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Open data
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Basic information
Entry | Database: PDB / ID: 8v3o | ||||||
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Title | CCP5 in complex with Glu-P-peptide 1 transition state analog | ||||||
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![]() | HYDROLASE/INHIBITOR / carboxypeptidase deglutamylation branch glutamate removal microtubule / HYDROLASE / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | ![]() tubulin-glutamate carboxypeptidase / protein deglutamylation / protein side chain deglutamylation / protein branching point deglutamylation / Post-chaperonin tubulin folding pathway / C-terminal protein deglutamylation / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III ...tubulin-glutamate carboxypeptidase / protein deglutamylation / protein side chain deglutamylation / protein branching point deglutamylation / Post-chaperonin tubulin folding pathway / C-terminal protein deglutamylation / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / Formation of tubulin folding intermediates by CCT/TriC / Gap junction assembly / COPI-independent Golgi-to-ER retrograde traffic / Prefoldin mediated transfer of substrate to CCT/TriC / Assembly and cell surface presentation of NMDA receptors / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / intercellular bridge / Recycling pathway of L1 / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / RHO GTPases activate IQGAPs / Hedgehog 'off' state / metallocarboxypeptidase activity / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Recruitment of NuMA to mitotic centrosomes / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / tubulin binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / neuron migration / structural constituent of cytoskeleton / mitotic spindle / Aggrephagy / microtubule cytoskeleton organization / HCMV Early Events / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / extracellular vesicle / mitotic cell cycle / midbody / microtubule / defense response to virus / GTPase activity / GTP binding / proteolysis / zinc ion binding / extracellular exosome / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.9 KB | Display | ![]() |
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PDB format | ![]() | 85.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.3 KB | Display | ![]() |
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Full document | ![]() | 452.8 KB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 28.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8v3mC ![]() 8v3nC ![]() 8v3pC ![]() 8v3qC ![]() 8v3rC ![]() 8v3sC ![]() 8v4kC ![]() 8v4lC ![]() 8v4mC C: citing same article ( |
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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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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 2 molecules AI
#1: Protein | Mass: 59170.668 Da / Num. of mol.: 1 / Mutation: E516A,residues 339-424 replaced with a SGSGG loop Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8NDL9, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases, tubulin-glutamate carboxypeptidase |
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#2: Protein/peptide | Mass: 1905.682 Da / Num. of mol.: 1 / Mutation: One of the glutamates replaced with BIX / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 4 types, 143 molecules ![](data/chem/img/ZN.gif)
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#3: Chemical | ChemComp-ZN / | ||||
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#4: Chemical | #5: Chemical | ChemComp-K / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.49 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 0.15 M DL-Malic acid, pH7.0, 0.1 M imidazole, pH7.0, 16% PEG MME 550 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 17, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→34.55 Å / Num. obs: 25384 / % possible obs: 100 % / Redundancy: 14.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.175 / Rrim(I) all: 0.187 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 14.7 % / Rmerge(I) obs: 1.455 / Mean I/σ(I) obs: 2 / Num. unique obs: 2454 / CC1/2: 0.712 / Rrim(I) all: 1.56 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→34.55 Å
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Refine LS restraints |
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LS refinement shell |
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