid-beta binding / collagen-containing extracellular matrix / 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
Myxococcus cysteine-rich repeat / 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
Similarity search - Domain/homology
Acetylcholinesterase / Acetylcholinesterase collagenic tail peptide
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å
AuthorsDvir, H. / Harel, M. / Bon, S. / Liu, W.-Q. / Vidal, M. / Garbay, C. / Sussman, J.L. / Massoulie, J. / Silman, I.
CitationJournal: Embo J. / Year: 2004
Title: The Synaptic Acetylcholinesterase Tetramer Assembles Around a Polyproline-II Helix
Authors: Dvir, H. / Harel, M. / Bon, S. / Liu, W.-Q. / Vidal, M. / Garbay, C. / Sussman, J.L. / Massoulie, J. / Silman, I.
History
DepositionMay 20, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2019Group: Data collection / Derived calculations / Other / Category: pdbx_database_status / reflns_shell / struct_conn
Item: _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYLCHOLINESTERASE
B: ACETYLCHOLINESTERASE
C: ACETYLCHOLINESTERASE
D: ACETYLCHOLINESTERASE
E: ACETYLCHOLINESTERASE
F: ACETYLCHOLINESTERASE
G: ACETYLCHOLINESTERASE
H: ACETYLCHOLINESTERASE
I: ACETYLCHOLINESTERASE COLLAGENIC TAIL PEPTIDE
J: ACETYLCHOLINESTERASE COLLAGENIC TAIL PEPTIDE


Theoretical massNumber of molelcules
Total (without water)44,39710
Polymers44,39710
Non-polymers00
Water70339
1
A: ACETYLCHOLINESTERASE
B: ACETYLCHOLINESTERASE
C: ACETYLCHOLINESTERASE
D: ACETYLCHOLINESTERASE
I: ACETYLCHOLINESTERASE COLLAGENIC TAIL PEPTIDE


Theoretical massNumber of molelcules
Total (without water)22,1995
Polymers22,1995
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: ACETYLCHOLINESTERASE
F: ACETYLCHOLINESTERASE
G: ACETYLCHOLINESTERASE
H: ACETYLCHOLINESTERASE
J: ACETYLCHOLINESTERASE COLLAGENIC TAIL PEPTIDE


Theoretical massNumber of molelcules
Total (without water)22,1995
Polymers22,1995
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.730, 58.790, 58.800
Angle α, β, γ (deg.)90.00, 111.38, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.988733, 0.015964, 0.148832), (0.02003, 0.999465, 0.025859), (-0.14834, 0.028549, -0.988524)
Vector: 56.3827, 22.76779, 76.72089)
DetailsHOMOTETRAMER COMPOSED OF DISULFIDE-LINKED HOMODIMERS.INTERACTS WITH PRIMA1 TO ANCHOR IT TO THE BASAL LAMINAOF CELLS AND ORGANIZE INTO TETRAMERS

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Components

#1: Protein/peptide
ACETYLCHOLINESTERASE / / ACETYLCHOLINESTERASE COLLAGENIC TAIL PEPTIDE (WAT)


Mass: 5130.421 Da / Num. of mol.: 8
Fragment: C TERMINAL TETRAMERIZATION DOMAIN, RESIDUES 575-614
Source method: obtained synthetically
Details: THE HUMAN ACHE SEQUENCE OF WAT WAS MODIFIED AT TWO POSITIONS, 21 AND 37, TO REPLACE MET AND CYS BY MSE AND SER, RESPECTIVELY
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P22303, acetylcholinesterase
#2: Protein/peptide ACETYLCHOLINESTERASE COLLAGENIC TAIL PEPTIDE / COLQ / ACETYLCHOLINESTERASE-ASSOCIATED COLLAGEN / ACHE Q SUBUNIT


Mass: 1677.032 Da / Num. of mol.: 2 / Fragment: PRAD PEPTIDE, RESIDUES 53-67 / Source method: obtained synthetically
Details: PROLINE RICH ATTACHMENT DOMAIN (PRAD) OF THE ACHE-ASSOCIATED COLLAGEN PROTEIN (COLQ)
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9Y215
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: ACETYLCHOLINE + H(2)O = CHOLINE + ACETATE.
Sequence detailsRESIDUE 37 IN CHAINS A-H HAS BEEN MUTATED TO A CYS FROM A SER BUT WAS NOT VISIBLE IN THE ELECTRON ...RESIDUE 37 IN CHAINS A-H HAS BEEN MUTATED TO A CYS FROM A SER BUT WAS NOT VISIBLE IN THE ELECTRON DENSITY MAP FOR THIS ENTRY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.2 %
Crystal growpH: 5.6
Details: 10% ISOPROPANOL, 10% PEG, 4K 0.05 M TRISODIUM CITRATE, PH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.96672,0.97927,0.97895,1.5415
DetectorDate: Apr 15, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.966721
20.979271
30.978951
41.54151
ReflectionResolution: 2.3→29 Å / Num. obs: 12935 / % possible obs: 89.4 % / Observed criterion σ(I): 3 / Redundancy: 2.7 % / Biso Wilson estimate: 55.2 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.75 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 1.47 / % possible all: 58.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.35→40 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.259 662 5 %RANDOM
Rwork0.247 ---
obs0.247 12889 89.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.99 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 60.07 Å2
Baniso -1Baniso -2Baniso -3
1--3.627 Å20 Å21.757 Å2
2--6.272 Å20 Å2
3----2.644 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 2.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2503 0 0 39 2542
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009308
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.20223
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.73127
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88574
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.35→2.43 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.4251 36 5.4 %
Rwork0.5169 800 -
obs--59.2 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

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