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- PDB-7ptb: Crystal structure of the SPD-2 domain of human CEP192 -

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Basic information

Entry
Database: PDB / ID: 7ptb
TitleCrystal structure of the SPD-2 domain of human CEP192
ComponentsCentrosomal protein of 192 kDa
KeywordsCELL CYCLE / Centriole / Centrosome / Cell-cycle / Pericentriolar material
Function / homology
Function and homology information


centrosome-templated microtubule nucleation / procentriole / procentriole replication complex / centrosome cycle / protein localization to centrosome / pericentriolar material / centriole replication / mitotic spindle assembly / phosphatase binding / centriole ...centrosome-templated microtubule nucleation / procentriole / procentriole replication complex / centrosome cycle / protein localization to centrosome / pericentriolar material / centriole replication / mitotic spindle assembly / phosphatase binding / centriole / 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 / response to bacterium / Regulation of PLK1 Activity at G2/M Transition / centrosome / cytosol / cytoplasm
Similarity search - Function
Centrosomal protein Spd-2/CEP192 / : / : / : / : / : / Cep192 domain 1 / Cep192 domain 2 / Cep192 domain 7 / Cep192 domain 8 ...Centrosomal protein Spd-2/CEP192 / : / : / : / : / : / Cep192 domain 1 / Cep192 domain 2 / Cep192 domain 7 / Cep192 domain 8 / Cep192 domain 3 / : / : / : / Cep192 domain 4 / Cep192 domain 5 / Cep192 domain 6 / Immunoglobulin-like fold
Similarity search - Domain/homology
NITRATE ION / Centrosomal protein of 192 kDa
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å
AuthorsRosa e Silva, I. / van Breugel, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MRC - MC_UP_1201/3 United Kingdom
CitationJournal: Commun Biol / Year: 2022
Title: Structural validation and assessment of AlphaFold2 predictions for centrosomal and centriolar proteins and their complexes.
Authors: van Breugel, M. / Rosa E Silva, I. / Andreeva, A.
History
DepositionSep 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 20, 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

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Assembly

Deposited unit
A: Centrosomal protein of 192 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5274
Polymers39,3411
Non-polymers1863
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC MALS suggests a monomeric protein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint3 kcal/mol
Surface area17790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.588, 104.588, 90.214
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Centrosomal protein of 192 kDa / Cep192 / Cep192/SPD-2


Mass: 39340.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The GP residues on the N-terminus were left after PreScission protease cleavage.
Source: (gene. exp.) Homo sapiens (human) / Gene: CEP192, KIAA1569, PP8407 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TEP8
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.64 Å3/Da / Density % sol: 66.19 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion
Details: 100 nl protein solution and 100 nl of reservoir solution which was 0.1 M Na-Acetate pH 5.3, 3.9 M ammonium ni-trate. Crystals were mounted in 0.1 M Na-Acetate pH 4.6, 1 M ammonium nitrate, 30% glycerol.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97835 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97835 Å / Relative weight: 1
ReflectionResolution: 2.08→90.6 Å / Num. obs: 33669 / % possible obs: 100 % / Redundancy: 18.6 % / Rpim(I) all: 0.024 / Net I/σ(I): 19.7
Reflection shellResolution: 2.08→2.14 Å / Redundancy: 2.5 % / Num. unique obs: 32002 / Rpim(I) all: 0.357 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.18refinement
iMOSFLMdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.08→90.58 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.086 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22364 1629 4.8 %RANDOM
Rwork0.21197 ---
obs0.21252 32002 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.671 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.16 Å20 Å2
2--0.32 Å2-0 Å2
3----1.03 Å2
Refinement stepCycle: 1 / Resolution: 2.08→90.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 12 160 2688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132626
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172594
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.6483553
X-RAY DIFFRACTIONr_angle_other_deg1.0291.5795979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7025334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.09721.857140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00915481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4371521
X-RAY DIFFRACTIONr_chiral_restr0.0360.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022969
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02621
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_it1.2634.7761285
X-RAY DIFFRACTIONr_mcbond_other1.2644.7731284
X-RAY DIFFRACTIONr_mcangle_it2.3437.1551609
X-RAY DIFFRACTIONr_mcangle_other2.3437.1581610
X-RAY DIFFRACTIONr_scbond_it0.94.9491341
X-RAY DIFFRACTIONr_scbond_other0.8984.9481333
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6737.3581927
X-RAY DIFFRACTIONr_long_range_B_refined4.55253.6172654
X-RAY DIFFRACTIONr_long_range_B_other4.36753.4262624
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.082→2.136 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 103 -
Rwork0.287 2368 -
obs--99.92 %

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