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- EMDB-17834: Dynactin pointed end bound to JIP3 -

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Basic information

Entry
Database: EMDB / ID: EMD-17834
TitleDynactin pointed end bound to JIP3
Map data3D map after focussed 3D refinement of pointed end
Sample
  • Complex: Dynactin pointed end bound to JIP3
    • Protein or peptide: Arp11
    • Protein or peptide: Dynactin 6
    • Protein or peptide: Dynactin subunit 5
    • Protein or peptide: Dynactin subunit 4
    • Protein or peptide: C-Jun-amino-terminal kinase-interacting protein 3
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
KeywordsDynein / AAA-Atpase / p150 / LIS1 / MOTOR PROTEIN
Function / homology
Function and homology information


retrograde axonal transport of mitochondrion / dynactin complex / anterograde axonal protein transport / MAP-kinase scaffold activity / Neutrophil degranulation / JUN kinase binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / axon regeneration ...retrograde axonal transport of mitochondrion / dynactin complex / anterograde axonal protein transport / MAP-kinase scaffold activity / Neutrophil degranulation / JUN kinase binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / axon regeneration / dynein complex binding / axon development / kinesin binding / regulation of JNK cascade / stress fiber / vesicle-mediated transport / axon cytoplasm / sarcomere / mitotic spindle organization / positive regulation of JNK cascade / kinetochore / signaling receptor complex adaptor activity / cell cortex / growth cone / cell body / cytoplasmic vesicle / protein stabilization / Golgi membrane / axon / centrosome / dendrite / negative regulation of apoptotic process / perinuclear region of cytoplasm / cytoplasm
Similarity search - Function
JNK-interacting protein, leucine zipper II / JNK-interacting protein 3/4 / JNK-interacting protein leucine zipper II / WD40 repeated domain / Dynactin subunit 4 / RH1 domain / RH2 domain / Dynactin p62 family / RILP homology 1 domain / RH1 domain profile. ...JNK-interacting protein, leucine zipper II / JNK-interacting protein 3/4 / JNK-interacting protein leucine zipper II / WD40 repeated domain / Dynactin subunit 4 / RH1 domain / RH2 domain / Dynactin p62 family / RILP homology 1 domain / RH1 domain profile. / RH2 domain profile. / : / Dynactin subunit 6 / Dynactin subunit 5 / Trimeric LpxA-like superfamily / Actin / Actin family / Actin / ATPase, nucleotide binding domain / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Dynactin subunit 5 / Dynactin subunit 4 / Dynactin subunit 6 / Actin-related protein 10 / C-Jun-amino-terminal kinase-interacting protein 3
Similarity search - Component
Biological speciesHomo sapiens (human) / Sus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSingh K / Lau CK / Manigrasso G / Gassmann R / Carter AP
Funding support United Kingdom, European Union, 3 items
OrganizationGrant numberCountry
Wellcome Trust210711/Z/18/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_A025_1011 United Kingdom
European Molecular Biology Organization (EMBO)ALTF 197-2021European Union
CitationJournal: Science / Year: 2024
Title: Molecular mechanism of dynein-dynactin complex assembly by LIS1.
Authors: Kashish Singh / Clinton K Lau / Giulia Manigrasso / José B Gama / Reto Gassmann / Andrew P Carter /
Abstract: Cytoplasmic dynein is a microtubule motor vital for cellular organization and division. It functions as a ~4-megadalton complex containing its cofactor dynactin and a cargo-specific coiled-coil ...Cytoplasmic dynein is a microtubule motor vital for cellular organization and division. It functions as a ~4-megadalton complex containing its cofactor dynactin and a cargo-specific coiled-coil adaptor. However, how dynein and dynactin recognize diverse adaptors, how they interact with each other during complex formation, and the role of critical regulators such as lissencephaly-1 (LIS1) protein (LIS1) remain unclear. In this study, we determined the cryo-electron microscopy structure of dynein-dynactin on microtubules with LIS1 and the lysosomal adaptor JIP3. This structure reveals the molecular basis of interactions occurring during dynein activation. We show how JIP3 activates dynein despite its atypical architecture. Unexpectedly, LIS1 binds dynactin's p150 subunit, tethering it along the length of dynein. Our data suggest that LIS1 and p150 constrain dynein-dynactin to ensure efficient complex formation.
History
DepositionJul 12, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17834.png

Downloads & links

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Map

FileDownload / File: emd_17834.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D map after focussed 3D refinement of pointed end
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 460 pix.
= 487.14 Å		1.06 Å/pix.
x 460 pix.
= 487.14 Å		1.06 Å/pix.
x 460 pix.
= 487.14 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.01003648 - 0.030064616
Average (Standard dev.)-0.0001770282 (±0.00046396302)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 487.14 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17834_msk_1.map
Projections & Slices
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Additional map: #1

Fileemd_17834_additional_1.map
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Additional map: 3D map prior to focussed 3D refinement of pointed end

Fileemd_17834_additional_2.map
Annotation3D map prior to focussed 3D refinement of pointed end
Projections & Slices
AxesZYX

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Additional map: half map 1 of 3D map prior to focussed 3D refinement of pointed end

Fileemd_17834_additional_3.map
Annotationhalf map 1 of 3D map prior to focussed 3D refinement of pointed end
Projections & Slices
AxesZYX

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Additional map: half map 2 of 3D map prior to focussed 3D refinement of pointed end

Fileemd_17834_additional_4.map
Annotationhalf map 2 of 3D map prior to focussed 3D refinement of pointed end
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_17834_half_map_1.map
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Half map: #1

Fileemd_17834_half_map_2.map
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Sample components

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Entire : Dynactin pointed end bound to JIP3

EntireName: Dynactin pointed end bound to JIP3
Components
  • Complex: Dynactin pointed end bound to JIP3
    • Protein or peptide: Arp11
    • Protein or peptide: Dynactin 6
    • Protein or peptide: Dynactin subunit 5
    • Protein or peptide: Dynactin subunit 4
    • Protein or peptide: C-Jun-amino-terminal kinase-interacting protein 3
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: Dynactin pointed end bound to JIP3

SupramoleculeName: Dynactin pointed end bound to JIP3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Arp11

MacromoleculeName: Arp11 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 46.250785 KDa
SequenceString: MPLYEGLGSG GEKTAVVIDL GEAFTKCGFA GETGPRCIIP SVIKKAGMPK PIKVVQYNIN TEELYSYLKE FIHILYFRHL LVNPRDRRV VVIESVLCPS HFRETLTRVL FKYFEVPSVL LAPSHLMALL TLGINSAMVL DCGYRESLVL PIYEGIPVLN C WGALPLGG ...String:
MPLYEGLGSG GEKTAVVIDL GEAFTKCGFA GETGPRCIIP SVIKKAGMPK PIKVVQYNIN TEELYSYLKE FIHILYFRHL LVNPRDRRV VVIESVLCPS HFRETLTRVL FKYFEVPSVL LAPSHLMALL TLGINSAMVL DCGYRESLVL PIYEGIPVLN C WGALPLGG KALHKELETQ LLEQCTVDTG AAKEQSLPSV MGSIPEGVLE DIKVRTCFVS DLTRGLKIQA AKFNIDGNTE RP SPPPNVD YPLDGEKILH VLGSIRDSVV EILFEQDNEE KSVATLILDS LMQCPIDTRK QLAENLVIIG GTSMLPGFLH RLL AEIRYL VEKPKYKKTL GTKTFRIHTP PAKANCVAWL GGAIFGALQD ILGSRSVSKE YYNQTGRIPD WCSLNNPPLE MVFD VGKSQ PPLMKRAFST EK

UniProtKB: Actin-related protein 10

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Macromolecule #2: Dynactin 6

MacromoleculeName: Dynactin 6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 20.70391 KDa
SequenceString:
MAEKTQKSVK IAPGAVVCVE SEIRGDVTIG PRTVIHPKAR IIAEAGPIVI GEGNLIEEQA LIINAHPDNI TPDAEDSEPK PMIIGTNNV FEVGCYSQAM KMGDNNVIES KAYVGRNVIL TSGCIIGACC NLNTFEVIPE NTVIYGADCL RRVQTERPQP Q TLQLDFLM KILPNYHHLK KTMKGSSTPV KN

UniProtKB: Dynactin subunit 6

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Macromolecule #3: Dynactin subunit 5

MacromoleculeName: Dynactin subunit 5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 20.150533 KDa
SequenceString:
MELGELLYNK SEYIETASGN KVSRQSVLCG SQNIVLNGKT IVMNDCIIRG DLANVRVGRH CVVKSRSVIR PPFKKFSKGV AFFPLHIGD HVFIEEDCVV NAAQIGSYVH VGKNCVIGRR CVLKDCCKIL DNTVLPPETV VPPFTVFSGC PGLFSGELPE C TQELMIDV TKSYYQKFLP LTQV

UniProtKB: Dynactin subunit 5

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Macromolecule #4: Dynactin subunit 4

MacromoleculeName: Dynactin subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 52.920434 KDa
SequenceString: MASLLQSERV LYLVQGEKKV RAPLSQLYFC RYCSELRSLE CVSHEVDSHY CPSCLENMPS AEAKLKKNRC ANCFDCPGCM HTLSTRATS ISTQLPDDPA KTAVKKAYYL ACGFCRWTSR DVGMADKSVA SGGWQEPDHP HTQRMNKLIE YYQQLAQKEK V ERDRKKLA ...String:
MASLLQSERV LYLVQGEKKV RAPLSQLYFC RYCSELRSLE CVSHEVDSHY CPSCLENMPS AEAKLKKNRC ANCFDCPGCM HTLSTRATS ISTQLPDDPA KTAVKKAYYL ACGFCRWTSR DVGMADKSVA SGGWQEPDHP HTQRMNKLIE YYQQLAQKEK V ERDRKKLA RRRNYMPLAF SQHTIHVVDK YGLGTRLQRP RAGTTITALA GLSLKEGEDQ KEIKIEPAQA VDEVEPLPED YY TRPVNLT EVTTLQQRLL QPDFQPICAS QLYPRHKHLL IKRSLRCRQC EHNLSKPEFN PTSIKFKIQL VAVNYIPEVR IMS IPNLRY MKESQVLLTL TNPVENLTHV TLLECEEGDP DDTNSTAKVS VPPTELVLAG KDAAAEYDEL AEPQDFPDDP DVVA FRKAN KVGVFIKVTP QREEGDVTVC FKLKHDFKNL AAPIRPVEEA DPGAEVSWLT QHVELSLGPL LP

UniProtKB: Dynactin subunit 4

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Macromolecule #5: C-Jun-amino-terminal kinase-interacting protein 3

MacromoleculeName: C-Jun-amino-terminal kinase-interacting protein 3 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.975398 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SNIEFLKMME IQMDEGGGVV VYQDDYCSGS VMSERVSGLA GSIYREFERL IHCYDEEVVK ELMPLVVNVL ENLDSVLSEN QEHEVELEL LREDNEQLLT QYEREKALRR QAEEKFIEFE DALEQEKKEL QIQVEHYEFQ TRQLELKAKN YADQISRLEE R ESEMKKEY ...String:
SNIEFLKMME IQMDEGGGVV VYQDDYCSGS VMSERVSGLA GSIYREFERL IHCYDEEVVK ELMPLVVNVL ENLDSVLSEN QEHEVELEL LREDNEQLLT QYEREKALRR QAEEKFIEFE DALEQEKKEL QIQVEHYEFQ TRQLELKAKN YADQISRLEE R ESEMKKEY NALHQRHTEM IQTYVEHIER SKMQQVGGNS QTESSLPGRR KERPTSLNVF PLADGTVRAQ IGGKLVPAGD HW HLSDLGQ LQSSSSYQCP QDEMSESGQS SAAATPSTTG TKSNTPTSSV PSAAVTPLNE SLQPLGDYGV GSKNSKRARE KRD SRNMEV QVTQEMRNVS IGMGSSDEWS DVQDIIDSTP ELDMCPETRL DRTGSSPTQG IVNKAFGINT DSLYHELSTA GSEV IGDVD EGADLLGEFS VRDDFFGMGK EVGNLLLENS QLLETKNALN VVKNDLIAKV DQLSGEQEVL RGELEAAKQA KVKLE NRIK ELEEELKRVK SEAIIARREP KEEAEDVSSY LCTESDKIPM AQRRRFTRVE MARVLMERNQ YKERLMELQE AVRWTE MIR ASREGSGSGR WSHPQFEK

UniProtKB: C-Jun-amino-terminal kinase-interacting protein 3

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Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98623
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7z8g


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8pr4:
Dynactin pointed end bound to JIP3

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