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- EMDB-13933: Focused refined map of the TPR lobe of the Anaphase-promoting com... -

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Basic information

Entry
Database: EMDB / ID: EMD-13933
TitleFocused refined map of the TPR lobe of the Anaphase-promoting complex/cyclosome (APC/C)
Map dataFocused refined map (sharpened with deepEMhancer) of the TPR lobe of the Anaphase-promoting complex/cyclosome (APC/C)
Sample
  • Complex: Anaphase-promoting complex (APC/C) bound to co-activator Cdh1
KeywordsAPC/C / cyclosome / Cdc20 / Cdh1 / ubiquitination / Emi1 / mitosis / Cell cycle
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsHoefler A / Yu J / Chang L / Zhang Z / Yang J / Boland A / Barford D
Funding support Switzerland, United Kingdom, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_185235 Switzerland
Medical Research Council (MRC, United Kingdom)MC_UP_1201/6 United Kingdom
CitationJournal: To Be Published
Title: High-resolution structure of the Anaphase-promoting complex (APC/C) bound to co-activator Cdh1
Authors: Hoefler A / Yu J / Chang L / Zhang Z / Yang J / Boland A / Barford D
History
DepositionDec 1, 2021-
Header (metadata) releaseDec 22, 2021-
Map releaseDec 22, 2021-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.085
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.085
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13933.png

Downloads & links

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Map

FileDownload / File: emd_13933.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refined map (sharpened with deepEMhancer) of the TPR lobe of the Anaphase-promoting complex/cyclosome (APC/C)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.085 / Movie #1: 0.085
Minimum - Maximum-0.03774307 - 1.9113202
Average (Standard dev.)0.0023139876 (±0.033902943)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 385.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z385.200385.200385.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0381.9110.002

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Supplemental data

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Additional map: Focused refined map (unsharpened) of the TPR lobe...

Fileemd_13933_additional_1.map
AnnotationFocused refined map (unsharpened) of the TPR lobe of the Anaphase-promoting complex/cyclosome (APC/C)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of the TPR lobe of...

Fileemd_13933_half_map_1.map
AnnotationHalf map A of the TPR lobe of the Anaphase-promoting complex/cyclosome (APC/C)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of the TPR lobe of...

Fileemd_13933_half_map_2.map
AnnotationHalf map B of the TPR lobe of the Anaphase-promoting complex/cyclosome (APC/C)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Anaphase-promoting complex (APC/C) bound to co-activator Cdh1

EntireName: Anaphase-promoting complex (APC/C) bound to co-activator Cdh1
Components
  • Complex: Anaphase-promoting complex (APC/C) bound to co-activator Cdh1

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Supramolecule #1: Anaphase-promoting complex (APC/C) bound to co-activator Cdh1

SupramoleculeName: Anaphase-promoting complex (APC/C) bound to co-activator Cdh1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.2 MDa

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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

Concentration0.1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMHepes2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
200.0 mMNaClsodium chloride
2.0 mMDTTDithiothreitol
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 50 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 8297 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1800000 / Details: The particles were automatically selected
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.14.2) / Software - details: Local refinement / Number images used: 364331
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.14.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.14.2)
Final 3D classificationNumber classes: 8 / Software - Name: RELION (ver. 3.1 beta)

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Atomic model buiding 1

Initial modelPDB ID:

4ui9


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 80

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