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- PDB-9hhl: Structure of Dynein-Dynactin-NuMA-LIS1 -

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Entry
Database: PDB / ID: 9hhl
TitleStructure of Dynein-Dynactin-NuMA-LIS1
Components
  • (Cytoplasmic dynein 1 ...) x 3
  • (Dynactin subunit ...) x 5
  • ARP1 actin related protein 1 homolog A
  • Actin, cytoplasmic 1
  • Arp11
  • Capping protein (Actin filament) muscle Z-line, alpha 1
  • Dynactin 6
  • Dynein light chain roadblock-type 1
  • F-actin-capping protein subunit beta
  • Nuclear mitotic apparatus protein 1,Methylated-DNA--protein-cysteine methyltransferase
KeywordsMOTOR PROTEIN / transport
Function / homology
Function and homology information


anastral spindle assembly / positive regulation of protein localization to spindle pole body / positive regulation of mitotic spindle elongation / cytoplasmic microtubule bundle / positive regulation of chromosome separation / microtubule minus-end / cortical microtubule / microtubule bundle / RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production ...anastral spindle assembly / positive regulation of protein localization to spindle pole body / positive regulation of mitotic spindle elongation / cytoplasmic microtubule bundle / positive regulation of chromosome separation / microtubule minus-end / cortical microtubule / microtubule bundle / RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / Mitotic Prophase / lateral cell cortex / MGMT-mediated DNA damage reversal / positive regulation of chromosome segregation / cell cortex region / mitotic spindle astral microtubule / 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 / centriolar subdistal appendage / Clathrin-mediated endocytosis / Formation of the dystrophin-glycoprotein complex (DGC) / dynactin complex / positive regulation of neuromuscular junction development / centriole-centriole cohesion / microtubule minus-end binding / transport along microtubule / visual behavior / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / 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 / F-actin capping protein complex / WASH complex / microtubule anchoring at centrosome / Recruitment of mitotic centrosome proteins and complexes / mitotic spindle midzone / dynein light chain binding / dynein heavy chain binding / ventral spinal cord development / positive regulation of hair follicle development / astral microtubule organization / DNA-methyltransferase activity / retromer complex / cytoskeleton-dependent cytokinesis / ciliary tip / microtubule plus-end / nuclear membrane disassembly / cellular response to cytochalasin B / Intraflagellar transport / positive regulation of intracellular transport / positive regulation of microtubule nucleation / regulation of transepithelial transport / regulation of metaphase plate congression / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / positive regulation of spindle assembly / barbed-end actin filament capping / spindle pole centrosome / melanosome transport / protein localization to adherens junction / establishment of spindle localization / dense body / positive regulation of BMP signaling pathway / Tat protein binding / positive regulation of keratinocyte differentiation / postsynaptic actin cytoskeleton / coronary vasculature development / microtubule bundle formation / microtubule plus-end binding / DNA alkylation repair / Neutrophil degranulation / non-motile cilium assembly / regulation of cell morphogenesis / dynein complex / retrograde transport, endosome to Golgi / COPI-independent Golgi-to-ER retrograde traffic / adherens junction assembly / retrograde axonal transport / apical protein localization / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / P-body assembly / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / microtubule motor activity / MHC class II antigen presentation / tight junction / Recruitment of NuMA to mitotic centrosomes
Similarity search - Function
: / : / NuMA N-terminal hook domain / : / Dynactin subunit 3 / Dynactin subunit p22 / Dynactin subunit 4 / Dynactin p62 family / Dynein associated protein / Dynein associated protein ...: / : / NuMA N-terminal hook domain / : / Dynactin subunit 3 / Dynactin subunit p22 / Dynactin subunit 4 / Dynactin p62 family / Dynein associated protein / Dynein associated protein / Dynamitin / : / Dynamitin / Dynactin subunit 6 / Dynein 1 light intermediate chain / Dynein light chain roadblock-type 1/2 / Dynactin subunit 5 / Dynein family light intermediate chain / Dynein light intermediate chain (DLIC) / 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. / Methylguanine DNA methyltransferase, ribonuclease-like domain / F-actin capping protein, alpha subunit, conserved site / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / Methylated DNA-protein cysteine methyltransferase domain superfamily / 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 / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / Methylated-DNA--protein-cysteine methyltransferase active site. / Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding / Methylated DNA-protein cysteine methyltransferase, DNA binding domain / 6-O-methylguanine DNA methyltransferase, DNA binding domain / CAP-Gly domain signature. / : / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / 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 / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Dynactin subunit 5 / Dynactin subunit 1 / Dynactin subunit 4 / Dynactin subunit 2 / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta / Dynactin subunit 6 / Dynactin subunit 3 ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Dynactin subunit 5 / Dynactin subunit 1 / Dynactin subunit 4 / Dynactin subunit 2 / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta / Dynactin subunit 6 / Dynactin subunit 3 / Alpha-centractin / Actin-related protein 10 / Cytoplasmic dynein 1 light intermediate chain 2 / Methylated-DNA--protein-cysteine methyltransferase / Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein 1 heavy chain 1 / Nuclear mitotic apparatus protein 1 / Actin, cytoplasmic 1 / Dynein light chain roadblock-type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.53 Å
Authorsd'Amico, E.A. / Carter, A.P.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust227434/Z/23/Z United Kingdom
UK Research and Innovation (UKRI)EP/Y026004/1 United Kingdom
CitationJournal: To Be Published
Title: Structural and functional insights into activation and regulation of the dynein-dynactin-NuMA complex
Authors: Aslan, M. / d'Amico, E.A. / Cho, N. / Taheri, A. / Zhao, Y. / Zhong, J. / Blaauw, M. / Carter, A.P. / Dumont, S. / Yildiz, A.
History
DepositionNov 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
p: Cytoplasmic dynein 1 intermediate chain 2
1: Nuclear mitotic apparatus protein 1,Methylated-DNA--protein-cysteine methyltransferase
2: Nuclear mitotic apparatus protein 1,Methylated-DNA--protein-cysteine methyltransferase
A: ARP1 actin related protein 1 homolog A
B: ARP1 actin related protein 1 homolog A
D: ARP1 actin related protein 1 homolog A
E: ARP1 actin related protein 1 homolog A
F: ARP1 actin related protein 1 homolog A
G: ARP1 actin related protein 1 homolog A
H: Actin, cytoplasmic 1
I: ARP1 actin related protein 1 homolog A
J: Arp11
K: Capping protein (Actin filament) muscle Z-line, 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 6
V: Dynactin subunit 2
W: Dynactin subunit 5
Y: Dynactin subunit 4
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
j: Cytoplasmic dynein 1 light intermediate chain 2
m: Cytoplasmic dynein 1 heavy chain 1
n: Cytoplasmic dynein 1 heavy chain 1
o: Cytoplasmic dynein 1 intermediate chain 2
q: Cytoplasmic dynein 1 light intermediate chain 2
s: Dynein light chain roadblock-type 1
t: Dynein light chain roadblock-type 1
u: Cytoplasmic dynein 1 light intermediate chain 2
w: Dynein light chain roadblock-type 1
z: Dynein light chain roadblock-type 1
S: Dynactin subunit 1
T: Dynactin subunit 1
C: ARP1 actin related protein 1 homolog A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,953,07154
Polymers3,948,44341
Non-polymers4,62813
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Cytoplasmic dynein 1 ... , 3 types, 11 molecules pghoefmnjqu

#1: Protein
Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein intermediate chain 2 / Dynein intermediate chain 2 / cytosolic / DH IC-2


Mass: 68442.141 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
#13: Protein
Cytoplasmic dynein 1 heavy chain 1 / Cytoplasmic dynein heavy chain 1 / Dynein heavy chain / cytosolic


Mass: 533055.125 Da / Num. of mol.: 4 / Mutation: R1567E, K1610E
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
#14: Protein Cytoplasmic dynein 1 light intermediate chain 2 / Dynein light intermediate chain 2 / cytosolic / LIC-2 / LIC53/55


Mass: 54173.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1LI2, DNCLI2, LIC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43237

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Protein , 8 types, 19 molecules 12ABDEFGICHJKLUstwz

#2: Protein Nuclear mitotic apparatus protein 1,Methylated-DNA--protein-cysteine methyltransferase / Nuclear matrix protein-22 / NMP-22 / Nuclear mitotic apparatus protein / NuMA protein / SP-H ...Nuclear matrix protein-22 / NMP-22 / Nuclear mitotic apparatus protein / NuMA protein / SP-H antigen / 6-O-methylguanine-DNA methyltransferase / MGMT / O-6-methylguanine-DNA-alkyltransferase


Mass: 99677.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUMA1, NMP22, NUMA, MGMT / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q14980, UniProt: P16455, methylated-DNA-[protein]-cysteine S-methyltransferase
#3: Protein
ARP1 actin related protein 1 homolog A


Mass: 42670.688 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F2Z5G5
#4: Protein Actin, cytoplasmic 1 / Beta-actin


Mass: 41782.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q6QAQ1
#5: 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
#6: 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
#7: Protein F-actin-capping protein subunit beta / CapZ beta


Mass: 30669.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0PFK7
#10: 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
#15: Protein
Dynein light chain roadblock-type 1 / Bithoraxoid-like protein / BLP / Dynein light chain 2A / cytoplasmic / Dynein-associated protein ...Bithoraxoid-like protein / BLP / Dynein light chain 2A / cytoplasmic / Dynein-associated protein Km23 / Roadblock domain-containing protein 1


Mass: 10934.576 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYNLRB1, BITH, DNCL2A, DNLC2A, ROBLD1, HSPC162 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NP97

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Dynactin subunit ... , 5 types, 11 molecules MNPQVORWYST

#8: Protein
Dynactin subunit 2


Mass: 44704.414 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A5G2QD80
#9: Protein Dynactin subunit 3 / Dynactin subunit 3 isoform 1


Mass: 21192.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SEC0
#11: Protein Dynactin subunit 5


Mass: 20150.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZK88
#12: Protein Dynactin subunit 4 / Dynactin subunit 4


Mass: 52920.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TB62
#16: Protein Dynactin subunit 1 / 150 kDa dynein-associated polypeptide / p150-glued


Mass: 142015.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287B8J2

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Non-polymers , 3 types, 13 molecules

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


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#18: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#19: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
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
1Dynein-Dynactin-NuMA-LIS1 complexCOMPLEX#2-#9, #16, #10-#13, #1, #14-#150RECOMBINANT
2DynactinCOMPLEX#3-#9, #16, #10-#121NATURAL
3NuMACOMPLEX#21RECOMBINANT
4Dynein-A and Dynein-BCOMPLEX#13, #1, #14-#151RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Sus scrofa (pig)9823
33Homo sapiens (human)9606
44Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
23Spodoptera frugiperda (fall armyworm)7108
34Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 7.2
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8092 / Symmetry type: POINT

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