[English] 日本語
Yorodumi
- PDB-9yng: Dynactin and dynein-1 tail region of dynein-dynactin complex on m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9yng
TitleDynactin and dynein-1 tail region of dynein-dynactin complex on microtubule in the presence of LIS1
Components
  • (Cytoplasmic dynein 1 ...) x 2
  • (Dynactin subunit ...) x 6
  • (F-actin-capping protein subunit ...) x 2
  • Actin, cytoplasmic 1
  • Actin-related protein 10
  • Alpha-centractin
KeywordsMOTOR PROTEIN / Dynein-1 / Dynactin
Function / homology
Function and homology information


: / Factors involved in megakaryocyte development and platelet production / retrograde axonal transport of mitochondrion / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation ...: / Factors involved in megakaryocyte development and platelet production / retrograde axonal transport of mitochondrion / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / UCH proteinases / Gap junction degradation / Formation of annular gap junctions / RHOF GTPase cycle / Clathrin-mediated endocytosis / Formation of the dystrophin-glycoprotein complex (DGC) / dynactin complex / centriolar subdistal appendage / positive regulation of neuromuscular junction development / centriole-centriole cohesion / 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 / transport along microtubule / F-actin capping protein complex / WASH complex / Recruitment of mitotic centrosome proteins and complexes / microtubule anchoring at centrosome / dynein light chain binding / ventral spinal cord development / dynein heavy chain binding / retromer complex / cytoskeleton-dependent cytokinesis / microtubule plus-end / cellular response to cytochalasin B / nuclear membrane disassembly / positive regulation of intracellular transport / positive regulation of microtubule nucleation / regulation of transepithelial transport / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / regulation of metaphase plate congression / positive regulation of spindle assembly / protein localization to adherens junction / barbed-end actin filament capping / melanosome transport / establishment of spindle localization / dense body / Tat protein binding / postsynaptic actin cytoskeleton / coronary vasculature development / Neutrophil degranulation / non-motile cilium assembly / regulation of cell morphogenesis / dynein complex / adherens junction assembly / retrograde transport, endosome to Golgi / COPI-independent Golgi-to-ER retrograde traffic / apical protein localization / retrograde axonal transport / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / P-body assembly / microtubule motor activity / Recruitment of NuMA to mitotic centrosomes / tight junction / microtubule associated complex / minus-end-directed microtubule motor activity / COPI-mediated anterograde transport / dynein light intermediate chain binding / cytoplasmic dynein complex / aorta development / ventricular septum development / microtubule-based movement / neuromuscular process / nuclear migration / apical junction complex / regulation of norepinephrine uptake / neuromuscular junction development / nitric-oxide synthase binding / transporter regulator activity / cortical cytoskeleton / establishment or maintenance of cell polarity / NuA4 histone acetyltransferase complex / cell leading edge / motor behavior / dynein intermediate chain binding / dynein complex binding / microtubule organizing center / cleavage furrow / brush border / establishment of mitotic spindle orientation / kinesin binding / regulation of synaptic vesicle endocytosis / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination
Similarity search - Function
Dynactin subunit 3 / Dynactin subunit p22 / Dynactin subunit 4 / Dynactin p62 family / Dynamitin / : / Dynamitin / Dynactin subunit 6 / Dynein associated protein / Dynein associated protein ...Dynactin subunit 3 / Dynactin subunit p22 / Dynactin subunit 4 / Dynactin p62 family / Dynamitin / : / Dynamitin / Dynactin subunit 6 / Dynein associated protein / Dynein associated protein / Dynactin subunit 5 / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / 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 / CAP-Gly domain signature. / : / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain, C-terminal domain / Dynein heavy chain, C-terminal domain, barrel region / Dynein heavy chain C-terminal domain / : / Dynein heavy chain, ATPase lid domain / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / P-loop containing dynein motor region / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker / Dynein heavy chain, AAA module D4 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Dynein heavy chain, ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Dynein heavy chain AAA lid domain superfamily / Dynein heavy chain, domain 2, N-terminal / Dynein heavy chain, linker, subdomain 3 / Dynein heavy chain, AAA1 domain, small subdomain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, N-terminal region 2 / Hydrolytic ATP binding site of dynein motor region / Microtubule-binding stalk of dynein motor / P-loop containing dynein motor region D4 / ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / 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 / WD domain, G-beta repeat / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Dynactin subunit 5 / Dynactin subunit 1 / Dynactin subunit 4 / Dynactin subunit 2 / Actin related protein 1A / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta / Dynactin subunit 6 ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Dynactin subunit 5 / Dynactin subunit 1 / Dynactin subunit 4 / Dynactin subunit 2 / Actin related protein 1A / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta / Dynactin subunit 6 / Dynactin subunit 3 / Actin-related protein 10 / Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein 1 heavy chain 1 / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesSus scrofa (pig)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.07 Å
AuthorsYang, J. / Rao, Q. / Chai, P. / Zhang, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM142959 United States
CitationJournal: To Be Published
Title: Molecular basis for the assembly of the dynein transport machinery on microtubules
Authors: Rao, Q. / Yang, J. / Chai, P. / Zhang, K.
History
DepositionOct 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-centractin
B: Alpha-centractin
C: Alpha-centractin
D: Alpha-centractin
E: Alpha-centractin
F: Alpha-centractin
G: Alpha-centractin
H: Actin, cytoplasmic 1
I: Alpha-centractin
J: Actin-related protein 10
K: F-actin-capping protein subunit alpha-1
L: F-actin-capping protein subunit beta
M: Dynactin subunit 2
N: Dynactin subunit 2
O: Dynactin subunit 3
P: Dynactin subunit 2
Q: Dynactin subunit 2
R: Dynactin subunit 3
U: Dynactin subunit 6
V: Dynactin subunit 5
W: Dynactin subunit 1
Y: Dynactin subunit 4
Z: Dynactin subunit 1
e: Cytoplasmic dynein 1 heavy chain 1
f: Cytoplasmic dynein 1 heavy chain 1
g: Cytoplasmic dynein 1 intermediate chain 2
h: Cytoplasmic dynein 1 intermediate chain 2
m: Cytoplasmic dynein 1 heavy chain 1
n: Cytoplasmic dynein 1 heavy chain 1
o: Cytoplasmic dynein 1 intermediate chain 2
p: Cytoplasmic dynein 1 intermediate chain 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,515,20444
Polymers3,510,65631
Non-polymers4,54813
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 3 types, 10 molecules ABCDEFGIHJ

#1: Protein
Alpha-centractin


Mass: 42670.688 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A8D1PMN0
#2: Protein Actin, cytoplasmic 1 / Beta-actin


Mass: 41782.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: ACTB / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q6QAQ1, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#3: Protein Actin-related protein 10


Mass: 46250.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: ACTR10, ARP11 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: I3LHK5

-
F-actin-capping protein subunit ... , 2 types, 2 molecules KL

#4: Protein F-actin-capping protein subunit alpha-1


Mass: 33059.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: CAPZA1, Capza, CP alpha1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0PFK5
#5: Protein F-actin-capping protein subunit beta / CapZ beta


Mass: 30669.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: CAPZB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0PFK7

-
Dynactin subunit ... , 6 types, 11 molecules MNPQORUVWZY

#6: Protein
Dynactin subunit 2


Mass: 44704.414 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: DCTN2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A5G2QD80
#7: Protein Dynactin subunit 3


Mass: 21192.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: DCTN3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: F1SEC0
#8: Protein Dynactin subunit 6


Mass: 20703.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: DCTN6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D0G6S1
#9: Protein Dynactin subunit 5


Mass: 20150.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: DCTN5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A286ZK88
#10: Protein Dynactin subunit 1 / 150 kDa dynein-associated polypeptide / p150-glued


Mass: 142015.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: DCTN1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A287B8J2
#11: Protein Dynactin subunit 4 / Dyn4


Mass: 52920.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: DCTN4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A4X1TB62

-
Cytoplasmic dynein 1 ... , 2 types, 8 molecules efmnghop

#12: Protein
Cytoplasmic dynein 1 heavy chain 1 / Cytoplasmic dynein heavy chain 1 / Dynein heavy chain / cytosolic


Mass: 533083.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1H1, DHC1, DNCH1, DNCL, DNECL, DYHC, KIAA0325 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14204
#13: Protein
Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein intermediate chain 2 / Dynein intermediate chain 2 / cytosolic / DH IC-2


Mass: 71546.445 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1I2, DNCI2, DNCIC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13409

-
Non-polymers , 3 types, 13 molecules

#14: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#15: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#16: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Dynactin and dynein tail region of dynein-dynactin complex on microtubule in the presence of LIS1
Type: COMPLEX / Entity ID: #1-#13 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.2
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 X / Calibrated magnification: 45000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 2600 nm / Cs: 2.7 mm / C2 aperture diameter: 30 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
8PHENIXmodel refinement
13PHENIX3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91824 / Symmetry type: POINT
RefinementHighest resolution: 4.07 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00284823
ELECTRON MICROSCOPYf_angle_d0.507115433
ELECTRON MICROSCOPYf_dihedral_angle_d5.2312425
ELECTRON MICROSCOPYf_chiral_restr0.04113439
ELECTRON MICROSCOPYf_plane_restr0.00415163

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more