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- PDB-5nvu: Full length human cytoplasmic dynein-1 in the phi-particle confor... -

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Basic information

Entry
Database: PDB / ID: 5nvu
TitleFull length human cytoplasmic dynein-1 in the phi-particle conformation
Components
  • (Dynein light intermediate ...) x 2
  • (Dynein tail heavy ...) x 2
  • (Intermediate chain N-terminus ...) x 2
  • (N-terminal dimerization ...) x 2
  • (Tctex) x 2
  • Dynein intermediate chain
  • Dynein motor domain
  • LC8
  • Robl
KeywordsMOTOR PROTEIN / dynein-1 / phi-particle
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 15 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 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: em_software / pdbx_audit_support ...em_software / pdbx_audit_support / pdbx_struct_sheet_hbond / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.2Sep 6, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.content_type
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: database_2 / em_admin ...database_2 / em_admin / pdbx_entry_details / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-3705
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Dynein motor domain
B: Dynein motor domain
C: Dynein tail heavy chain
D: Dynein intermediate chain
E: Dynein intermediate chain
F: Dynein tail heavy chain
G: Dynein light intermediate chain
H: Dynein light intermediate chain
I: N-terminal dimerization domain
J: N-terminal dimerization domain
K: LC8
L: LC8
M: Tctex
N: Tctex
O: Intermediate chain N-terminus peptides
P: Intermediate chain N-terminus peptides
Q: Robl
R: Robl


Theoretical massNumber of molelcules
Total (without water)883,55618
Polymers883,55618
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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Protein , 6 types, 10 molecules ABDEKLMNQR

#1: Protein Dynein motor domain


Mass: 269723.031 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)
#3: 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)
#9: 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)
#10: 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)
#11: 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)
#14: 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 tail heavy ... , 2 types, 2 molecules CF

#2: Protein Dynein tail 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)
#4: Protein Dynein tail 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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Dynein light intermediate ... , 2 types, 2 molecules GH

#5: 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)
#6: 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 IJ

#7: 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)
#8: 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 chain N-terminus ... , 2 types, 2 molecules OP

#12: Protein/peptide Intermediate chain N-terminus peptides


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)
#13: Protein/peptide Intermediate chain N-terminus peptides


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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Details

Has protein modificationN

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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: Complete human cytoplasmic dynein-1 in the phi-particle conformation
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding 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
13RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionDetails: Particles were selected on the phase-flipped micrographs
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28736 / Symmetry type: POINT

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