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- PDB-7rb6: Low temperature structure of hAChE in complex with substrate anal... -

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Basic information

Entry
Database: PDB / ID: 7rb6
TitleLow temperature structure of hAChE in complex with substrate analog 4K-TMA
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / acetylcholine esterase / serine hydrolase / tetrahedral intermediate
Function / homology
Function and homology information


negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / acetylcholine catabolic process / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine binding / acetylcholine receptor signaling pathway ...negative regulation of synaptic transmission, cholinergic / serine hydrolase activity / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / acetylcholine catabolic process / acetylcholinesterase / amyloid precursor protein metabolic process / acetylcholine binding / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / Synthesis of PC / basement membrane / regulation of receptor recycling / Synthesis, secretion, and deacylation of Ghrelin / synaptic cleft / synapse assembly / side of membrane / laminin binding / collagen binding / positive regulation of protein secretion / neuromuscular junction / receptor internalization / nervous system development / amyloid-beta binding / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / 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
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
NITRATE ION / 4,4-DIHYDROXY-N,N,N-TRIMETHYLPENTAN-1-AMINIUM / Acetylcholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKovalevsky, A. / Gerlits, O. / Radic, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)U01 NS083451 United States
CitationJournal: Curr Res Struct Biol / Year: 2021
Title: Room temperature crystallography of human acetylcholinesterase bound to a substrate analogue 4K-TMA: Towards a neutron structure
Authors: Gerlits, O. / Blakeley, M.P. / Keen, D.A. / Radic, Z. / Kovalevsky, A.
History
DepositionJul 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,48511
Polymers120,5762
Non-polymers9099
Water11,043613
1
B: Acetylcholinesterase
hetero molecules

A: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,48511
Polymers120,5762
Non-polymers9099
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z+1/31
Buried area4490 Å2
ΔGint-3 kcal/mol
Surface area38330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.800, 124.800, 130.169
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Acetylcholinesterase / AChE


Mass: 60287.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P22303, acetylcholinesterase
#2: Chemical ChemComp-NWA / 4,4-DIHYDROXY-N,N,N-TRIMETHYLPENTAN-1-AMINIUM


Mass: 162.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H20NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 613 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 4.85 Å3/Da / Density % sol: 74.66 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES, pH 7.5, 10 mM sodium citrate, 6-8% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 87262 / % possible obs: 98.1 % / Redundancy: 2.6 % / CC1/2: 0.983 / Rmerge(I) obs: 0.065 / Net I/σ(I): 12.9
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 8730 / CC1/2: 0.543 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6O5R

6o5r


Resolution: 2.4→38.98 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 22.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2148 4111 4.87 %random
Rwork0.1819 ---
obs0.1835 84333 94.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→38.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8376 0 58 613 9047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028697
X-RAY DIFFRACTIONf_angle_d0.5611885
X-RAY DIFFRACTIONf_dihedral_angle_d10.5341212
X-RAY DIFFRACTIONf_chiral_restr0.0431257
X-RAY DIFFRACTIONf_plane_restr0.0051573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.34933260.28096557X-RAY DIFFRACTION78
2.48-2.580.30933900.25917356X-RAY DIFFRACTION87
2.58-2.70.2854280.24448264X-RAY DIFFRACTION98
2.7-2.840.27924950.23518318X-RAY DIFFRACTION98
2.84-3.020.2574570.20988242X-RAY DIFFRACTION98
3.02-3.250.23164400.19078204X-RAY DIFFRACTION97
3.25-3.580.21713390.18788462X-RAY DIFFRACTION99
3.58-4.10.18894100.16218277X-RAY DIFFRACTION98
4.1-5.160.15914450.13578320X-RAY DIFFRACTION98
5.16-38.980.17093810.15588222X-RAY DIFFRACTION97

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