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- PDB-7w91: Residues 440-490 of centrosomal protein 63 -

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Basic information

Entry
Database: PDB / ID: 7w91
TitleResidues 440-490 of centrosomal protein 63
ComponentsCentrosomal protein of 63 kDa
KeywordsSTRUCTURAL PROTEIN / Cep63 / Centrosomal Protein 63
Function / homology
Function and homology information


negative regulation of protein K63-linked ubiquitination / de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / centriole replication / centriolar satellite / signal transduction in response to DNA damage / spindle assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / negative regulation of innate immune response ...negative regulation of protein K63-linked ubiquitination / de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / centriole replication / centriolar satellite / signal transduction in response to DNA damage / spindle assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / negative regulation of innate immune response / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / DNA damage checkpoint signaling / spindle pole / Regulation of PLK1 Activity at G2/M Transition / molecular adaptor activity / protein stabilization / cell division / centrosome / cytosol
Similarity search - Function
Centrosomal protein Cep63/Deup1, N-terminal / Centrosomal protein of 63 kDa
Similarity search - Domain/homology
Centrosomal protein of 63 kDa
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.292 Å
AuthorsYun, H.Y. / Ku, B.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019M3E5D6063955 Korea, Republic Of
National Research Foundation (NRF, Korea)KGM9952112 Korea, Republic Of
CitationJournal: Commun Biol / Year: 2023
Title: Architectural basis for cylindrical self-assembly governing Plk4-mediated centriole duplication in human cells.
Authors: Il Ahn, J. / Zhang, L. / Ravishankar, H. / Fan, L. / Kirsch, K. / Zeng, Y. / Meng, L. / Park, J.E. / Yun, H.Y. / Ghirlando, R. / Ma, B. / Ball, D. / Ku, B. / Nussinov, R. / Schmit, J.D. / ...Authors: Il Ahn, J. / Zhang, L. / Ravishankar, H. / Fan, L. / Kirsch, K. / Zeng, Y. / Meng, L. / Park, J.E. / Yun, H.Y. / Ghirlando, R. / Ma, B. / Ball, D. / Ku, B. / Nussinov, R. / Schmit, J.D. / Heinz, W.F. / Kim, S.J. / Karpova, T. / Wang, Y.X. / Lee, K.S.
History
DepositionDec 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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
B: Centrosomal protein of 63 kDa
C: Centrosomal protein of 63 kDa
D: Centrosomal protein of 63 kDa
E: Centrosomal protein of 63 kDa
F: Centrosomal protein of 63 kDa
G: Centrosomal protein of 63 kDa
H: Centrosomal protein of 63 kDa
I: Centrosomal protein of 63 kDa
J: Centrosomal protein of 63 kDa
K: Centrosomal protein of 63 kDa
L: Centrosomal protein of 63 kDa


Theoretical massNumber of molelcules
Total (without water)82,10512
Polymers82,10512
Non-polymers00
Water00
1
A: Centrosomal protein of 63 kDa
B: Centrosomal protein of 63 kDa
C: Centrosomal protein of 63 kDa
D: Centrosomal protein of 63 kDa
E: Centrosomal protein of 63 kDa
F: Centrosomal protein of 63 kDa


Theoretical massNumber of molelcules
Total (without water)41,0536
Polymers41,0536
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11110 Å2
ΔGint-121 kcal/mol
Surface area21140 Å2
MethodPISA
2
G: Centrosomal protein of 63 kDa
H: Centrosomal protein of 63 kDa
I: Centrosomal protein of 63 kDa
J: Centrosomal protein of 63 kDa
K: Centrosomal protein of 63 kDa
L: Centrosomal protein of 63 kDa


Theoretical massNumber of molelcules
Total (without water)41,0536
Polymers41,0536
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11290 Å2
ΔGint-116 kcal/mol
Surface area21040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.622, 81.112, 80.846
Angle α, β, γ (deg.)65.330, 60.070, 60.200
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Centrosomal protein of 63 kDa / Cep63


Mass: 6842.105 Da / Num. of mol.: 12
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
Has ligand of interestY
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: 5.07 Å3/Da / Density % sol: 75.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.6 M sodium citrate tribasic dihydrate, 0.1 M Tris-HCl pH 7.75, 0.4 M NDSB-221, 0.1M ethylene-diamine-tetraacetic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 3.292→50 Å / Num. obs: 37129 / % possible obs: 90.4 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 17.92
Reflection shellResolution: 3.292→3.36 Å / Rmerge(I) obs: 0.221 / Num. unique obs: 1383

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.292→36.229 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 2.64 / Phase error: 26.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2607 3638 9.8 %
Rwork0.2293 33482 -
obs0.2324 37120 81.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 221.37 Å2 / Biso mean: 57.3548 Å2 / Biso min: 20.99 Å2
Refinement stepCycle: final / Resolution: 3.292→36.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5084 0 0 0 5084
Num. residues----616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035108
X-RAY DIFFRACTIONf_angle_d0.486740
X-RAY DIFFRACTIONf_chiral_restr0.026740
X-RAY DIFFRACTIONf_plane_restr0.001868
X-RAY DIFFRACTIONf_dihedral_angle_d18.6533344
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.292-3.33510.33151220.32688155
3.3351-3.38070.36841150.2914106865
3.3807-3.4290.3206650.2679101466
3.429-3.48010.26041170.2857111170
3.4801-3.53450.27711670.2633107972
3.5345-3.59240.3711880.2507123575
3.5924-3.65430.29331200.2509127079
3.6543-3.72060.24451500.2486120080
3.7206-3.79210.25491450.2374132782
3.7921-3.86950.24571530.2393127780
3.8695-3.95350.28121150.2429126482
3.9535-4.04530.21641490.2334136884
4.0453-4.14640.31291410.1966129986
4.1464-4.25830.2031740.1959144986
4.2583-4.38340.15981420.1822131789
4.3834-4.52460.24381320.1885141886
4.5246-4.6860.25641620.1894132688
4.686-4.87320.25571620.2009139589
4.8732-5.09440.23891590.2021144890
5.0944-5.36220.25481330.2275137587
5.3622-5.6970.25931560.266129284
5.697-6.13490.33481300.297136285
6.1349-6.74870.32091570.2656140487
6.7487-7.7170.28731590.259135390
7.717-9.69170.22021580.211150194
9.6917-36.2290.27281670.2144144992

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