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- EMDB-3584: Cryo-EM structure of a Separase-Securin complex from Caenorhabdit... -

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Basic information

Entry
Database: EMDB / ID: 3584
TitleCryo-EM structure of a Separase-Securin complex from Caenorhabditis elegans at 3.8 A resolution
SampleHomo sapiens Separase-Securin complex
SourceHomo sapiens / human
Map dataCryo-EM structure of the human Separase-Securin complex
Methodsingle particle reconstruction, at 3.8 A resolution
AuthorsBoland A / Martin TG / Zhang Z / Yang J / Bai XC / Chang L / Scheres SHW / Barford D
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: 0.004
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.004
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_3584.map.gz (map file in CCP4 format, 55297 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.05 A/pix
= 252. A
240 pix
1.05 A/pix
= 252. A
240 pix
1.05 A/pix
= 252. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.05 A
Density
Contour Level:0.004 (by author), 0.004 (movie #1):
Minimum - Maximum-0.0043986565 - 0.022666683
Average (Standard dev.)0.00015417936 (0.0012133757)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin000
Limit239239239
Spacing240240240
CellA=B=C: 251.99998 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.051.051.05
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z252.000252.000252.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0040.0230.000

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Supplemental data

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Sample components

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Entire Homo sapiens Separase-Securin complex

EntireName: Homo sapiens Separase-Securin complex
Details: H. sapiens Separase-Securin complex at medium resolution refined with Relion. Sample exhibits strong preferred orientation of particles.
Number of components: 2
MassTheoretical: 255 kDa

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Component #1: protein, Homo sapiens Separase-Securin complex

ProteinName: Homo sapiens Separase-Securin complex
Details: H. sapiens Separase-Securin complex at medium resolution refined with Relion. Sample exhibits strong preferred orientation of particles.
Recombinant expression: No
MassTheoretical: 255 kDa
SourceSpecies: Homo sapiens / human
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-Securin complex

ProteinName: Separase-Securin complex / Recombinant expression: No
Source (engineered)Expression System: Homo sapiens / human

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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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