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- PDB-5mz6: Cryo-EM structure of a Separase-Securin complex from Caenorhabdit... -

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Basic information

Entry
Database: PDB / ID: 5mz6
TitleCryo-EM structure of a Separase-Securin complex from Caenorhabditis elegans at 3.8 A resolution
Components
  • Interactor of FizzY protein
  • SEParase
KeywordsCELL CYCLE / caspase / cell cycle / cohesin / cleavage
Function / homologyPeptidase family C50 / Separation of Sister Chromatids / SEPARIN core domain profile. / SEPARIN core domain / Peptidase C50, separase / cortical granule exocytosis / metaphase plate / regulation of nematode larval development / separase / eggshell formation ...Peptidase family C50 / Separation of Sister Chromatids / SEPARIN core domain profile. / SEPARIN core domain / Peptidase C50, separase / cortical granule exocytosis / metaphase plate / regulation of nematode larval development / separase / eggshell formation / polar body extrusion after meiotic divisions / cortical granule / polarity specification of anterior/posterior axis / meiotic chromosome separation / mitotic sister chromatid separation / regulation of centriole-centriole cohesion / regulation of locomotion / regulation of exocytosis / multicellular organismal reproductive process / meiotic spindle / centrosome localization / cleavage furrow / mitotic cytokinesis / cellular protein localization / centrosome duplication / protein processing / condensed chromosome / mitotic spindle / condensed nuclear chromosome / spindle microtubule / spindle / nuclear envelope / midbody / cell cortex / chromosome / protein stabilization / cysteine-type endopeptidase activity / protease binding / centrosome / ubiquitin protein ligase binding / nucleus / cytoplasm / Separin homolog sep-1 / Securin-like protein
Function and homology information
Specimen sourceCaenorhabditis elegans (roundworm)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsBoland, A. / Martin, T.G. / Zhang, Z. / Yang, J. / Bai, X.C. / Chang, L. / Scheres, S.H.W. / Barford, D.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Cryo-EM structure of a metazoan separase-securin complex at near-atomic resolution.
Authors: Andreas Boland / Thomas G Martin / Ziguo Zhang / Jing Yang / Xiao-Chen Bai / Leifu Chang / Sjors H W Scheres / David Barford
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 31, 2017 / Release: Mar 8, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 8, 2017Structure modelrepositoryInitial release
1.1Mar 15, 2017Structure modelDatabase references
1.2Apr 19, 2017Structure modelDatabase references
1.3Aug 30, 2017Structure modelData collectionem_software_em_software.name

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Assembly

Deposited unit
1: SEParase
B: Interactor of FizzY protein


Theoretical massNumber of molelcules
Total (without water)171,3442
Polyers171,3442
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)5510
ΔGint (kcal/M)-29
Surface area (Å2)39900
MethodPISA

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Components

#1: Protein/peptide SEParase / / Separase


Mass: 144315.984 Da / Num. of mol.: 1 / Source: (gene. exp.) Caenorhabditis elegans (roundworm) / Gene: sep-1, CELE_Y47G6A.12, Y47G6A.12 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G5ED39
#2: Protein/peptide Interactor of FizzY protein


Mass: 27027.646 Da / Num. of mol.: 1 / Source: (gene. exp.) Caenorhabditis elegans (roundworm) / Gene: ify-1, C27A2.3, CELE_C27A2.3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q18235

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Caenorhabditis elegans Separase-Securin complex / Type: COMPLEX
Details: C. elegans Separase-Securin complex at 3.8 Angstrom resolution refined with Relion.
Entity ID: 1, 2 / Source: RECOMBINANT
Molecular weightValue: 0.17 MDa / Experimental value: NO
Source (natural)Organism: Caenorhabditis elegans (roundworm)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.8
SpecimenConc.: 0.02 mg/ml / Details: Monodisperse sample / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Glow 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
Grid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins / Details: Custom Manual Plunger

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / C2 aperture diameter: 70 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.8 sec. / Electron dose: 1.25 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF / Energyfilter upper: 20 eV / Energyfilter lower: -20 eV
Image scansWidth: 3710 / Height: 3710

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategory
4GctfCTF correction
7Coot0.88model fitting
9RELION2.0initial Euler assignment
10RELION2.0final Euler assignment
12RELION2.03D reconstruction
EM 3D crystal entityAngle alpha: 9 deg. / Angle beta: 9 deg. / Angle gamma: 9 deg. / Length a: 1 Å / Length b: 1 Å / Length c: 1 Å / Space group name: 1 / Space group num: 1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 103696 / Symmetry type: POINT
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0058569
ELECTRON MICROSCOPYf_angle_d0.89111591
ELECTRON MICROSCOPYf_dihedral_angle_d11.8255189
ELECTRON MICROSCOPYf_chiral_restr0.0491312
ELECTRON MICROSCOPYf_plane_restr0.0061473

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