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Open data
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Basic information
Entry | Database: PDB / ID: 8v4k | ||||||
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Title | CCP5 in complex with microtubules class1 | ||||||
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![]() | HYDROLASE/SUBSTRATE / STRUCTURAL PROTEIN / carboxypeptidase deglutamylation branch glutamate removal microtubule / HYDROLASE / HYDROLASE-SUBSTRATE complex / HYDROLASE-SUBSTRATE / STRUCTURAL PROTEIN complex | ||||||
Function / homology | ![]() tubulin-glutamate carboxypeptidase / protein deglutamylation / protein side chain deglutamylation / protein branching point deglutamylation / C-terminal protein deglutamylation / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport ...tubulin-glutamate carboxypeptidase / protein deglutamylation / protein side chain deglutamylation / protein branching point deglutamylation / C-terminal protein deglutamylation / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / intercellular bridge / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / metallocarboxypeptidase activity / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / mitotic spindle / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / midbody / microtubule / defense response to virus / GTPase activity / GTP binding / proteolysis / zinc ion binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
![]() | Chen, J. / Zehr, E.A. / Gruschus, J.M. / Szyk, A. / Liu, Y. / Tanner, M.E. / Tjandra, N. / Roll-Mecak, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Tubulin code eraser CCP5 binds branch glutamates by substrate deformation Authors: Chen, J. / Zehr, E.A. / Gruschus, J.M. / Szyk, A. / Liu, Y. / Tanner, M.E. / Tjandra, N. / Roll-Mecak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 447 KB | Display | ![]() |
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PDB format | ![]() | 355.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 60.1 KB | Display | |
Data in CIF | ![]() | 92.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 42971MC ![]() 8v3mC ![]() 8v3nC ![]() 8v3oC ![]() 8v3pC ![]() 8v3qC ![]() 8v3rC ![]() 8v3sC ![]() 8v4lC ![]() 8v4mC ![]() 42948 C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 3 types, 5 molecules ACBDE
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 49504.801 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: Beta tubulin from porcine brain microtubules, heterogeneous in tail sequence Source: (natural) ![]() ![]() #3: Protein | | Mass: 68229.547 Da / Num. of mol.: 1 / Fragment: residues 2-605 / Mutation: E516A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 10 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/G2P.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GLU.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/G2P.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GLU.gif)
#4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-ZN / | #8: Chemical | ChemComp-GLU / | |
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-Details
Has ligand of interest | Y |
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Sequence details | Brain tubulin contains multiple tubulin isotypes. The tubulin body was modeled using the sequence ...Brain tubulin contains multiple tubulin isotypes. The tubulin body was modeled using the sequence of betaII, the most abundant isotype in brain. The residues in the variable tails are modeled as UNK. |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: CCP5 in complex with microtubules / Type: COMPLEX / Details: Composite structure of CCP5:microtubule class#1 / Entity ID: #1, #3 / Source: MULTIPLE SOURCES | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid type: Au-flat 1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 303 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 135000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 1.651 sec. / Electron dose: 53.34 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
EM imaging optics | Energyfilter slit width: 20 eV |
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Processing
EM software | Name: PHENIX / Category: model refinement | |||||||||||||||||||||
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CTF correction | Type: NONE | |||||||||||||||||||||
Particle selection | Num. of particles selected: 162521 | |||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 239209 / Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient | |||||||||||||||||||||
Atomic model building |
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