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- PDB-5u1t: Crystal structure of the Saccharomyces cerevisiae separase-securi... -

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Basic information

Entry
Database: PDB / ID: 5u1t
TitleCrystal structure of the Saccharomyces cerevisiae separase-securin complex at 2.6 angstrom resolution
Components
  • Securin
  • Separin
KeywordsHYDROLASE / separase-securin complex / ESP1 / PDS1 / chromosome segregation / cohesion / helical region / inhibition / chaperon
Function / homology
Function and homology information


meiosis II / positive regulation of metaphase/anaphase transition of meiotic cell cycle / Separation of Sister Chromatids / separase-securin complex / negative regulation of protein localization to nucleolus / negative regulation of exit from mitosis / separase / regulation of mitotic spindle elongation / meiotic chromosome separation / mitotic spindle pole body ...meiosis II / positive regulation of metaphase/anaphase transition of meiotic cell cycle / Separation of Sister Chromatids / separase-securin complex / negative regulation of protein localization to nucleolus / negative regulation of exit from mitosis / separase / regulation of mitotic spindle elongation / meiotic chromosome separation / mitotic spindle pole body / positive regulation of exit from mitosis / meiosis I / recombinational repair / mitotic sister chromatid segregation / spindle / mitotic spindle / intracellular protein localization / cell division / cysteine-type endopeptidase activity / apoptotic process / DNA damage response / enzyme binding / mitochondrion / proteolysis / nucleus / cytoplasm
Similarity search - Function
Securin sister-chromatid separation inhibitor / Securin sister-chromatid separation inhibitor / Peptidase C50, separase / SEPARIN core domain / Separin, protease domain / SEPARIN core domain profile.
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLuo, S. / Tong, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118093 United States
National Institutes of Health/Office of the DirectorS10OD012018 United States
CitationJournal: Nature / Year: 2017
Title: Molecular mechanism for the regulation of yeast separase by securin.
Authors: Luo, S. / Tong, L.
History
DepositionNov 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Separin
B: Securin


Theoretical massNumber of molelcules
Total (without water)197,4112
Polymers197,4112
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-50 kcal/mol
Surface area66110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.863, 125.863, 271.944
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Separin / Separase


Mass: 184044.469 Da / Num. of mol.: 1
Fragment: UNP residues 71-1630, helical domain and catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ESP1, YGR098C / Plasmid: pFL / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five Cell / References: UniProt: Q03018, separase
#2: Protein Securin


Mass: 13366.599 Da / Num. of mol.: 1
Fragment: UNP residues 258-373, separase interaction segment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: PDS1, YDR113C, YD9727.08C / Plasmid: pFL / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five Cell / References: UniProt: P40316
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 0.25 M Na/K-phosphate (pH 6.0) and 14% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 18, 2016 / Details: DECTRIS PILATUS 6M-F
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 77491 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 62.34 Å2 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.059 / Rrim(I) all: 0.153 / Χ2: 1.06 / Net I/av σ(I): 14.42 / Net I/σ(I): 4.3 / Num. measured all: 774372
Reflection shell
Resolution (Å)Redundancy (%)CC1/2Diffraction-ID% possible allRmerge(I) obs
2.6-2.698.20.476199.9
2.69-2.88.90.5951100
2.8-2.93100.777199.9
2.93-3.0810.70.86611000.924
3.08-3.2810.50.93311000.612
3.28-3.539.80.96511000.352
3.53-3.8810.90.98611000.221
3.88-4.4510.40.99111000.136
4.45-5.610.50.99311000.105
5.6-50100.998199.90.062

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
MR-Rosettaphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U1S

5u1s


Resolution: 2.6→48.667 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.01
RfactorNum. reflection% reflection
Rfree0.264 2015 2.6 %
Rwork0.2207 --
obs0.2218 77408 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.36 Å2 / Biso mean: 72.031 Å2 / Biso min: 35.38 Å2
Refinement stepCycle: final / Resolution: 2.6→48.667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12617 0 0 16 12633
Biso mean---63.21 -
Num. residues----1552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112865
X-RAY DIFFRACTIONf_angle_d1.217366
X-RAY DIFFRACTIONf_chiral_restr0.0552003
X-RAY DIFFRACTIONf_plane_restr0.0062162
X-RAY DIFFRACTIONf_dihedral_angle_d16.3254821
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6001-2.66510.37611410.34925291543299
2.6651-2.73720.37671450.326353085453100
2.7372-2.81770.40511420.30952795421100
2.8177-2.90860.40051430.301453535496100
2.9086-3.01260.31241390.29353025441100
3.0126-3.13320.38371420.285953625504100
3.1332-3.27570.36031390.270353405479100
3.2757-3.44840.2811440.251853715515100
3.4484-3.66440.2971430.246353775520100
3.6644-3.94720.26591400.216354205560100
3.9472-4.34420.23151450.191953965541100
4.3442-4.97230.20341450.178354225567100
4.9723-6.26240.26381490.208354835632100
6.2624-48.67520.19151580.16856895847100

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