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- PDB-8ibh: Cep57 C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 8ibh
TitleCep57 C-terminal domain
ComponentsCentrosomal protein of 57 kDa
KeywordsCELL CYCLE / coiled-coil / cell centrosome / scaffold
Function / homology
Function and homology information


gamma-tubulin binding / spermatid development / fibroblast growth factor binding / fibroblast growth factor receptor signaling pathway / 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 / AURKA Activation by TPX2 ...gamma-tubulin binding / spermatid development / fibroblast growth factor binding / fibroblast growth factor receptor signaling pathway / 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 / AURKA Activation by TPX2 / protein homooligomerization / centriolar satellite / Regulation of PLK1 Activity at G2/M Transition / microtubule binding / microtubule / centrosome / Golgi apparatus / protein homodimerization activity / nucleus / cytosol
Similarity search - Function
Cep57 centrosome microtubule-binding domain / Cep57 centrosome localisation domain / : / Centrosome microtubule-binding domain of Cep57 / Centrosome localisation domain of Cep57
Similarity search - Domain/homology
Centrosomal protein of 57 kDa
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChen, T. / Yeh, H.-W. / Cheng, H.-C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science and Technology Council (Taiwan)111-2311-B-007 -009 - Taiwan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Cep57 regulates human centrosomes through multivalent interactions.
Authors: Yeh, H.W. / Chen, P.P. / Yeh, T.C. / Lin, S.L. / Chen, Y.T. / Lin, W.P. / Chen, T. / Pang, J.M. / Lin, K.T. / Wang, L.H. / Lin, Y.C. / Shih, O. / Jeng, U.S. / Hsia, K.C. / Cheng, H.C.
History
DepositionFeb 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[3]

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Centrosomal protein of 57 kDa


Theoretical massNumber of molelcules
Total (without water)12,5361
Polymers12,5361
Non-polymers00
Water23413
1
A: Centrosomal protein of 57 kDa

A: Centrosomal protein of 57 kDa


Theoretical massNumber of molelcules
Total (without water)25,0732
Polymers25,0732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z1
Unit cell
Length a, b, c (Å)62.937, 62.937, 81.494
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11A-203-

HOH

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Components

#1: Protein Centrosomal protein of 57 kDa / Cep57 / FGF2-interacting protein / Testis-specific protein 57 / Translokin


Mass: 12536.278 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEP57, KIAA0092, TSP57 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86XR8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 1.86 Å3/Da / Density % sol: 33.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium chloride, 0.1 M HEPES pH 7.5, 1.6 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→30 Å / Num. obs: 7114 / % possible obs: 99.3 % / Redundancy: 9.2 % / Biso Wilson estimate: 25.44 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 38
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2 / Num. unique obs: 681 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L0R

4l0r


Resolution: 2.1→24.91 Å / SU ML: 0.2125 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5964
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2572 272 5 %
Rwork0.2383 5169 -
obs0.2392 5441 91.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.97 Å2
Refinement stepCycle: LAST / Resolution: 2.1→24.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms603 0 0 13 616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0157607
X-RAY DIFFRACTIONf_angle_d1.295812
X-RAY DIFFRACTIONf_chiral_restr0.053792
X-RAY DIFFRACTIONf_plane_restr0.0076108
X-RAY DIFFRACTIONf_dihedral_angle_d22.3524242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.650.32461200.23132287X-RAY DIFFRACTION83
2.65-24.910.23531520.24072882X-RAY DIFFRACTION98.6
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)
16.84825230558-3.99130208668-1.304644409486.908701198650.9396838928643.545046758870.0178963133997-0.02775804001110.551705186676-0.367390808886-0.0637717041407-0.250594046836-0.5415441933170.0648076939955-0.0752058844980.2223095587380.0558942524863-0.04194066340820.3251964770280.0005308918804770.12084608009333.5515484029-19.20333234213.67945918492
26.2354333587-6.333613428220.1721674186677.468933078980.00917224631362.91636171759-0.138560170197-0.2557690042110.06964925476910.00441042000305-0.04153944000530.1578414235310.0321235334797-0.3492120804730.1625379806570.220011636688-0.01486737366460.007224779686160.342677384189-0.0749510591490.18525748234728.129004405-23.28086324218.67325440167
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 33 through 68 )33 - 682 - 37
22chain 'A' and (resid 69 through 106 )69 - 10638 - 75

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