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- PDB-3qmz: Crystal structure of the cytoplasmic dynein heavy chain motor domain -

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Basic information

Entry
Database: PDB / ID: 3qmz
TitleCrystal structure of the cytoplasmic dynein heavy chain motor domain
Components
  • Cytoplasmic dynein heavy chain
  • Glutathione-S-transferase
KeywordsMOTOR PROTEIN / AAA+ protein / ASCE protein / P-loop NTPase / Cytoskeletal motor / ATPase
Function / homology
Function and homology information


karyogamy / establishment of mitotic spindle localization / nuclear migration along microtubule / astral microtubule / spindle pole body / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / dynein intermediate chain binding / nuclear migration ...karyogamy / establishment of mitotic spindle localization / nuclear migration along microtubule / astral microtubule / spindle pole body / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / dynein intermediate chain binding / nuclear migration / establishment of mitotic spindle orientation / glutathione transferase / mitotic sister chromatid segregation / glutathione transferase activity / cytoplasmic microtubule / cytoplasmic microtubule organization / Neutrophil degranulation / glutathione metabolic process / mitotic spindle organization / cell cortex / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
AAA+ lid domain / : / DYN1, AAA+ ATPase lid domain / : / Dynein heavy chain, ATPase lid domain / Glutathione S-transferase, C-terminal domain / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain region D6 P-loop domain ...AAA+ lid domain / : / DYN1, AAA+ ATPase lid domain / : / Dynein heavy chain, ATPase lid domain / Glutathione S-transferase, C-terminal domain / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / 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 / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Glutathione S-transferase class-mu 26 kDa isozyme / Dynein heavy chain, cytoplasmic
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Schistosoma japonicum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 6 Å
AuthorsCho, C. / Carter, A.P. / Jin, L. / Vale, R.D.
CitationJournal: Science / Year: 2011
Title: Crystal structure of the dynein motor domain.
Authors: Carter, A.P. / Cho, C. / Jin, L. / Vale, R.D.
History
DepositionFeb 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 29, 2012Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytoplasmic dynein heavy chain
B: Cytoplasmic dynein heavy chain
T: Glutathione-S-transferase
S: Glutathione-S-transferase


Theoretical massNumber of molelcules
Total (without water)622,5814
Polymers622,5814
Non-polymers00
Water00
1
A: Cytoplasmic dynein heavy chain
T: Glutathione-S-transferase


Theoretical massNumber of molelcules
Total (without water)311,2902
Polymers311,2902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytoplasmic dynein heavy chain
S: Glutathione-S-transferase


Theoretical massNumber of molelcules
Total (without water)311,2902
Polymers311,2902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.080, 118.921, 200.509
Angle α, β, γ (deg.)90.00, 90.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytoplasmic dynein heavy chain


Mass: 285684.625 Da / Num. of mol.: 2 / Fragment: unp residues 1364-4092
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P36022
#2: Protein Glutathione-S-transferase


Mass: 25605.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P08515

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 16% PEG3350, 0.1 M sodium citrate, 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 5.7

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 / Wavelength: 1.21476 1.15776
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 25, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.214761
31.157761
ReflectionResolution: 6→50.13 Å / Num. obs: 20819

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Processing

Software
NameClassification
HKL-2000data collection
PHENIXmodel building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 6→50 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.43 -Random
Rwork0.43 --
all-20819 -
obs-20819 -
Refinement stepCycle: LAST / Resolution: 6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23302 0 0 0 23302

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