+Open data
-Basic information
Entry | Database: PDB / ID: 7z0f | ||||||
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Title | CPAP:S-TUBULIN:IIH5 ALPHAREP COMPLEX | ||||||
Components |
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Keywords | CELL CYCLE / MICROTUBULE / VINCA DOMAIN INHIBITORS / CENTRIOLE | ||||||
Function / homology | Function and homology information astral microtubule nucleation / centriole elongation / gamma-tubulin small complex / positive regulation of centriole elongation / positive regulation of non-motile cilium assembly / positive regulation of establishment of protein localization / regulation of centriole replication / procentriole replication complex / positive regulation of centriole replication / motile cilium assembly ...astral microtubule nucleation / centriole elongation / gamma-tubulin small complex / positive regulation of centriole elongation / positive regulation of non-motile cilium assembly / positive regulation of establishment of protein localization / regulation of centriole replication / procentriole replication complex / positive regulation of centriole replication / motile cilium assembly / centriole replication / positive regulation of spindle assembly / microtubule nucleation / non-motile cilium assembly / gamma-tubulin binding / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / smoothened signaling pathway / positive regulation of G1/S transition of mitotic cell cycle / microtubule polymerization / microtubule-based process / cilium assembly / regulation of mitotic spindle organization / 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 / tubulin binding / AURKA Activation by TPX2 / ciliary basal body / positive regulation of receptor signaling pathway via JAK-STAT / structural constituent of cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / transcription coactivator activity / microtubule / protein domain specific binding / cell division / centrosome / GTP binding / protein kinase binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | synthetic construct (others) Homo sapiens (human) Ovis aries (sheep) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.396 Å | ||||||
Authors | Gigant, B. / Campanacci, V. | ||||||
Funding support | France, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Structural convergence for tubulin binding of CPAP and vinca domain microtubule inhibitors. Authors: Campanacci, V. / Urvoas, A. / Ammar Khodja, L. / Aumont-Nicaise, M. / Noiray, M. / Lachkar, S. / Curmi, P.A. / Minard, P. / Gigant, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z0f.cif.gz | 425.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z0f.ent.gz | 342 KB | Display | PDB format |
PDBx/mmJSON format | 7z0f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z0f_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7z0f_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7z0f_validation.xml.gz | 39.4 KB | Display | |
Data in CIF | 7z0f_validation.cif.gz | 54.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/7z0f ftp://data.pdbj.org/pub/pdb/validation_reports/z0/7z0f | HTTPS FTP |
-Related structure data
Related structure data | 7q1eC 7q1fC 7z0gC 6gwdS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 4 types, 4 molecules ABCP
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P7DY20 |
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#2: Protein | Mass: 49999.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P3TCJ9 |
#3: Protein | Mass: 18866.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
#4: Protein | Mass: 9199.604 Da / Num. of mol.: 1 / Mutation: V319M, A320V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CENPJ, CPAP, LAP, LIP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HC77 |
-Non-polymers , 5 types, 163 molecules
#5: Chemical | ChemComp-GTP / |
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#6: Chemical | ChemComp-MG / |
#7: Chemical | ChemComp-GDP / |
#8: Chemical | ChemComp-GOL / |
#9: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.95 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop Details: 0.2 M Na tartrate, 10% (W/V) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.396→45.79 Å / Num. obs: 49614 / % possible obs: 99.19 % / Redundancy: 4.47 % / CC1/2: 0.998 / Rpim(I) all: 0.054 / Rrim(I) all: 0.083 / Net I/σ(I): 13.06 |
Reflection shell | Resolution: 2.396→2.482 Å / Redundancy: 4.51 % / Mean I/σ(I) obs: 1.05 / Num. unique obs: 4790 / CC1/2: 0.62 / Rrim(I) all: 1.556 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GWD Resolution: 2.396→45.79 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.362 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.345 / SU Rfree Blow DPI: 0.256 / SU Rfree Cruickshank DPI: 0.263
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Displacement parameters | Biso mean: 99.87 Å2
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Refine analyze | Luzzati coordinate error obs: 0.37 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.396→45.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.42 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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