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- PDB-5fc3: Structural basis of cohesin cleavage by separase -

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Basic information

Entry
Database: PDB / ID: 5fc3
TitleStructural basis of cohesin cleavage by separase
Components
  • pAMK peptide
  • separase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / cysteine protease / cohesin / complex / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


nuclear chromosome segregation / separase / nuclear division / cysteine-type endopeptidase activity / proteolysis / nucleus
Similarity search - Function
Peptidase family C50 / Peptidase C50, separase / SEPARIN core domain / SEPARIN core domain profile.
Similarity search - Domain/homology
PAMK PEPTIDE Inhibitor / separase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsLin, Z. / Luo, X. / Yu, H.
CitationJournal: Nature / Year: 2016
Title: Structural basis of cohesin cleavage by separase
Authors: Lin, Z. / Luo, X. / Yu, H.
History
DepositionDec 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Apr 27, 2016Group: Database references
Revision 1.3May 4, 2016Group: Derived calculations / Structure summary
Revision 1.4Sep 27, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: pAMK peptide
B: separase


Theoretical massNumber of molelcules
Total (without water)69,9192
Polymers69,9192
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint2 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.148, 149.148, 115.625
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11B-2321-

HOH

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Components

#1: Protein/peptide pAMK peptide


Type: Oligopeptide / Class: Inhibitor / Mass: 1065.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: PAMK PEPTIDE Inhibitor
#2: Protein separase /


Mass: 68854.016 Da / Num. of mol.: 1 / Fragment: unp residues 1633-2223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0070540 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SHM3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammonium citrate tribasic, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.099→50 Å / Num. obs: 14250 / % possible obs: 99.9 % / Redundancy: 9.6 % / Net I/σ(I): 14.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data collection
Cootmodel building
PHENIXphasing
RefinementResolution: 3.1→48.82 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.258 711 5 %
Rwork0.194 --
obs0.197 14228 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→48.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3797 0 0 38 3835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013890
X-RAY DIFFRACTIONf_angle_d1.1285258
X-RAY DIFFRACTIONf_dihedral_angle_d13.741413
X-RAY DIFFRACTIONf_chiral_restr0.049579
X-RAY DIFFRACTIONf_plane_restr0.007681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0994-3.33870.34761360.26712592X-RAY DIFFRACTION98
3.3387-3.67460.30981400.21732652X-RAY DIFFRACTION100
3.6746-4.2060.23121420.18262681X-RAY DIFFRACTION100
4.206-5.29820.21081420.1642712X-RAY DIFFRACTION100
5.2982-48.82620.26751510.19552880X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0997-0.1431-0.08570.22920.13580.0815-0.09890.06150.02990.0413-0.03050.0346-0.01330.1632-0.00110.78010.02630.16271.0647-0.00511.2763-0.1619-61.28546.3618
20.5374-0.2384-0.21311.8854-0.26161.07270.13450.23460.3943-0.0779-0.1132-0.2319-0.17190.085800.5970.05430.06540.59970.03140.6413-9.2916-50.4584-15.0889
31.09790.1785-0.10890.4510.14580.04640.2230.21010.3078-0.1054-0.06690.0154-0.1786-0.258200.67350.12370.10620.55920.09680.5626-24.9056-41.1544-21.0111
40.857-0.6355-0.50522.07870.19512.8973-0.0099-0.0578-0.1092-0.05420.036-0.0999-0.0349-0.105400.3847-0.005-0.00830.4584-0.01590.4416-13.6574-70.2767-4.6973
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 5:7 )A5 - 7
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1696:1818 )B1696 - 1818
3X-RAY DIFFRACTION3( CHAIN B AND RESID 1819:1993 )B1819 - 1993
4X-RAY DIFFRACTION4( CHAIN B AND RESID 1994:2220 )B1994 - 2220

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