[English] 日本語
Yorodumi- PDB-7z2a: P. berghei kinesin-8B motor domain in no nucleotide state bound t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z2a | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | P. berghei kinesin-8B motor domain in no nucleotide state bound to tubulin dimer | |||||||||
Components |
| |||||||||
Keywords | MOTOR PROTEIN / kinesin | |||||||||
Function / homology | Function and homology information 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 ...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 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / microtubule motor activity / microtubule-based movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitotic cell cycle / microtubule binding / microtubule / GTPase activity / GTP binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Plasmodium berghei (eukaryote) Sus scrofa (pig) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
Authors | Liu, T. / Shilliday, F. / Cook, A.D. / Moores, C.A. | |||||||||
Funding support | United Kingdom, 2items
| |||||||||
Citation | Journal: Nat Commun / Year: 2022 Title: Mechanochemical tuning of a kinesin motor essential for malaria parasite transmission. Authors: Tianyang Liu / Fiona Shilliday / Alexander D Cook / Mohammad Zeeshan / Declan Brady / Rita Tewari / Colin J Sutherland / Anthony J Roberts / Carolyn A Moores / Abstract: Plasmodium species cause malaria and kill hundreds of thousands annually. The microtubule-based motor kinesin-8B is required for development of the flagellated Plasmodium male gamete, and its absence ...Plasmodium species cause malaria and kill hundreds of thousands annually. The microtubule-based motor kinesin-8B is required for development of the flagellated Plasmodium male gamete, and its absence completely blocks parasite transmission. To understand the molecular basis of kinesin-8B's essential role, we characterised the in vitro properties of kinesin-8B motor domains from P. berghei and P. falciparum. Both motors drive ATP-dependent microtubule gliding, but also catalyse ATP-dependent microtubule depolymerisation. We determined these motors' microtubule-bound structures using cryo-electron microscopy, which showed very similar modes of microtubule interaction in which Plasmodium-distinct sequences at the microtubule-kinesin interface influence motor function. Intriguingly however, P. berghei kinesin-8B exhibits a non-canonical structural response to ATP analogue binding such that neck linker docking is not induced. Nevertheless, the neck linker region is required for motility and depolymerisation activities of these motors. These data suggest that the mechanochemistry of Plasmodium kinesin-8Bs is functionally tuned to support flagella formation. #1: Journal: Protein Sci / Year: 2018 Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin / Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7z2a.cif.gz | 295.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7z2a.ent.gz | 232.2 KB | Display | PDB format |
PDBx/mmJSON format | 7z2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z2a_validation.pdf.gz | 937.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7z2a_full_validation.pdf.gz | 953.6 KB | Display | |
Data in XML | 7z2a_validation.xml.gz | 43.7 KB | Display | |
Data in CIF | 7z2a_validation.cif.gz | 66.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/7z2a ftp://data.pdbj.org/pub/pdb/validation_reports/z2/7z2a | HTTPS FTP |
-Related structure data
Related structure data | 14459MC 7z2bC 7z2cC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 3 types, 3 molecules AHK
#1: Protein | Mass: 47833.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4 |
---|---|
#2: Protein | Mass: 47825.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554 |
#3: Protein | Mass: 39086.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium berghei (eukaryote) Gene: PBNK65E_000018700, PBNK65NY_000018400, PBSP11A_000018500, PBSP11RLL_000018700 Production host: Escherichia coli (E. coli) / References: UniProt: A0A1C6WMA4 |
-Non-polymers , 3 types, 4 molecules
#4: Chemical | ChemComp-GTP / | ||
---|---|---|---|
#5: Chemical | #6: Chemical | ChemComp-G2P / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: P. berghei kinesin-8B motor domain in no nucleotide state bound to tubulin dimer Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Plasmodium berghei (eukaryote) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 6.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 2500 nm |
Image recording | Electron dose: 50.8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: UCSF ChimeraX / Version: 1.1/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package |
---|---|
CTF correction | Type: PHASE FLIPPING ONLY |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 196084 / Symmetry type: POINT |
Atomic model building | Protocol: FLEXIBLE FIT |