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- PDB-5fcn: microtubule binding domain of human CEP135 -

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Basic information

Entry
Database: PDB / ID: 5fcn
Titlemicrotubule binding domain of human CEP135
ComponentsCentrosomal protein of 135 kDa
Keywordsmicrotubule-binding protein / centriole / coiled-coil
Function / homology
Function and homology information


positive regulation of non-motile cilium assembly / positive regulation of establishment of protein localization / centriole-centriole cohesion / centriole replication / 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 ...positive regulation of non-motile cilium assembly / positive regulation of establishment of protein localization / centriole-centriole cohesion / centriole replication / 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 / AURKA Activation by TPX2 / tubulin binding / Regulation of PLK1 Activity at G2/M Transition / microtubule binding / centrosome / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
Centrosomal protein of 135 kDa
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKraatz, S.H.W.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_138659 Switzerland
CitationJournal: Structure / Year: 2016
Title: The Human Centriolar Protein CEP135 Contains a Two-Stranded Coiled-Coil Domain Critical for Microtubule Binding.
Authors: Kraatz, S. / Guichard, P. / Obbineni, J.M. / Olieric, N. / Hatzopoulos, G.N. / Hilbert, M. / Sen, I. / Missimer, J. / Gonczy, P. / Steinmetz, M.O.
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 135 kDa
A: Centrosomal protein of 135 kDa


Theoretical massNumber of molelcules
Total (without water)15,4562
Polymers15,4562
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-29 kcal/mol
Surface area8340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.850, 78.850, 95.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11B-133-

HOH

21B-160-

HOH

31B-170-

HOH

41B-176-

HOH

51B-181-

HOH

61B-184-

HOH

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Components

#1: Protein Centrosomal protein of 135 kDa / Cep135 / Centrosomal protein 4


Mass: 7727.894 Da / Num. of mol.: 2 / Fragment: UNP residues 82-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEP135, CEP4, KIAA0635 / Plasmid: PSTCm1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q66GS9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 25% PEG 1500, 0.1M SPG buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→39.42 Å / Num. obs: 14195 / % possible obs: 99 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.04226 / Net I/σ(I): 18.71
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 5 % / Rmerge(I) obs: 0.4213 / Mean I/σ(I) obs: 3.49 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIXdev_1965refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GKW

4gkw


Resolution: 1.8→39.42 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2379 712 5.02 %
Rwork0.2156 --
obs0.2167 14194 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→39.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms887 0 0 145 1032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002928
X-RAY DIFFRACTIONf_angle_d0.3731242
X-RAY DIFFRACTIONf_dihedral_angle_d11.998373
X-RAY DIFFRACTIONf_chiral_restr0.017137
X-RAY DIFFRACTIONf_plane_restr0.001158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8005-1.93950.33731410.28342652X-RAY DIFFRACTION99
1.9395-2.13470.25471390.24022633X-RAY DIFFRACTION99
2.1347-2.44350.22641420.21572689X-RAY DIFFRACTION100
2.4435-3.07840.26141440.2132702X-RAY DIFFRACTION99
3.0784-39.43440.21651460.20542806X-RAY DIFFRACTION98

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