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- PDB-7pt5: Crystal structure of the CH domain of human CEP44 -

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Basic information

Entry
Database: PDB / ID: 7pt5
TitleCrystal structure of the CH domain of human CEP44
ComponentsCentrosomal protein of 44 kDa
KeywordsCELL CYCLE / Centriole / Centrosome / Microtubule-associated protein
Function / homology
Function and homology information


centriole-centriole cohesion / centrosome cycle / centriole replication / centriole / spindle pole / midbody / microtubule binding / centrosome / cytoplasm
Similarity search - Function
Centrosomal CEP44 domain / Centrosomal protein of 44kDa / Centrosomal spindle body, CEP44
Similarity search - Domain/homology
Centrosomal protein of 44 kDa
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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 13, 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 44 kDa


Theoretical massNumber of molelcules
Total (without water)16,7541
Polymers16,7541
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.949, 33.949, 243.359
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Centrosomal protein of 44 kDa / Cep44 / HBV PreS1-transactivated protein 3 / PS1TP3


Mass: 16753.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: amino acid residues GAMDP are residues of TEV protease cleavage
Source: (gene. exp.) Homo sapiens (human) / Gene: CEP44, KIAA1712 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9C0F1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion
Details: 100 nl protein solution and 100 nl of reservoir solution which was 0.1 M Hepes pH 7.3, 10% isopropanol, 10% PEG-4000. Crystals were mounted 0.1 M Hepes pH 7.5, 7.5% isopropanol, 30% PEG-400.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97928 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.3→81.1 Å / Num. obs: 7159 / % possible obs: 100 % / Redundancy: 21.4 % / Biso Wilson estimate: 73.06 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.019 / Net I/σ(I): 17.7
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 661 / Rpim(I) all: 0.506 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5refinement
PHENIX1.18-3845refinement
iMOSFLMdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→33.62 Å / SU ML: 0.3315 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.7948
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2645 702 9.93 %
Rwork0.2262 6370 -
obs0.2299 7072 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 103.08 Å2
Refinement stepCycle: LAST / Resolution: 2.3→33.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 0 4 980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037993
X-RAY DIFFRACTIONf_angle_d0.55781339
X-RAY DIFFRACTIONf_chiral_restr0.0383153
X-RAY DIFFRACTIONf_plane_restr0.0034168
X-RAY DIFFRACTIONf_dihedral_angle_d20.11380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.480.40051470.3351190X-RAY DIFFRACTION99.93
2.48-2.730.31531300.2871239X-RAY DIFFRACTION100
2.73-3.120.27931440.24521247X-RAY DIFFRACTION100
3.12-3.930.2651180.24621294X-RAY DIFFRACTION100
3.93-33.620.24961630.20461400X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 6.58776806038 Å / Origin y: 24.0539816559 Å / Origin z: 14.266926446 Å
111213212223313233
T0.830313523354 Å20.0186647579526 Å2-0.122050934825 Å2-0.450853980706 Å20.0383121571873 Å2--0.586415155837 Å2
L8.31214846774 °2-1.01562950489 °20.781556518011 °2-11.0863759203 °2-1.43789496576 °2--8.54448982554 °2
S0.0102029246488 Å °-0.359378444929 Å °-0.263429625925 Å °1.61772501279 Å °0.0727739639451 Å °-0.577460812418 Å °0.0694578158772 Å °0.181564109771 Å °0.461828712636 Å °
Refinement TLS groupSelection details: { A|* }

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