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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 / dynein / dynactin / BICD
Function / homology
Function and homology information


retrograde axonal transport of mitochondrion / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / dynactin complex / Recruitment of mitotic centrosome proteins and complexes / F-actin capping protein complex / dense body ...retrograde axonal transport of mitochondrion / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / dynactin complex / Recruitment of mitotic centrosome proteins and complexes / F-actin capping protein complex / dense body / barbed-end actin filament capping / Neutrophil degranulation / coronary vasculature development / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / aorta development / COPI-mediated anterograde transport / ventricular septum development / cortical cytoskeleton / dynein complex binding / microtubule-based process / COPI-mediated anterograde transport / axon cytoplasm / MHC class II antigen presentation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / mitotic spindle organization / kinetochore / actin filament binding / actin binding / actin cytoskeleton organization / cell cortex / nuclear membrane / cytoskeleton / focal adhesion / centrosome / nucleoplasm / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Dynamitin / : / Dynamitin / Dynactin subunit 6 / Dynactin subunit 5 / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. ...Dynamitin / : / Dynamitin / Dynactin subunit 6 / Dynactin subunit 5 / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Dynactin / Dynactin subunit 2 / Dynactin / Actin, cytoplasmic 1 / F-actin-capping protein subunit alpha-1 / Dynactin subunit 6 / F-actin-capping protein subunit beta / Alpha-centractin / Actin-related protein 10 / Actin gamma 1 / Dynactin subunit 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsZhang, K. / Foster, H.E. / Carter, A.P.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome TrustWT100387 United Kingdom
Medical Research Council (United Kingdom)MC_UP_A025_1011 United Kingdom
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.
History
DepositionMay 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / entity_src_nat / pdbx_database_related / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._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
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 21, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_seq_id

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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
Polymers1,095,05539
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#1: Protein dynein heavy chain


Mass: 75675.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#4: Protein dynein heavy chain


Mass: 78484.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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 dynein intermediate chain


Mass: 29038.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Protein dynein intermediate chain


Mass: 29804.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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 dynein N-terminal dimerization domain


Mass: 10656.127 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#6: Protein dynein N-terminal dimerization domain


Mass: 10571.022 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

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Protein , 13 types, 22 molecules RSGHOPQTUWVXYZghijlo56

#7: Protein Robl


Mass: 10230.603 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#10: Protein
Arp1


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


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


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


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


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


Mass: 20698.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#22: Protein p150


Mass: 4443.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#24: Protein Dynactin / Dynactin subunit 2


Mass: 7931.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A0J9X293
#27: Protein dynactin p150


Mass: 4528.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#28: Protein BICD2N


Mass: 23421.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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 dynein light intermediate chain


Mass: 25123.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#9: Protein dynein light intermediate chain


Mass: 25379.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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 dynactin shoulder complex


Mass: 48613.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#16: Protein dynactin shoulder complex


Mass: 51251.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#17: Protein dynactin shoulder complex


Mass: 11081.651 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#18: Protein dynactin shoulder complex


Mass: 14826.253 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)

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Protein/peptide , 3 types, 3 molecules kmn

#23: Protein/peptide Dynactin / Dynactin subunit 2


Mass: 5400.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A0J9X292
#25: Protein/peptide Dynactin


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


Mass: 2237.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A0J9X293*PLUS

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D 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 BICD2COMPLEX#1-#290MULTIPLE SOURCES
2dynein-1COMPLEX#1-#91RECOMBINANT
3dynactinCOMPLEX#10-#271NATURAL
4BICD2COMPLEX#281RECOMBINANT
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Sus scrofa (pig)9823
34Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Spodoptera frugiperda (fall armyworm)7108
24Spodoptera frugiperda (fall armyworm)7108
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
MicroscopyModel: 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
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 / Num. of particles: 78671 / Symmetry type: POINT

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