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- PDB-6csu: The structure of the Cep63-Cep152 heterotetrameric complex -

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Basic information

Entry
Database: PDB / ID: 6csu
TitleThe structure of the Cep63-Cep152 heterotetrameric complex
Components
  • Centrosomal protein of 152 kDaCentrosome
  • Centrosomal protein of 63 kDaCentrosome
KeywordsCELL CYCLE / Centrosome / Hydrophobic
Function / homology
Function and homology information


negative regulation of protein K63-linked ubiquitination / de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / procentriole / deuterosome / procentriole replication complex / cell projection organization / pericentriolar material / centriole replication / centrosome duplication / centriolar satellite ...negative regulation of protein K63-linked ubiquitination / de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / procentriole / deuterosome / procentriole replication complex / cell projection organization / pericentriolar material / centriole replication / centrosome duplication / centriolar satellite / spindle assembly / signal transduction in response to DNA damage / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / negative regulation of innate immune response / AURKA Activation by TPX2 / DNA damage checkpoint signaling / spindle pole / Regulation of PLK1 Activity at G2/M Transition / protein stabilization / molecular adaptor activity / cell division / centrosome / protein kinase binding / nucleoplasm / cytosol
Similarity search - Function
Centrosomal protein Cep63/Deup1, N-terminal / Centrosomal protein of 63 kDa
Similarity search - Domain/homology
Centrosomal protein of 152 kDa / Centrosomal protein of 63 kDa
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLee, E. / Chen, Y. / Zhang, L. / Kim, T.S. / Ahn, J.I. / Park, J.E. / Lee, K.S.
CitationJournal: Nat Commun / Year: 2019
Title: Molecular architecture of a cylindrical self-assembly at human centrosomes.
Authors: Kim, T.S. / Zhang, L. / Il Ahn, J. / Meng, L. / Chen, Y. / Lee, E. / Bang, J.K. / Lim, J.M. / Ghirlando, R. / Fan, L. / Wang, Y.X. / Kim, B.Y. / Park, J.E. / Lee, K.S.
History
DepositionMar 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Centrosomal protein of 152 kDa
C: Centrosomal protein of 63 kDa
D: Centrosomal protein of 152 kDa
A: Centrosomal protein of 63 kDa


Theoretical massNumber of molelcules
Total (without water)23,5764
Polymers23,5764
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-54 kcal/mol
Surface area11330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.066, 41.523, 205.619
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Centrosomal protein of 152 kDa / Centrosome / Cep152


Mass: 6456.716 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEP152, KIAA0912 / Production host: Escherichia coli (E. coli) / References: UniProt: O94986
#2: Protein/peptide Centrosomal protein of 63 kDa / Centrosome / Cep63


Mass: 5331.049 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEP63 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96MT8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES (pH 5.4), 23% PEG 3350 and 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Mar 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.5→19.87 Å / Num. obs: 8163 / % possible obs: 91.18 % / Redundancy: 6.9 % / Net I/σ(I): 16.68
Reflection shellResolution: 2.5→2.54 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.87 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.52 / Phase error: 29.39
RfactorNum. reflection% reflection
Rfree0.2853 817 10.01 %
Rwork0.25 --
obs0.2535 8163 90.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1489 0 0 15 1504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041498
X-RAY DIFFRACTIONf_angle_d0.6011985
X-RAY DIFFRACTIONf_dihedral_angle_d21.525966
X-RAY DIFFRACTIONf_chiral_restr0.031219
X-RAY DIFFRACTIONf_plane_restr0.002255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4956-2.65160.33581110.2958997X-RAY DIFFRACTION77
2.6516-2.85580.32981240.27821115X-RAY DIFFRACTION85
2.8558-3.14220.30381380.24871239X-RAY DIFFRACTION93
3.1422-3.59450.27281430.25621287X-RAY DIFFRACTION97
3.5945-4.51990.23581450.21261314X-RAY DIFFRACTION97
4.5199-19.87050.30851560.26171394X-RAY DIFFRACTION96

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