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- EMDB-3583: Cryo-EM structure of a Separase-Securin complex from Caenorhabdit... -

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Basic information

Entry
Database: EMDB / ID: 3583
TitleCryo-EM structure of a Separase-Securin complex from Caenorhabditis elegans at 3.8 A resolution
SampleCaenorhabditis elegans Separase-Securin complex
SourceCaenorhabditis elegans / animal /
Map dataMap of the C. elegans Separase-Securin complex. Manual B-factor sharpening of 140 applied.
Methodsingle particle reconstruction, at 3.8 A resolution
AuthorsBoland A / Martin TG
CitationNat. Struct. Mol. Biol., 2017

Nat. Struct. Mol. Biol., 2017 StrPapers
Cryo-EM structure of a metazoan separase-securin complex at near-atomic resolution.
Andreas Boland / Thomas G Martin / Ziguo Zhang / Jing Yang / Xiao-Chen Bai / Leifu Chang / Sjors H W Scheres / David Barford

DateDeposition: Jan 31, 2017 / Header (metadata) release: Feb 15, 2017 / Map release: Mar 8, 2017 / Last update: Jan 31, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5mz6
  • Surface level: 0.1
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_3583.map.gz (map file in CCP4 format, 23329 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
180 pix
1.43 A/pix
= 257.4 A
180 pix
1.43 A/pix
= 257.4 A
180 pix
1.43 A/pix
= 257.4 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.43 A
Density
Contour Level:0.1 (by author), 0.1 (movie #1):
Minimum - Maximum-0.29977334 - 0.39163244
Average (Standard dev.)0.00042302595 (0.009249026)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions180180180
Origin000
Limit179179179
Spacing180180180
CellA=B=C: 257.4 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.431.431.43
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z257.400257.400257.400
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.3000.3920.000

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Supplemental data

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Sample components

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Entire Caenorhabditis elegans Separase-Securin complex

EntireName: Caenorhabditis elegans Separase-Securin complex
Details: C. elegans Separase-Securin complex at 3.8 Angstrom resolution refined with Relion.
Number of components: 3
MassTheoretical: 170 kDa

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Component #1: protein, Caenorhabditis elegans Separase-Securin complex

ProteinName: Caenorhabditis elegans Separase-Securin complex
Details: C. elegans Separase-Securin complex at 3.8 Angstrom resolution refined with Relion.
Recombinant expression: No
MassTheoretical: 170 kDa
SourceSpecies: Caenorhabditis elegans / animal /
Source (engineered)Expression System: Trichoplusia ni / arthropod / イラクサキンウワバ, イラクサギンウワバ

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Component #2: protein, SEParase

ProteinName: SEParase / Recombinant expression: No
MassTheoretical: 144.315984 kDa
Source (engineered)Expression System: Caenorhabditis elegans / animal /

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Component #3: protein, Interactor of FizzY protein

ProteinName: Interactor of FizzY protein / Recombinant expression: No
MassTheoretical: 27.027646 kDa
Source (engineered)Expression System: Caenorhabditis elegans / animal /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.02 mg/ml / pH: 7.8
Support filmGlow discharging was performed before applying graphene oxide solution onto the grid. Grid was washed three times, dried and sample was applied. For detailed information see: https://figshare.com/articles/Graphene_Oxide_Grid_Preparation/3178669
VitrificationCryogen name: ETHANE / Temperature: 277 K / Humidity: 100 % / Details: Custom Manual Plunger

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.25 e/A2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Energy filter: GIF / Energy window: -20-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 103696
3D reconstructionSoftware: RELION / Resolution: 3.8 A / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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