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

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Database: PDB / ID: 5mz6
TitleCryo-EM structure of a Separase-Securin complex from Caenorhabditis elegans at 3.8 A resolution
DescriptorSEParase, Interactor of FizzY protein
KeywordsCELL CYCLE / caspase / cell cycle / cohesin / cleavage
Specimen sourceCaenorhabditis elegans / animal /
MethodElectron microscopy (3.8 Å resolution / Particle / Single particle)
AuthorsBoland, A. / Martin, T.G. / Zhang, Z. / Yang, J. / Bai, X.C. / Chang, L. / Scheres, S.H.W. / Barford, D.
CitationNat. Struct. Mol. Biol., 2017, 24, 414-418

Nat. Struct. Mol. Biol., 2017, 24, 414-418 Yorodumi Papers
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

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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Deposited unit
1: SEParase
B: Interactor of FizzY protein

Theoretical massNumber of molelcules
Total (without water)171,3442

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


#1: Polypeptide(L)SEParase / Separase

Mass: 144315.984 Da / Num. of mol.: 1 / Source: (gene. exp.) Caenorhabditis elegans / animal / / References: UniProt: G5ED39

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)Interactor of FizzY protein

Mass: 27027.646 Da / Num. of mol.: 1 / Source: (gene. exp.) Caenorhabditis elegans / animal / / References: UniProt: Q18235

Cellular component

Molecular function

Biological process

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Caenorhabditis elegans
Source (recombinant)Organism: Trichoplusia ni
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

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 FIELD / Cs: 2.7 mm / C2 aperture diameter: 70 mm / 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 scansDimension width: 3710 / Dimension height: 3710


SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDFitting ID
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
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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