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- PDB-5nw4: Human cytoplasmic dynein-1 bound to dynactin and an N-terminal co... -

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Basic information

Entry
Database: PDB / ID: 5nw4
TitleHuman cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2
Descriptordynein heavy chain
dynein intermediate chain
dynein N-terminal dimerization domain
Robl
dynein light intermediate chain
and more 14 items
KeywordsMOTOR PROTEIN / Motor protein / dynein / dynactin / BICD
Specimen sourceHomo sapiens / human
Sus scrofa / mammal / Pig / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica
Alligator mississippiensis / reptile / American alligator
MethodElectron microscopy (8.7 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 StrPapers
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 5, 2017 / Release: Aug 2, 2017

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Assembly

Deposited unit
B: dynein heavy chain
D: dynein intermediate chain
C: dynein intermediate chain
A: dynein heavy chain
1: dynein N-terminal dimerization domain
2: dynein N-terminal dimerization domain
R: Robl
S: Robl
E: dynein light intermediate chain
F: dynein light intermediate chain
G: Uncharacterized protein
H: Uncharacterized protein
O: Uncharacterized protein
P: Uncharacterized protein
Q: Uncharacterized protein
T: Uncharacterized protein
U: Uncharacterized protein
V: Uncharacterized protein
W: Uncharacterized protein
X: Uncharacterized protein
Y: Capping protein (Actin filament) muscle Z-line, alpha 1
Z: F-actin capping protein beta subunit variant II
a: dynactin shoulder complex
b: dynactin shoulder complex
c: dynactin shoulder complex
d: dynactin shoulder complex
e: dynactin shoulder complex
f: dynactin shoulder complex
g: Dynactin 6
h: Dynactin subunit 5
i: dynactin pointed end p62
j: p150
k: Dynactin
l: Dynactin
m: Dynactin
n: Dynactin
o: dynactin p150
5: BICD2N
6: BICD2N


Theoretical massNumber of molelcules
Total (without water)1,095,05539
Polyers1,095,05539
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Dynein heavy ... , 2 types, 2 molecules BA

#1: Polypeptide(L)dynein heavy chain


Mass: 75675.695 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens
#4: Polypeptide(L)dynein heavy chain


Mass: 78484.062 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens

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Dynein intermediate ... , 2 types, 2 molecules DC

#2: Polypeptide(L)dynein intermediate chain


Mass: 29038.656 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens
#3: Polypeptide(L)dynein intermediate chain


Mass: 29804.609 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens

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Dynein N-terminal dimerization ... , 2 types, 2 molecules 12

#5: Polypeptide(L)dynein N-terminal dimerization domain


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


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

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Polypeptide(L) , 13 types, 15 molecules RSYZghijkl...

#7: Polypeptide(L)Robl


Mass: 10230.603 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens
#13: Polypeptide(L)Capping protein (Actin filament) muscle Z-line, alpha 1 / F-actin capping protein alpha 1 subunit / F-actin capping protein subunit alpha 1


Mass: 33059.848 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt: A0PFK5
#14: Polypeptide(L)F-actin capping protein beta subunit variant II / F-actin-capping protein subunit beta / F-actin-capping protein subunit beta isoform 2


Mass: 33060.379 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt: D2JYW4
#19: Polypeptide(L)Dynactin 6


Mass: 20703.910 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt: D0G6S1
#20: Polypeptide(L)Dynactin subunit 5 / Dynactin subunit p25


Mass: 24538.305 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens / References: UniProt: Q9BTE1
#21: Polypeptide(L)dynactin pointed end p62


Mass: 20698.426 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa
#22: Polypeptide(L)p150


Mass: 4443.468 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa
#23: Polypeptide(L)Dynactin / Dynactin subunit 2


Mass: 5400.015 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt: A0A0J9X292
#24: Polypeptide(L)Dynactin / Dynactin subunit 2


Mass: 7931.814 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt: A0A0J9X293
#25: Polypeptide(L)Dynactin


Mass: 3019.344 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt: A0A0J9X299
#26: Polypeptide(L)Dynactin


Mass: 2237.488 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt: A0A0J9X299
#27: Polypeptide(L)dynactin p150


Mass: 4528.573 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa
#28: Polypeptide(L)BICD2N


Mass: 23421.752 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens

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

#8: Polypeptide(L)dynein light intermediate chain


Mass: 25123.830 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens
#9: Polypeptide(L)dynein light intermediate chain


Mass: 25379.143 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens

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Uncharacterized ... , 3 types, 10 molecules GHOPQTUWVX

#10: Polypeptide(L)
Uncharacterized protein


Mass: 42684.711 Da / Num. of mol.: 8 / Source: (natural) Sus scrofa / References: UniProt: F2Z5G5
#11: Polypeptide(L)Uncharacterized protein


Mass: 43987.133 Da / Num. of mol.: 1 / Source: (natural) Alligator mississippiensis / References: UniProt: A0A151MAL5
#12: Polypeptide(L)Uncharacterized protein


Mass: 46250.785 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt: I3LHK5

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Dynactin shoulder ... , 4 types, 6 molecules abcdef

#15: Polypeptide(L)dynactin shoulder complex


Mass: 48613.012 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa
#16: Polypeptide(L)dynactin shoulder complex


Mass: 51251.293 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa
#17: Polypeptide(L)dynactin shoulder complex


Mass: 11081.651 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa
#18: Polypeptide(L)dynactin shoulder complex


Mass: 14826.253 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa

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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: Human cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2
Type: COMPLEX
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29
Source: MULTIPLE SOURCES
Molecular weightValue: 2.5 deg. / Units: MEGADALTONS / Experimental value: NO
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
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionDetails: Particles were selected from phase-flipped micrographs
3D reconstructionResolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 78671 / Symmetry type: POINT

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