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- EMDB-8454: Cryo-electron microscopy structure of a bovine CLC-K chloride cha... -

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Basic information

Entry
Database: EMDB / ID: 8454
TitleCryo-electron microscopy structure of a bovine CLC-K chloride channel, alternate (class 2) conformation
SampleA bovine CLC-K channel complexed with a monoclonal antibody fragment (Fab)
SourceBos taurus / mammal / ウシ /
Mus musculus / mammal / ハツカネズミ, はつかねずみ /
Map dataStructure of a bovine CLC-K chloride channel. Combined, unfiltered map of Class 2
Methodsingle particle reconstruction, at 3.95 Å resolution
AuthorsPark E / MacKinnon R
CitationNature, 2017, 541, 500-505

Nature, 2017, 541, 500-505 Yorodumi Papers
Structure of a CLC chloride ion channel by cryo-electron microscopy.
Eunyong Park / Ernest B Campbell / Roderick MacKinnon

Validation ReportPDB-ID: 5tr1

SummaryFull reportAbout validation report
DateDeposition: Oct 26, 2016 / Header (metadata) release: Dec 28, 2016 / Map release: Jan 11, 2017 / Last update: Sep 27, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0176
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.0176
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5tr1
  • Surface level: 0.0176
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_8454.map.gz (map file in CCP4 format, 55297 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.3 Å/pix.
= 312. Å
240 pix
1.3 Å/pix.
= 312. Å
240 pix
1.3 Å/pix.
= 312. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour Level:0.0176 (by author), 0.0176 (movie #1):
Minimum - Maximum-0.024342816 - 0.056552105
Average (Standard dev.)0.00012446755 (0.0026305348)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin000
Limit239239239
Spacing240240240
CellA=B=C: 312 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z312.000312.000312.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0240.0570.000

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Supplemental data

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Mask #1

Fileemd_8454_msk_1.map ( map file in CCP4 format, 55297 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Annotation detailsthe mask used for the FSC calculation
Space group number1

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Mask #1~

Fileemd_8454_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire A bovine CLC-K channel complexed with a monoclonal antibody fragm...

EntireName: A bovine CLC-K channel complexed with a monoclonal antibody fragment (Fab)
Details: Fab fragment generated by proteolytic (papain) cleavage of murine IgG antibody.
Number of components: 5

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Component #1: protein, A bovine CLC-K channel complexed with a monoclonal antib...

ProteinName: A bovine CLC-K channel complexed with a monoclonal antibody fragment (Fab)
Details: Fab fragment generated by proteolytic (papain) cleavage of murine IgG antibody.
Recombinant expression: No
SourceSpecies: Bos taurus / mammal / ウシ /
Source (engineered)Expression System: Homo sapiens / human / Vector: pFastBac (BacMam)

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Component #2: protein, Chloride channel protein

ProteinName: Chloride channel protein / Recombinant expression: No
MassTheoretical: 73.521484 kDa
Source (engineered)Expression System: Bos taurus / mammal / ウシ /

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Component #3: protein, Monoclonal antibody, Fab fragment, heavy chain

ProteinName: Monoclonal antibody, Fab fragment, heavy chain / Recombinant expression: No
MassTheoretical: 12.633068 kDa
SourceSpecies: Mus musculus / mammal / ハツカネズミ, はつかねずみ /

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Component #4: protein, Monoclonal antibody, Fab fragment, light chain

ProteinName: Monoclonal antibody, Fab fragment, light chain / Recombinant expression: No
MassTheoretical: 11.824102 kDa
SourceSpecies: Mus musculus / mammal / ハツカネズミ, はつかねずみ /

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Component #5: ligand, CHOLESTEROL HEMISUCCINATE

LigandName: CHOLESTEROL HEMISUCCINATE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.486726 kDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 3 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 90 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.8 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 67475
3D reconstructionSoftware: RELION / Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF
Details: the indicated resolution was estimated on the primary map using the provided mask including Fab.
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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