+Open data
-Basic information
Entry | Database: PDB / ID: 7z0g | ||||||
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Title | CPAP:TUBULIN:IE5 ALPHAREP COMPLEX P1 SPACE GROUP | ||||||
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 / 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 / microtubule polymerization / centriole replication / microtubule-based process / cilium assembly / positive regulation of G1/S transition of mitotic cell cycle / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / regulation of mitotic spindle organization / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / tubulin binding / ciliary basal body / positive regulation of receptor signaling pathway via JAK-STAT / structural constituent of cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / microtubule / transcription coactivator activity / protein domain specific binding / cell division / centrosome / GTP binding / protein kinase binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | synthetic construct (others) Homo sapiens (human) Ovis aries (sheep) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.487 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 | 7z0g.cif.gz | 837.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z0g.ent.gz | 685.5 KB | Display | PDB format |
PDBx/mmJSON format | 7z0g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z0g_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7z0g_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7z0g_validation.xml.gz | 74.7 KB | Display | |
Data in CIF | 7z0g_validation.cif.gz | 100.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/7z0g ftp://data.pdbj.org/pub/pdb/validation_reports/z0/7z0g | HTTPS FTP |
-Related structure data
Related structure data | 7q1eC 7q1fC 7z0fC 6gwcS 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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2 |
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Unit cell |
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-Components
-Protein , 4 types, 8 molecules ARBSCTPU
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P7DY20 #2: Protein | Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P3TCJ9 #3: Protein | Mass: 25173.736 Da / Num. of mol.: 2 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.: 2 / 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 |
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-Non-polymers , 4 types, 8 molecules
#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | |
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-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: 2.21 Å3/Da / Density % sol: 44.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M Mes-K, 0.2 M Ca acetate, 20% (V/V) polyethylene glycol 400 |
-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: Sep 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 3.487→48.54 Å / Num. obs: 28469 / % possible obs: 96.88 % / Redundancy: 3.37 % / CC1/2: 0.982 / Rrim(I) all: 0.272 / Net I/σ(I): 4.96 |
Reflection shell | Resolution: 3.487→3.612 Å / Num. unique obs: 2508 / CC1/2: 0.394 / % possible all: 84.36 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GWC Resolution: 3.487→48.54 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.857 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.701
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Displacement parameters | Biso mean: 109.74 Å2
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Refine analyze | Luzzati coordinate error obs: 0.5 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.487→48.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.49→3.52 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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