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- EMDB-0256: Natural tetrameric form of human butyrylcholinesterase (BChE) -

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Basic information

Entry
Database: EMDB / ID: EMD-0256
TitleNatural tetrameric form of human butyrylcholinesterase (BChE)
Map dataMap after post-processing procedure in RELION 2.1. Contour level was selected based on visualization in Chimera 1.11.2.
Sample
  • Complex: Natural tetrameric form of human butyrylcholinesterase
    • Protein or peptide: Natural tetrameric form of human butyrylcholinesterase
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.6 Å
AuthorsBaymukhametov TN / Chesnokov YM / Boyko KM / Hons M / Lipkin AV / Lushchekina SV / Konarev PV / Masson P / Vasiliev AL / Popov VO / Kovalchuk MV
Funding support Russian Federation, 2 items
OrganizationGrant numberCountry
Russian Science Foundation14-24-00172 Russian Federation
Russian Science Foundation18-41-06001 Russian Federation
CitationJournal: Biochimie / Year: 2019
Title: 3D structure of the natural tetrameric form of human butyrylcholinesterase as revealed by cryoEM, SAXS and MD.
Authors: Konstantin M Boyko / Timur N Baymukhametov / Yury M Chesnokov / Michael Hons / Sofya V Lushchekina / Petr V Konarev / Alexey V Lipkin / Alexandre L Vasiliev / Patrick Masson / Vladimir O ...Authors: Konstantin M Boyko / Timur N Baymukhametov / Yury M Chesnokov / Michael Hons / Sofya V Lushchekina / Petr V Konarev / Alexey V Lipkin / Alexandre L Vasiliev / Patrick Masson / Vladimir O Popov / Michail V Kovalchuk /
Abstract: Human plasma butyrylcholinesterase (BChE) is an endogenous bioscavenger that hydrolyzes numerous medicamentous and poisonous esters and scavenges potent organophosphorus nerve agents. BChE is thus a ...Human plasma butyrylcholinesterase (BChE) is an endogenous bioscavenger that hydrolyzes numerous medicamentous and poisonous esters and scavenges potent organophosphorus nerve agents. BChE is thus a marker for the diagnosis of OP poisoning. It is also considered a therapeutic target against Alzheimer's disease. Although the X-ray structure of a partially deglycosylated monomer of human BChE was solved 15 years ago, all attempts to determine the 3D structure of the natural full-length glycosylated tetrameric human BChE have been unsuccessful so far. Here, a combination of three complementary structural methods-single-particle cryo-electron microscopy, molecular dynamics and small-angle X-ray scattering-were implemented to elucidate the overall structural and spatial organization of the natural tetrameric human plasma BChE. A 7.6 Å cryoEM map clearly shows the major features of the enzyme: a dimer of dimers with a nonplanar monomer arrangement, in which the interconnecting super helix complex PRAD-(WAT)-peptide C-terminal tail is located in the center of the tetramer, nearly perpendicular to its plane, and is plunged deep between the four subunits. Molecular dynamics simulations allowed optimization of the geometry of the molecule and reconstruction of the structural features invisible in the cryoEM density, i.e., glycan chains and glycan interdimer contact areas, as well as intermonomer disulfide bridges at the C-terminal tail. Finally, SAXS data were used to confirm the consistency of the obtained model with the experimental data. The tetramer organization of BChE is unique in that the four subunits are joined at their C-termini through noncovalent contacts with a short polyproline-rich peptide. This tetramer structure could serve as a model for the design of highly stable glycosylated tetramers.
History
Header (metadata) releaseMay 23, 2018-
DepositionSep 25, 2018-
Map releaseNov 14, 2018-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0256.png

Downloads & links

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Map

FileDownload / File: emd_0256.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap after post-processing procedure in RELION 2.1. Contour level was selected based on visualization in Chimera 1.11.2.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.152 Å		1.07 Å/pix.
x 256 pix.
= 273.152 Å		1.07 Å/pix.
x 256 pix.
= 273.152 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.020299394 - 0.09232882
Average (Standard dev.)0.00080702716 (±0.005097126)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.152 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0671.0671.067
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z273.152273.152273.152
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0200.0920.001

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Supplemental data

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Mask #1

Fileemd_0256_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Natural tetrameric form of human butyrylcholinesterase

EntireName: Natural tetrameric form of human butyrylcholinesterase
Components
  • Complex: Natural tetrameric form of human butyrylcholinesterase
    • Protein or peptide: Natural tetrameric form of human butyrylcholinesterase

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Supramolecule #1: Natural tetrameric form of human butyrylcholinesterase

SupramoleculeName: Natural tetrameric form of human butyrylcholinesterase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 335 KDa

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Macromolecule #1: Natural tetrameric form of human butyrylcholinesterase

MacromoleculeName: Natural tetrameric form of human butyrylcholinesterase
type: protein_or_peptide / ID: 1
Details: Glycan chains are attached to the following residues: 17,57,106, 241, 256, 341, 455, 481, 486.
Enantiomer: LEVO / EC number: cholinesterase
Source (natural)Organism: Homo sapiens (human)
SequenceString: MHSKVTIICI RFLFWFLLLC MLIGKSHTED DIIIATKNGK VRGMNLTVFG GTVTAFLGIP YAQPPLGRL RFKKPQSLTK WSDIWNATKY ANSCCQNIDQ SFPGFHGSEM WNPNTDLSED C LYLNVWIP APKPKNATVL IWIYGGGFQT GTSSLHVYDG KFLARVERVI ...String:
MHSKVTIICI RFLFWFLLLC MLIGKSHTED DIIIATKNGK VRGMNLTVFG GTVTAFLGIP YAQPPLGRL RFKKPQSLTK WSDIWNATKY ANSCCQNIDQ SFPGFHGSEM WNPNTDLSED C LYLNVWIP APKPKNATVL IWIYGGGFQT GTSSLHVYDG KFLARVERVI VVSMNYRVGA LG FLALPGN PEAPGNMGLF DQQLALQWVQ KNIAAFGGNP KSVTLFGESA GAASVSLHLL SPG SHSLFT RAILQSGSFN APWAVTSLYE ARNRTLNLAK LTGCSRENET EIIKCLRNKD PQEI LLNEA FVVPYGTPLS VNFGPTVDGD FLTDMPDILL ELGQFKKTQI LVGVNKDEGT AFLVY GAPG FSKDNNSIIT RKEFQEGLKI FFPGVSEFGK ESILFHYTDW VDDQRPENYR EALGDV VGD YNFICPALEF TKKFSEWGNN AFFYYFEHRS SKLPWPEWMG VMHGYEIEFV FGLPLER RD NYTKAEEILS RSIVKRWANF AKYGNPNETQ NNSTSWPVFK STEQKYLTLN TESTRIMT K LRAQQCRFWT SFFPKVLEMT GNIDEAEWEW KAGFHRWNNY MMDWKNQFND YTSKKESCVG L

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 8
GridMaterial: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 1 second before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-28 / Number grids imaged: 1 / Number real images: 1500 / Average exposure time: 7.0 sec. / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 46860 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.003 µm / Nominal defocus min: 0.001 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 170963
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 6712
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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