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Yorodumi- PDB-7quq: BtubA(R284G,K286D,F287G):BtubB bacterial tubulin M-loop mutant fo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7quq | |||||||||
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Title | BtubA(R284G,K286D,F287G):BtubB bacterial tubulin M-loop mutant forming a single protofilament (Prosthecobacter dejongeii) | |||||||||
Components |
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Keywords | CELL CYCLE / Cytyoskeleton / tubulin-like / cytomotive filaments | |||||||||
Function / homology | Function and homology information microtubule-based process / structural constituent of cytoskeleton / microtubule / GTP binding Similarity search - Function | |||||||||
Biological species | Prosthecobacter dejongeii (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Wagstaff, J. / Planelles-Herrero, V.J. / Derivery, E. / Lowe, J. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Sci Adv / Year: 2023 Title: Diverse cytomotive actins and tubulins share a polymerization switch mechanism conferring robust dynamics. Authors: James Mark Wagstaff / Vicente José Planelles-Herrero / Grigory Sharov / Aisha Alnami / Frank Kozielski / Emmanuel Derivery / Jan Löwe / Abstract: Protein filaments are used in myriads of ways to organize other molecules within cells. Some filament-forming proteins couple the hydrolysis of nucleotides to their polymerization cycle, thus ...Protein filaments are used in myriads of ways to organize other molecules within cells. Some filament-forming proteins couple the hydrolysis of nucleotides to their polymerization cycle, thus powering the movement of other molecules. These filaments are termed cytomotive. Only members of the actin and tubulin protein superfamilies are known to form cytomotive filaments. We examined the basis of cytomotivity via structural studies of the polymerization cycles of actin and tubulin homologs from across the tree of life. We analyzed published data and performed structural experiments designed to disentangle functional components of these complex filament systems. Our analysis demonstrates the existence of shared subunit polymerization switches among both cytomotive actins and tubulins, i.e., the conformation of subunits switches upon assembly into filaments. These cytomotive switches can explain filament robustness, by enabling the coupling of kinetic and structural polarities required for cytomotive behaviors and by ensuring that single cytomotive filaments do not fall apart. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7quq.cif.gz | 422.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7quq.ent.gz | 345 KB | Display | PDB format |
PDBx/mmJSON format | 7quq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7quq_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7quq_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7quq_validation.xml.gz | 82 KB | Display | |
Data in CIF | 7quq_validation.cif.gz | 120.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/7quq ftp://data.pdbj.org/pub/pdb/validation_reports/qu/7quq | HTTPS FTP |
-Related structure data
Related structure data | 14151MC 7qucC 7qudC 7qupC 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: 51095.012 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Prosthecobacter dejongeii (bacteria) / Gene: HNQ64_001272 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A7W7YIU5 #2: Protein | Mass: 46497.570 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Prosthecobacter dejongeii (bacteria) / Gene: HNQ64_001273 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A7W7YJ10 #3: Chemical | ChemComp-G2P / Has ligand of interest | Y | |
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-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: BtubAB heterodimer / Type: COMPLEX / Details: M-loop mutant BtubA(R284G,K286D,F287G) / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Source (recombinant) | Organism: Drosophila melanogaster (fruit fly) |
Buffer solution | pH: 7.7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: UltrAuFoil R1.2/1.3 |
Vitrification | Cryogen name: NITROGEN |
-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 defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 44 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 6993 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 290000 / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||
Atomic model building | PDB-ID: 2BTQ Accession code: 2BTQ / Source name: PDB / Type: experimental model |