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- PDB-5oi7: Human CEP85 - coiled coil domain 4 -

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Basic information

Entry
Database: PDB / ID: 5oi7
TitleHuman CEP85 - coiled coil domain 4
ComponentsCentrosomal protein of 85 kDaCentrosome
KeywordsPROTEIN BINDING / Centrosomes / centriole / CEP85 / STIL
Function / homology
Function and homology information


regulation of mitotic centrosome separation / pericentriolar material / chromosome segregation / negative regulation of protein kinase activity / spindle pole / centrosome / nucleolus / Golgi apparatus / cytosol
Similarity search - Function
Centrosomal protein of 85 kDa
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
Authorsvan Breugel, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_1201/3 United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Direct binding of CEP85 to STIL ensures robust PLK4 activation and efficient centriole assembly.
Authors: Liu, Y. / Gupta, G.D. / Barnabas, D.D. / Agircan, F.G. / Mehmood, S. / Wu, D. / Coyaud, E. / Johnson, C.M. / McLaughlin, S.H. / Andreeva, A. / Freund, S.M.V. / Robinson, C.V. / Cheung, S.W.T. ...Authors: Liu, Y. / Gupta, G.D. / Barnabas, D.D. / Agircan, F.G. / Mehmood, S. / Wu, D. / Coyaud, E. / Johnson, C.M. / McLaughlin, S.H. / Andreeva, A. / Freund, S.M.V. / Robinson, C.V. / Cheung, S.W.T. / Raught, B. / Pelletier, L. / van Breugel, M.
History
DepositionJul 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: Centrosomal protein of 85 kDa
B: Centrosomal protein of 85 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8133
Polymers20,6952
Non-polymers1181
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS experiments
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-50 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.930, 73.880, 128.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Centrosomal protein of 85 kDa / Centrosome / Cep85 / Coiled-coil domain-containing protein 21


Mass: 10347.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEP85, CCDC21 / Production host: Escherichia coli (E. coli) / Variant (production host): C41 / References: UniProt: Q6P2H3
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 100 mM Na-HEPES, pH 7.7 200 mM Na-Citrate 36 % (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.67→36.98 Å / Num. obs: 21341 / % possible obs: 98.9 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.063 / Net I/σ(I): 8.6
Reflection shellResolution: 1.67→1.76 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.552 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2852 / CC1/2: 0.474 / Rpim(I) all: 0.506 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q6Q

2q6q


Resolution: 1.67→36.976 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 27.3
RfactorNum. reflection% reflection
Rfree0.2394 2011 5 %
Rwork0.2025 --
obs0.2043 21329 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.67→36.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1448 0 8 227 1683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021487
X-RAY DIFFRACTIONf_angle_d0.5381994
X-RAY DIFFRACTIONf_dihedral_angle_d12.16960
X-RAY DIFFRACTIONf_chiral_restr0.029220
X-RAY DIFFRACTIONf_plane_restr0.002270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6705-1.71220.34851400.33362664X-RAY DIFFRACTION97
1.7122-1.75850.35321590.31542700X-RAY DIFFRACTION100
1.7585-1.81030.33271250.28662762X-RAY DIFFRACTION100
1.8103-1.86870.35181300.27872756X-RAY DIFFRACTION100
1.8687-1.93550.27041310.26112735X-RAY DIFFRACTION100
1.9355-2.0130.29551580.25072737X-RAY DIFFRACTION100
2.013-2.10460.28141460.22372723X-RAY DIFFRACTION100
2.1046-2.21550.24751490.19342746X-RAY DIFFRACTION100
2.2155-2.35430.24071540.1812718X-RAY DIFFRACTION100
2.3543-2.53610.20741530.18262740X-RAY DIFFRACTION100
2.5361-2.79120.2141340.18262731X-RAY DIFFRACTION100
2.7912-3.19490.22441500.17722760X-RAY DIFFRACTION100
3.1949-4.02440.2031630.15712716X-RAY DIFFRACTION100
4.0244-36.98490.20591190.20252756X-RAY DIFFRACTION99

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