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- PDB-5nvs: Human cytoplasmic dynein-1 tail in the twisted N-terminus state -

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Basic information

Entry
Database: PDB / ID: 5nvs
TitleHuman cytoplasmic dynein-1 tail in the twisted N-terminus state
Components
  • (N-terminal dimerization ...) x 2
  • (Tctex) x 2
  • (dynein heavy ...) x 2
  • (dynein light intermediate ...) x 2
  • (intermediate ...) x 2
  • LC8
  • Robl
  • dynein intermediate chain
KeywordsMOTOR PROTEIN / dynein / tail complex
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.4 Å
AuthorsZhang, K. / Foster, H.E. / Carter, A.P.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome TrustWT100387 United Kingdom
Medical Research Council (United Kingdom)MC_UP_A025_1011 United Kingdom
CitationJournal: 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
DepositionMay 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Data collection / Category: em_image_scans / em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.2Feb 6, 2019Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.3May 15, 2024Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Jul 10, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

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  • EMDB-3703
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Structure viewerMolecule:
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Assembly

Deposited unit
A: dynein heavy chain
D: dynein intermediate chain
C: dynein intermediate chain
B: dynein heavy chain
F: dynein light intermediate chain
E: dynein light intermediate chain
2: N-terminal dimerization domain
1: N-terminal dimerization domain
I: LC8
J: LC8
K: Tctex
L: Tctex
M: intermediate chain
N: intermediate chain
R: Robl
S: Robl


Theoretical massNumber of molelcules
Total (without water)344,11016
Polymers344,11016
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Dynein heavy ... , 2 types, 2 molecules AB

#1: Protein dynein heavy chain


Mass: 79335.086 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)
#3: Protein dynein heavy chain


Mass: 76016.109 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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Protein , 5 types, 8 molecules DCIJKLRS

#2: Protein dynein intermediate chain


Mass: 29804.609 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)
#8: Protein LC8


Mass: 7251.930 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)
#9: Protein Tctex


Mass: 8783.818 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)
#10: Protein Tctex


Mass: 8868.924 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)
#13: Protein Robl


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)

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Dynein light intermediate ... , 2 types, 2 molecules FE

#4: Protein dynein light intermediate chain


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)
#5: Protein dynein light intermediate chain


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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N-terminal dimerization ... , 2 types, 2 molecules 21

#6: Protein N-terminal dimerization domain


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)
#7: Protein N-terminal dimerization domain


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)

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Intermediate ... , 2 types, 2 molecules MN

#11: Protein/peptide intermediate chain


Mass: 2315.846 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)
#12: Protein/peptide intermediate chain


Mass: 2486.056 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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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human cytoplasmic dynein-1 tail in the twisted N-terminus state
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.4 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.6 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1Gautomatch0.53particle selection
4Gctf1.06CTF correction
11RELION1.4final Euler assignment
13RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionDetails: Particles were selected on the phase-flipped micrographs by Gautomatch.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 187830 / Symmetry type: POINT

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