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- PDB-8k4d: Structure of the SA2/Scc1/CENP_U complex -

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Basic information

Entry
Database: PDB / ID: 8k4d
TitleStructure of the SA2/Scc1/CENP_U complex
Components
  • 64-kDa C-terminal product
  • CENP-U
  • Cohesin subunit SA-2
KeywordsCELL CYCLE / inner kinetochore / cohesion
Function / homology
Function and homology information


negative regulation of mitotic metaphase/anaphase transition / Cohesin Loading onto Chromatin / meiotic cohesin complex / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / cohesin complex / positive regulation of sister chromatid cohesion / mitotic cohesin complex / negative regulation of G2/M transition of mitotic cell cycle / negative regulation of glial cell apoptotic process ...negative regulation of mitotic metaphase/anaphase transition / Cohesin Loading onto Chromatin / meiotic cohesin complex / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / cohesin complex / positive regulation of sister chromatid cohesion / mitotic cohesin complex / negative regulation of G2/M transition of mitotic cell cycle / negative regulation of glial cell apoptotic process / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / chromatin looping / reciprocal meiotic recombination / sister chromatid cohesion / negative regulation of interleukin-1 beta production / lncRNA binding / mitotic spindle pole / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / chromosome, centromeric region / mitotic spindle assembly / SUMOylation of DNA damage response and repair proteins / cis-regulatory region sequence-specific DNA binding / protein localization to chromatin / Meiotic synapsis / Resolution of Sister Chromatid Cohesion / condensed nuclear chromosome / meiotic cell cycle / chromosome segregation / nuclear matrix / fibrillar center / spindle pole / Separation of Sister Chromatids / double-strand break repair / chromosome / midbody / DNA-binding transcription factor binding / DNA recombination / Estrogen-dependent gene expression / negative regulation of neuron apoptotic process / response to hypoxia / cell division / apoptotic process / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleolus / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
: / Cohesin subunit SCC3/SA, HEAT-repeats domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA / STAG domain / Stromalin conservative domain / Stromalin conservative (SCD) domain profile. / : / Rad21/Rec8-like protein, C-terminal, eukaryotic ...: / Cohesin subunit SCC3/SA, HEAT-repeats domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA / STAG domain / Stromalin conservative domain / Stromalin conservative (SCD) domain profile. / : / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / Armadillo-type fold / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
Double-strand-break repair protein rad21 homolog / Cohesin subunit SA-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.52 Å
AuthorsLiu, M.J. / He, X.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The CENP-O complex links inner kinetochore to centromere cohesion
Authors: Liu, M.J. / He, X.J.
History
DepositionJul 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cohesin subunit SA-2
B: 64-kDa C-terminal product
C: CENP-U


Theoretical massNumber of molelcules
Total (without water)130,7433
Polymers130,7433
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-43 kcal/mol
Surface area48860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.321, 132.615, 148.001
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Cohesin subunit SA-2 / SCC3 homolog 2 / Stromal antigen 2


Mass: 113480.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SA2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N3U4
#2: Protein 64-kDa C-terminal product / 64-kDa carboxy-terminal product / 65-kDa carboxy-terminal product


Mass: 16180.806 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCC1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60216
#3: Protein/peptide CENP-U


Mass: 1081.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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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: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.03 M CaCl2,0.03 M MgCl2, 0.1 M MOPS-HEPES, pH7.5, 10% PEG8000, 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.52→49.43 Å / Num. obs: 19789 / % possible obs: 99.15 % / Redundancy: 2 % / CC1/2: 0.999 / CC star: 1 / Rpim(I) all: 0.042 / Rrim(I) all: 0.059 / Net I/σ(I): 10.39
Reflection shellResolution: 3.52→3.65 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.59 / Num. unique obs: 1830 / CC1/2: 0.528 / CC star: 0.831 / Rpim(I) all: 0.52 / Rrim(I) all: 0.74 / % possible all: 93.27

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.52→49.43 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 36.647 / SU ML: 0.526 / Cross valid method: THROUGHOUT / ESU R Free: 0.639 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26943 1036 5.2 %RANDOM
Rwork0.22017 ---
obs0.22275 18753 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 138.582 Å2
Baniso -1Baniso -2Baniso -3
1--2.43 Å2-0 Å20 Å2
2--1.27 Å2-0 Å2
3---1.16 Å2
Refinement stepCycle: 1 / Resolution: 3.52→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8141 0 0 0 8141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0138281
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177827
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.63711161
X-RAY DIFFRACTIONr_angle_other_deg1.6071.57618171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5465991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09123.152441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.003151577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7061546
X-RAY DIFFRACTIONr_chiral_restr0.0950.21091
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029031
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021699
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it10.77314.6623997
X-RAY DIFFRACTIONr_mcbond_other10.77414.6633996
X-RAY DIFFRACTIONr_mcangle_it16.78221.9894977
X-RAY DIFFRACTIONr_mcangle_other16.78121.9884978
X-RAY DIFFRACTIONr_scbond_it9.99715.2834283
X-RAY DIFFRACTIONr_scbond_other9.99715.2864281
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.99122.6736184
X-RAY DIFFRACTIONr_long_range_B_refined24.07434077
X-RAY DIFFRACTIONr_long_range_B_other24.07434076
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.524→3.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 62 -
Rwork0.342 1269 -
obs--90.85 %

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