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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 A resolution / 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 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 / Release: Mar 8, 2017 / Last modification: Apr 19, 2017

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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 (A2)5510
ΔGint (kcal/M)-29
Surface area (A2)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

Biological process

Experimental details


EM experimentReconstruction method: SINGLE PARTICLE

Sample preparation

Assembly of specimenName: Caenorhabditis elegans Separase-Securin complex / Aggregation state: PARTICLE
ComponentName: Caenorhabditis elegans Separase-Securin complex
Details: C. elegans Separase-Securin complex at 3.8 Angstrom resolution refined with Relion.
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 % / 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 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER


SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
ComputingStructure refinement: PHENIX (1.11.1_2575: phenix.real_space_refine)
3D reconstructionResolution: 3.8 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 103696
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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