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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
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 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 5, 2017 / Release: Aug 2, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 2, 2017Structure modelrepositoryInitial release
1.1Sep 6, 2017Structure modelDatabase references / Source and taxonomy / Structure summaryentity / entity_name_com / entity_src_gen / entity_src_nat / pdbx_database_related / struct_ref / struct_ref_seq / struct_ref_seq_dif_entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_nat.common_name / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific / _pdbx_database_related.content_type / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
1.2Sep 13, 2017Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization

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Structure visualization

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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: Arp1
H: Arp1
O: Arp1
P: Arp1
Q: Arp1
T: Arp1
U: Arp1
V: beta-actin
W: Arp1
X: Arp11
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) , 16 types, 25 molecules RSGHOPQTUW...

#7: Polypeptide(L)Robl


Mass: 10230.603 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens
#10: Polypeptide(L)
Arp1


Mass: 42684.711 Da / Num. of mol.: 8 / Source: (natural) Sus scrofa / References: UniProt: F2Z5G5

Cellular component

Molecular function

#11: Polypeptide(L)beta-actin


Mass: 43987.133 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt: I3LVD5

Cellular component

Molecular function

#12: Polypeptide(L)Arp11


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

Cellular component

Molecular function

Biological process

#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

Cellular component

Molecular function

Biological process

#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

Cellular component

Molecular function

Biological process

#19: Polypeptide(L)Dynactin 6


Mass: 20703.910 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt: D0G6S1

Cellular component

#20: Polypeptide(L)Dynactin subunit 5 / Dynactin subunit p25


Mass: 24538.305 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa
#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

Cellular component

Biological process

#25: Polypeptide(L)Dynactin


Mass: 3019.344 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt: A0A0J9X299
#26: Polypeptide(L)Dynactin / Dynactin subunit 2


Mass: 2237.488 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa
#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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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

Component
IDNameTypeEntity IDParent IDSource
1Human cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2COMPLEX1, 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, 290MULTIPLE SOURCES
2dynein-1COMPLEX1, 2, 3, 4, 5, 6, 7, 8, 91RECOMBINANT
3dynactinCOMPLEX10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 271NATURAL
4BICD2COMPLEX281RECOMBINANT
Molecular weightValue: 2.5 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
129606Homo sapiens
239823Sus scrofa
349606Homo sapiens
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
127108Spodoptera frugiperda
247108Spodoptera 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
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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