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

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Entry
Database: PDB / ID: 5nvu
TitleFull length human cytoplasmic dynein-1 in the phi-particle conformation
DescriptorDynein motor domain, Dynein tail heavy chain, Dynein intermediate chain, Dynein light intermediate chain, N-terminal dimerization domain, LC8, Tctex, Intermediate chain N-terminus peptides, Robl
KeywordsMOTOR PROTEIN / Motor protein / dynein-1 / phi-particle
Specimen sourceHomo sapiens / human
MethodElectron microscopy (15 Å resolution / Particle / Single particle)
AuthorsZhang, K. / Foster, H.E. / Carter, A.P.
CitationCell, 2017, 169, 1303-1314.e18

Cell, 2017, 169, 1303-1314.e18 Yorodumi Papers
Cryo-EM Reveals How Human Cytoplasmic Dynein Is Auto-inhibited and Activated.
Kai Zhang / Helen E Foster / Arnaud Rondelet / Samuel E Lacey / Nadia Bahi-Buisson / Alexander W Bird / Andrew P Carter

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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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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Polypeptide(L) , 6 types, 10 molecules ABDEKLMNQR

#1: Polypeptide(L)Dynein motor domain


Mass: 269723.031 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens
#3: Polypeptide(L)Dynein intermediate chain


Mass: 29804.609 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens
#9: Polypeptide(L)LC8


Mass: 7251.930 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens
#10: Polypeptide(L)Tctex


Mass: 8783.818 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens
#11: Polypeptide(L)Tctex


Mass: 8868.924 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens
#14: Polypeptide(L)Robl


Mass: 10230.603 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens

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Dynein tail heavy ... , 2 types, 2 molecules CF

#2: Polypeptide(L)Dynein tail heavy chain


Mass: 79335.086 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens
#4: Polypeptide(L)Dynein tail heavy chain


Mass: 76016.109 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens

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

#5: Polypeptide(L)Dynein light intermediate chain


Mass: 25379.143 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens
#6: Polypeptide(L)Dynein light intermediate chain


Mass: 25123.830 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens

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

#7: Polypeptide(L)N-terminal dimerization domain


Mass: 10656.127 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens
#8: Polypeptide(L)N-terminal dimerization domain


Mass: 10571.022 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens

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Intermediate chain N-terminus ... , 2 types, 2 molecules OP

#12: Polypeptide(L)Intermediate chain N-terminus peptides


Mass: 2315.846 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens
#13: Polypeptide(L)Intermediate chain N-terminus peptides


Mass: 2486.056 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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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
Source (recombinant)Organism: Spodoptera frugiperda
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 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
IDNameVersionCategoryImage processing ID
1Gautomatch0.53PARTICLE SELECTION1
4Gctf1.06CTF CORRECTION1
13RELION1.4RECONSTRUCTION1
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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