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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 / Motor protein / dynein-1 / phi-particle
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 15 Å resolution
AuthorsZhang, K. / Foster, H.E. / Carter, A.P.
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 4, 2017 / Release: Aug 9, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 9, 2017Structure modelrepositoryInitial release
1.1Aug 30, 2017Structure modelAuthor supporting evidence / Data collection / Derived calculationsem_software / pdbx_audit_support / pdbx_struct_sheet_hbond / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range_em_software.name / _pdbx_audit_support.funding_organization
1.2Sep 6, 2017Structure modelDatabase referencespdbx_database_related_pdbx_database_related.content_type

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-3705
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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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
Polyers883,55618
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein/peptide , 6 types, 10 molecules ABDEKLMNQR

#1: Protein/peptide Dynein motor domain


Mass: 269723.031 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Protein/peptide Dynein intermediate chain


Mass: 29804.609 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#9: Protein/peptide LC8


Mass: 7251.930 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#10: Protein/peptide Tctex


Mass: 8783.818 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#11: Protein/peptide Tctex


Mass: 8868.924 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#14: Protein/peptide Robl


Mass: 10230.603 Da / Num. of mol.: 2 / 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/peptide Dynein tail heavy chain


Mass: 79335.086 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#4: Protein/peptide Dynein tail heavy chain


Mass: 76016.109 Da / Num. of mol.: 1 / 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/peptide Dynein light intermediate chain


Mass: 25379.143 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#6: Protein/peptide Dynein light intermediate chain


Mass: 25123.830 Da / Num. of mol.: 1 / 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/peptide N-terminal dimerization domain


Mass: 10656.127 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#8: Protein/peptide N-terminal dimerization domain


Mass: 10571.022 Da / Num. of mol.: 1 / 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: (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: (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 / 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: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 / 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
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
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
3D reconstructionResolution: 15 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 28736 / Symmetry type: POINT

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