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Yorodumi- PDB-5nw4: Human cytoplasmic dynein-1 bound to dynactin and an N-terminal co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nw4 | |||||||||
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Title | Human cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2 | |||||||||
Components |
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Keywords | MOTOR PROTEIN / dynein / dynactin / BICD | |||||||||
Function / homology | Function and homology information kinetochore => GO:0000776 / retrograde axonal transport of mitochondrion / dynactin complex / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / F-actin capping protein complex ...kinetochore => GO:0000776 / retrograde axonal transport of mitochondrion / dynactin complex / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / F-actin capping protein complex / negative regulation of filopodium assembly / actin cortical patch / dense body / dynein complex / Neutrophil degranulation / COPI-independent Golgi-to-ER retrograde traffic / coronary vasculature development / barbed-end actin filament capping / regulation of lamellipodium assembly / aorta development / 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 / ventricular septum development / dynein complex binding / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / axon cytoplasm / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / mitotic spindle organization / cell morphogenesis / kinetochore / actin filament binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / cell cortex / nuclear membrane / actin cytoskeleton organization / cytoskeleton / focal adhesion / centrosome / nucleoplasm / ATP binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Sus scrofa (pig) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.7 Å | |||||||||
Authors | Zhang, K. / Foster, H.E. / Carter, A.P. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Cell / Year: 2017 Title: Cryo-EM Reveals How Human Cytoplasmic Dynein Is Auto-inhibited and Activated. Authors: Kai Zhang / Helen E Foster / Arnaud Rondelet / Samuel E Lacey / Nadia Bahi-Buisson / Alexander W Bird / Andrew P Carter / Abstract: Cytoplasmic dynein-1 binds dynactin and cargo adaptor proteins to form a transport machine capable of long-distance processive movement along microtubules. However, it is unclear why dynein-1 moves ...Cytoplasmic dynein-1 binds dynactin and cargo adaptor proteins to form a transport machine capable of long-distance processive movement along microtubules. However, it is unclear why dynein-1 moves poorly on its own or how it is activated by dynactin. Here, we present a cryoelectron microscopy structure of the complete 1.4-megadalton human dynein-1 complex in an inhibited state known as the phi-particle. We reveal the 3D structure of the cargo binding dynein tail and show how self-dimerization of the motor domains locks them in a conformation with low microtubule affinity. Disrupting motor dimerization with structure-based mutagenesis drives dynein-1 into an open form with higher affinity for both microtubules and dynactin. We find the open form is also inhibited for movement and that dynactin relieves this by reorienting the motor domains to interact correctly with microtubules. Our model explains how dynactin binding to the dynein-1 tail directly stimulates its motor activity. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5nw4.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5nw4.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 5nw4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nw4_validation.pdf.gz | 828.7 KB | Display | wwPDB validaton report |
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Full document | 5nw4_full_validation.pdf.gz | 847.4 KB | Display | |
Data in XML | 5nw4_validation.xml.gz | 165 KB | Display | |
Data in CIF | 5nw4_validation.cif.gz | 308.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/5nw4 ftp://data.pdbj.org/pub/pdb/validation_reports/nw/5nw4 | HTTPS FTP |
-Related structure data
Related structure data | 3706MC 3698C 3703C 3704C 3705C 3707C 5nugC 5nvsC 5nvuC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-Dynein heavy ... , 2 types, 2 molecules BA
#1: Protein | Mass: 75675.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) |
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#4: Protein | Mass: 78484.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) |
-Dynein intermediate ... , 2 types, 2 molecules DC
#2: Protein | Mass: 29038.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) |
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#3: Protein | Mass: 29804.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) |
-Dynein N-terminal dimerization ... , 2 types, 2 molecules 12
#5: Protein | Mass: 10656.127 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) |
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#6: Protein | Mass: 10571.022 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) |
-Protein , 13 types, 22 molecules RSGHOPQTUWVXYZghijlo56
#7: Protein | Mass: 10230.603 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) #10: Protein | Mass: 42684.711 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F2Z5G5 #11: Protein | | Mass: 43987.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LVD5, UniProt: A0A151MAL5*PLUS #12: Protein | | Mass: 46250.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LHK5 #13: Protein | | Mass: 33059.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0PFK5 #14: Protein | | Mass: 33060.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: D2JYW4 #19: Protein | | Mass: 20703.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: D0G6S1 #20: Protein | | Mass: 24538.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q9BTE1*PLUS #21: Protein | | Mass: 20698.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) #22: Protein | | Mass: 4443.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) #24: Protein | | Mass: 7931.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A0J9X293 #27: Protein | | Mass: 4528.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) #28: Protein | Mass: 23421.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) |
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-Dynein light intermediate ... , 2 types, 2 molecules EF
#8: Protein | Mass: 25123.830 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) |
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#9: Protein | Mass: 25379.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) |
-Dynactin shoulder ... , 4 types, 6 molecules abcdef
#15: Protein | Mass: 48613.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) | ||
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#16: Protein | Mass: 51251.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) | ||
#17: Protein | Mass: 11081.651 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) #18: Protein | Mass: 14826.253 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) |
-Protein/peptide , 3 types, 3 molecules kmn
#23: Protein/peptide | Mass: 5400.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A0J9X292 |
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#25: Protein/peptide | Mass: 3019.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A0J9X299 |
#26: Protein/peptide | Mass: 2237.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A0J9X293*PLUS |
-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 |
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Molecular weight | Value: 2.5 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-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 |
Image recording | Electron dose: 1.6 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
Particle selection | Details: Particles were selected from phase-flipped micrographs | ||||||||||||
3D reconstruction | Resolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78671 / Symmetry type: POINT |