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

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Basic information

Entry
Database: PDB / ID: 6csv
TitleThe structure of the Cep63-Cep152 heterotetrameric complex
ComponentsCentrosomal protein of 63 kDa,Centrosomal protein of 152 kDaCentrosome
KeywordsCELL CYCLE / Centrosome / Complex / 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 / SAD / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,3554
Polymers44,3554
Non-polymers00
Water66737
1
A: Centrosomal protein of 63 kDa,Centrosomal protein of 152 kDa
C: Centrosomal protein of 63 kDa,Centrosomal protein of 152 kDa


Theoretical massNumber of molelcules
Total (without water)22,1772
Polymers22,1772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-39 kcal/mol
Surface area11040 Å2
MethodPISA
2
B: Centrosomal protein of 63 kDa,Centrosomal protein of 152 kDa
D: Centrosomal protein of 63 kDa,Centrosomal protein of 152 kDa


Theoretical massNumber of molelcules
Total (without water)22,1772
Polymers22,1772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-43 kcal/mol
Surface area10700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.403, 44.420, 225.937
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 63 kDa,Centrosomal protein of 152 kDa / Centrosome / Cep63 / Cep152


Mass: 11088.716 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEP63, CEP152, KIAA0912 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96MT8, UniProt: O94986
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.51 Å3/Da / Density % sol: 51.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris (pH 5.5) and 10% PEG 3350

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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-W / 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→19.93 Å / Num. obs: 19496 / % possible obs: 93.17 % / Redundancy: 4.9 % / Net I/σ(I): 15.82
Reflection shellResolution: 2.5→2.54 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.5→19.926 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.867 / SU B: 13.934 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R: 0.798 / ESU R Free: 0.388 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32079 1555 10 %RANDOM
Rwork0.25854 ---
obs0.26475 14033 95.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 57.564 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20 Å20 Å2
2--1.84 Å20 Å2
3----3.76 Å2
Refinement stepCycle: 1 / Resolution: 2.5→19.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 0 37 2970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192957
X-RAY DIFFRACTIONr_bond_other_d0.0020.022947
X-RAY DIFFRACTIONr_angle_refined_deg1.581.9783919
X-RAY DIFFRACTIONr_angle_other_deg1.03336805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6835343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.16922.911158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.36615656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3071540
X-RAY DIFFRACTIONr_chiral_restr0.0810.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02607
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_it3.8295.371396
X-RAY DIFFRACTIONr_mcbond_other3.8215.3661395
X-RAY DIFFRACTIONr_mcangle_it6.0178.0321731
X-RAY DIFFRACTIONr_mcangle_other6.0188.0361732
X-RAY DIFFRACTIONr_scbond_it4.4836.0821561
X-RAY DIFFRACTIONr_scbond_other4.4826.0841562
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1868.8882189
X-RAY DIFFRACTIONr_long_range_B_refined9.4763.9883419
X-RAY DIFFRACTIONr_long_range_B_other9.46164.0083419
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 105 -
Rwork0.318 956 -
obs--91.86 %

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