+Open data
-Basic information
Entry | Database: PDB / ID: 8v3q | ||||||
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Title | Structure of CCP5 class1 | ||||||
Components |
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Keywords | HYDROLASE/SUBSTRATE / carboxypeptidase / deglutamylation / branch glutamate removal / microtubule / HYDROLASE / HYDROLASE-SUBSTRATE complex | ||||||
Function / homology | Function and homology information tubulin-glutamate carboxypeptidase / protein deglutamylation / protein side chain deglutamylation / protein branching point deglutamylation / C-terminal protein deglutamylation / Carboxyterminal post-translational modifications of tubulin / intercellular bridge / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / metallocarboxypeptidase activity / tubulin binding ...tubulin-glutamate carboxypeptidase / protein deglutamylation / protein side chain deglutamylation / protein branching point deglutamylation / C-terminal protein deglutamylation / Carboxyterminal post-translational modifications of tubulin / intercellular bridge / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / metallocarboxypeptidase activity / tubulin binding / mitotic spindle / microtubule cytoskeleton / midbody / defense response to virus / proteolysis / zinc ion binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Sus scrofa (pig) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Chen, J. / Zehr, E.A. / Gruschus, J.M. / Szyk, A. / Liu, Y. / Tanner, M.E. / Tjandra, N. / Roll-Mecak, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nature / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8v3q.cif.gz | 115.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8v3q.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 8v3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8v3q_validation.pdf.gz | 967 KB | Display | wwPDB validaton report |
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Full document | 8v3q_full_validation.pdf.gz | 967.5 KB | Display | |
Data in XML | 8v3q_validation.xml.gz | 37.7 KB | Display | |
Data in CIF | 8v3q_validation.cif.gz | 54 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/8v3q ftp://data.pdbj.org/pub/pdb/validation_reports/v3/8v3q | HTTPS FTP |
-Related structure data
Related structure data | 42950MC 8v3mC 8v3nC 8v3oC 8v3pC 8v3rC 8v3sC 8v4kC 8v4lC 8v4mC M: map data used to model this data C: citing same article (ref.) |
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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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-Components
#1: 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.) Homo sapiens (human) / Gene: AGBL5 / Plasmid: pFastBac / Details (production host): His6_MBP_Asn10_TEV / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): IPLB-Sf-21-AE / References: UniProt: Q8NDL9 |
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#2: Protein/peptide | Mass: 827.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: brain |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-GLU / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: CCP5 in complex with beta tubulin tail / Type: COMPLEX Details: Focused refinement of CCP5:microtubule class#1 structure Entity ID: #1 / 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 mesh size: 300 divisions/in. / Grid type: Au-flat 1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 303 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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 |
-Processing
EM software |
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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: 239249 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient | ||||||||||||||||
Atomic model building | Details: crystal structure of apo CCP5 / Source name: Other / Type: experimental model | ||||||||||||||||
Refinement | Cross valid method: NONE |