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

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Entry
Database: PDB / ID: 5nw4
TitleHuman cytoplasmic dynein-1 bound to dynactin and an N-terminal construct of BICD2
Components
  • (Dynactin) x 4
  • (dynactin shoulder ...) x 4
  • (dynein N-terminal dimerization ...) x 2
  • (dynein heavy ...) x 2
  • (dynein intermediate ...) x 2
  • (dynein light intermediate ...) x 2
  • Arp1
  • Arp11
  • BICD2N
  • Capping protein (Actin filament) muscle Z-line, alpha 1
  • Dynactin 6
  • Dynactin subunit 5
  • F-actin capping protein beta subunit variant II
  • Robl
  • beta-actin
  • dynactin p150
  • dynactin pointed end p62
  • p150
KeywordsMOTOR PROTEIN / Motor protein / dynein / dynactin / BICD
Function / homologyActin / F-actin capping protein alpha subunit / Actins and actin-related proteins signature. / F-actin capping protein alpha subunit signature 2. / F-actin capping protein alpha subunit signature 1. / Actins signature 2. / Actins signature 1. / F-actin capping protein beta subunit signature. / Dynamitin / F-actin capping protein, beta subunit ...Actin / F-actin capping protein alpha subunit / Actins and actin-related proteins signature. / F-actin capping protein alpha subunit signature 2. / F-actin capping protein alpha subunit signature 1. / Actins signature 2. / Actins signature 1. / F-actin capping protein beta subunit signature. / Dynamitin / F-actin capping protein, beta subunit / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Bacterial transferase hexapeptide (six repeats) / F-actin-capping protein subunit alpha/beta / Actin-related protein 1 family / Dynamitin / Dynactin subunit 6 / Actin-related protein 10 / Actin/actin-like conserved site / F-actin capping protein, beta subunit, conserved site / MHC class II antigen presentation / COPI-mediated anterograde transport / Trimeric LpxA-like superfamily / Adherens junctions interactions / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / Anchoring of the basal body to the plasma membrane / Cell-extracellular matrix interactions / Interaction between L1 and Ankyrins / VEGFA-VEGFR2 Pathway / Recycling pathway of L1 / EPHB-mediated forward signaling / COPI-independent Golgi-to-ER retrograde traffic / Recruitment of NuMA to mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of Nlp from mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Regulation of PLK1 Activity at G2/M Transition / Regulation of actin dynamics for phagocytic cup formation / Formation of annular gap junctions / Gap junction degradation / F-actin capping protein, alpha subunit, conserved site / Actin, conserved site / MAP2K and MAPK activation / COPI-mediated anterograde transport / Factors involved in megakaryocyte development and platelet production / Clathrin-mediated endocytosis / AURKA Activation by TPX2 / Advanced glycosylation endproduct receptor signaling / COPI-independent Golgi-to-ER retrograde traffic / Actin family / RHO GTPases Activate Formins / Neutrophil degranulation / Hexapeptide repeat / F-actin-capping protein subunit beta / F-actin-capping protein subunit alpha / WASH complex / dynactin complex / F-actin capping protein complex / dense body / profilin binding / coronary vasculature development / aorta development / cell cortex region / barbed-end actin filament capping / ventricular septum development / cell junction assembly / sarcomere organization / myofibril / condensed chromosome kinetochore / filamentous actin / microtubule-based process / phagocytic vesicle / antigen processing and presentation of exogenous peptide antigen via MHC class II / microtubule-based movement / cellular response to interferon-gamma / structural constituent of cytoskeleton / actin cytoskeleton organization / actin binding / ER to Golgi vesicle-mediated transport / nuclear membrane / cytoskeleton / centrosome / myelin sheath / focal adhesion / ubiquitin protein ligase binding / nucleotide binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm / F-actin capping protein beta subunit variant II / Actin gamma 1 / Actin related protein 10 homolog / ARP1 actin related protein 1 homolog A / Dynactin / Dynactin 6 / Capping protein (Actin filament) muscle Z-line, alpha 1
Function and homology information
Specimen sourceHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 8.7 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 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

Movie
  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-3706
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Structure viewerMolecule:
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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: Protein/peptide dynein heavy chain /


Mass: 75675.695 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#4: Protein/peptide dynein heavy chain /


Mass: 78484.062 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

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

#2: Protein/peptide dynein intermediate chain


Mass: 29038.656 Da / Num. of mol.: 1 / 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.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

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

#5: Protein/peptide dynein N-terminal dimerization domain


Mass: 10656.127 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#6: Protein/peptide dynein 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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Protein/peptide , 16 types, 25 molecules RSGHOPQTUWVXYZghijklmno56

#7: Protein/peptide Robl


Mass: 10230.603 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#10: Protein/peptide
Arp1


Mass: 42684.711 Da / Num. of mol.: 8 / Source: (natural) Sus scrofa (pig) / References: UniProt: F2Z5G5
#11: Protein/peptide beta-actin /


Mass: 43987.133 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LVD5, UniProt: A0A151MAL5*PLUS
#12: Protein/peptide Arp11


Mass: 46250.785 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LHK5
#13: Protein/peptide 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 (pig) / References: UniProt: A0PFK5
#14: Protein/peptide 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 (pig) / References: UniProt: D2JYW4
#19: Protein/peptide Dynactin 6 /


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


Mass: 24538.305 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: Q9BTE1*PLUS
#21: Protein/peptide dynactin pointed end p62


Mass: 20698.426 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig)
#22: Protein/peptide p150


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


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


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


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


Mass: 2237.488 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A0J9X293*PLUS
#27: Protein/peptide dynactin p150


Mass: 4528.573 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig)
#28: Protein/peptide BICD2N


Mass: 23421.752 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

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

#8: 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)
#9: 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)

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

#15: Protein/peptide dynactin shoulder complex


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


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


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


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

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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

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 MDa / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
129606Homo sapiens (human)
239823Sus scrofa (pig)
349606Homo sapiens (human)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
127108Spodoptera frugiperda (fall armyworm)
247108Spodoptera 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
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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