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- PDB-30dr: Dynein-Dynactin-RAB11FIP3 complex - composite -

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Entry
Database: PDB / ID: 30dr
TitleDynein-Dynactin-RAB11FIP3 complex - composite
Components
  • (Cytoplasmic dynein 1 ...) x 2
  • (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
  • Isoform 2C of Cytoplasmic dynein 1 intermediate chain 2
  • Rab11 family-interacting protein 3
KeywordsMOTOR PROTEIN / dynein / dynactin / adaptors / RAB11FIP3 / R11F3 / FIP3
Function / homology
Function and homology information


: / regulation of protein localization to centrosome / protein localization to cleavage furrow / : / Advanced glycosylation endproduct receptor signaling / postsynaptic recycling endosome membrane / regulation of endocytic recycling / retrograde axonal transport of mitochondrion / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling ...: / regulation of protein localization to centrosome / protein localization to cleavage furrow / : / Advanced glycosylation endproduct receptor signaling / postsynaptic recycling endosome membrane / regulation of endocytic recycling / 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 / RHOF GTPase cycle / Formation of the canonical BAF (cBAF) complex / Formation of the polybromo-BAF (pBAF) complex / Formation of the embryonic stem cell BAF (esBAF) complex / Formation of the non-canonical BAF (ncBAF) complex / GBP-mediated host defense / sterol sensor activity / Platelet degranulation / visual behavior / Gap junction degradation / Formation of annular gap junctions / UCH proteinases / dynactin complex / centriolar subdistal appendage / Clathrin-mediated endocytosis / negative regulation of adiponectin secretion / centriole-centriole cohesion / positive regulation of mitotic cytokinetic process / positive regulation of neuromuscular junction development / 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 / Recruitment of mitotic centrosome proteins and complexes / microtubule anchoring at centrosome / F-actin capping protein complex / intraciliary retrograde transport / WASH complex / Regulation of CDH1 Function / Formation of the dystrophin-glycoprotein complex (DGC) / regulation of cilium assembly / lysosome to ER cholesterol transport / dynein light chain binding / transport along microtubule / ventral spinal cord development / dynein heavy chain binding / VxPx cargo-targeting to cilium / retromer complex / cytoskeleton-dependent cytokinesis / dynein complex / regulation of vesicle-mediated transport / microtubule plus-end / mitotic nuclear membrane disassembly / Intraflagellar transport / positive regulation of microtubule nucleation / protein localization to cilium / cellular response to cytochalasin B / positive regulation of cilium assembly / positive regulation of intracellular transport / positive regulation of spindle assembly / regulation of transepithelial transport / regulation of metaphase plate congression / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / protein localization to adherens junction / non-motile cilium assembly / barbed-end actin filament capping / endocytic recycling / Golgi to plasma membrane protein transport / establishment of spindle localization / dense body / Neutrophil degranulation / Tat protein binding / motor behavior / postsynaptic actin cytoskeleton / positive regulation of mitotic cell cycle spindle assembly checkpoint / apical protein localization / neuron cellular homeostasis / retrograde transport, endosome to Golgi / retrograde axonal transport / adherens junction assembly / COPI-independent Golgi-to-ER retrograde traffic / neuromuscular process / minus-end-directed microtubule motor activity / P-body assembly / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / microtubule associated complex / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / dynein light intermediate chain binding / cytoplasmic dynein complex / MHC class II antigen presentation / nuclear migration / Recruitment of NuMA to mitotic centrosomes
Similarity search - Function
: / : / Rab11-FIP3-like domain / Rab-binding domain FIP-RBD / FIP-RBD, C-terminal domain superfamily / FIP domain / FIP-RBD domain profile. / Dynactin subunit 3 / Dynactin subunit p22 / Dynactin subunit 4 ...: / : / Rab11-FIP3-like domain / Rab-binding domain FIP-RBD / FIP-RBD, C-terminal domain superfamily / FIP domain / FIP-RBD domain profile. / Dynactin subunit 3 / Dynactin subunit p22 / Dynactin subunit 4 / Dynactin p62 family / Dynamitin / Dynamitin / Dynactin subunit 6 / : / Domain of unknown function (DUF8221) / Dynein associated protein / Dynein associated protein / Dynein 1 light intermediate chain / : / Dynactin subunit 5 / Dynein light chain roadblock-type 1/2 / 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. / 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 / 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 / EF-hand domain pair / ATPase, nucleotide binding domain / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / 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
Similarity search - Domain/homology
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 ...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 / Rab11 family-interacting protein 3 / Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein 1 heavy chain 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: 10 Å
Authorsd'Amico, E.A. / Carter, A.P.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust227434/Z/23/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_A025_1011 United Kingdom
UK Research and Innovation (UKRI)101105484 United Kingdom
CitationJournal: To Be Published
Title: Molecular basis of dynein adaptor recognition
Authors: d'Amico, E.A. / Chaaban, S. / Abid Ali, F. / Michalski, L. / Carter, A.P.
History
DepositionApr 21, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Rab11 family-interacting protein 3
2: Rab11 family-interacting protein 3
A: ARP1 actin related protein 1 homolog A
B: ARP1 actin related protein 1 homolog A
C: 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
S: Dynactin subunit 1
T: Dynactin subunit 1
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: Isoform 2C of Cytoplasmic dynein 1 intermediate chain 2
h: Isoform 2C of 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: Isoform 2C of Cytoplasmic dynein 1 intermediate chain 2
p: Isoform 2C of Cytoplasmic dynein 1 intermediate chain 2
q: Cytoplasmic dynein 1 light intermediate chain 2
r: Cytoplasmic dynein 1 light intermediate chain 2
s: Dynein light chain roadblock-type 1
t: Dynein light chain roadblock-type 1
w: Dynein light chain roadblock-type 1
z: Dynein light chain roadblock-type 1


Theoretical massNumber of molelcules
Total (without water)3,922,42341
Polymers3,922,42341
Non-polymers00
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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Protein , 9 types, 23 molecules 12ABCDEFGIHJKLUghopstwz

#1: Protein Rab11 family-interacting protein 3 / FIP3 / FIP3-Rab11 / Rab11-FIP3 / Arfophilin-1 / EF hands-containing Rab-interacting protein / ...FIP3 / FIP3-Rab11 / Rab11-FIP3 / Arfophilin-1 / EF hands-containing Rab-interacting protein / Eferin / MU-MB-17.148


Mass: 86452.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11FIP3, ARFO1, KIAA0665 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75154
#2: 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
#3: 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
#4: 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
#5: 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
#6: 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
#14: Protein
Isoform 2C of Cytoplasmic dynein 1 intermediate chain 2 / Cytoplasmic dynein intermediate chain 2 / Dynein intermediate chain 2 / cytosolic / DH IC-2


Mass: 68514.203 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
#16: 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 MNPQVORSTWY

#7: Protein
Dynactin subunit 2


Mass: 44732.469 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A5G2QD80
#8: 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
#9: 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
#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

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Cytoplasmic dynein 1 ... , 2 types, 7 molecules efmnjqr

#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
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
#15: 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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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

ComponentName: dynein-dynactin-RAB11FIP3 / Type: COMPLEX
Entity ID: #1-#6, #8, #11, #16, #9, #7, #15, #13-#14, #10, #12
Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
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: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLO1.9particle selection
2PHENIX2.0_5936model refinement
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 10 Å / Resolution method: OTHER / Num. of particles: 159084 / Symmetry type: POINT
Atomic model buildingSource name: PDB / Type: experimental model
RefinementHighest resolution: 10 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00368715
ELECTRON MICROSCOPYf_angle_d0.43495650
ELECTRON MICROSCOPYf_dihedral_angle_d4.13913820
ELECTRON MICROSCOPYf_chiral_restr0.04113195
ELECTRON MICROSCOPYf_plane_restr0.00213820

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