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- PDB-9mfy: Motor domain-Pac1 complex with ADP AAA1 and Apo AAA3 from yeast f... -

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Basic information

Entry
Database: PDB / ID: 9mfy
TitleMotor domain-Pac1 complex with ADP AAA1 and Apo AAA3 from yeast full-length dynein-1 and Pac1 in 0.1 mM ATP condition
Components
  • Dynein heavy chain, cytoplasmic
  • Nuclear distribution protein PAC1
KeywordsMOTOR PROTEIN / dynein
Function / homology
Function and homology information


microtubule sliding / karyogamy / microtubule organizing center organization / nuclear migration along microtubule / astral microtubule / establishment of mitotic spindle localization / microtubule plus-end binding / spindle pole body / vesicle transport along microtubule / microtubule associated complex ...microtubule sliding / karyogamy / microtubule organizing center organization / nuclear migration along microtubule / astral microtubule / establishment of mitotic spindle localization / microtubule plus-end binding / spindle pole body / vesicle transport along microtubule / microtubule associated complex / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / nuclear migration / dynein intermediate chain binding / dynein complex binding / establishment of mitotic spindle orientation / Antigen processing: Ubiquitination & Proteasome degradation / mitotic sister chromatid segregation / cytoplasmic microtubule / cytoplasmic microtubule organization / Neutrophil degranulation / mitotic spindle organization / kinetochore / spindle pole / nuclear envelope / cell cortex / cell division / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Dynein regulator LIS1 / LIS1, N-terminal / : / DYN1, AAA+ ATPase lid 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 regulator LIS1 / LIS1, N-terminal / : / DYN1, AAA+ ATPase lid 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 / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / 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 / Dynein heavy chain, cytoplasmic / Nuclear distribution protein PAC1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsGeohring, I.C. / Chai, P. / Iyer, B.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM139483 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM142959 United States
CitationJournal: To Be Published
Title: A nucleotide code governs Lis1's ability to relieve dynein autoinhibition
Authors: Geohring, I.C. / Chai, P. / Iyer, B.R.
History
DepositionDec 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 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
B: Nuclear distribution protein PAC1
A: Dynein heavy chain, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)530,3037
Polymers528,8922
Non-polymers1,4105
Water00
1


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

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Components

#1: Protein Nuclear distribution protein PAC1 / Lissencephaly-1 homolog / LIS-1 / nudF homolog


Mass: 56973.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PAC1, LIS1, YOR269W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39946
#2: Protein Dynein heavy chain, cytoplasmic / Dynein heavy chain / cytosolic / DYHC


Mass: 471918.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DYN1, DHC1, YKR054C / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P36022
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: Motor domain-Pac1 complex with ADP AAA1 and Apo AAA3 from yeast full-length dynein-1 and Pac1 in 0.1 mM ATP condition
Type: COMPLEX / Details: class2, ADP AAA1, Apo AAA3, with Pac1 bound / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 1.2 MDa / Experimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2500 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 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)

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Processing

EM software
IDNameVersionCategory
2SerialEM4image acquisition
8PHENIXmodel refinement
13cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178195 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00424408
ELECTRON MICROSCOPYf_angle_d0.58733032
ELECTRON MICROSCOPYf_dihedral_angle_d5.1953182
ELECTRON MICROSCOPYf_chiral_restr0.0413734
ELECTRON MICROSCOPYf_plane_restr0.0044162

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