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- PDB-3wuq: Structure of the entire stalk region of the dynein motor domain -

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Basic information

Entry
Database: PDB / ID: 3wuq
TitleStructure of the entire stalk region of the dynein motor domain
ComponentsCytoplasmic dynein 1 heavy chain 1
KeywordsMOTOR PROTEIN / Microtubule
Function / homology
Function and homology information


COPI-independent Golgi-to-ER retrograde traffic / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / cilium movement / Aggrephagy / positive regulation of intracellular transport / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion ...COPI-independent Golgi-to-ER retrograde traffic / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / cilium movement / Aggrephagy / positive regulation of intracellular transport / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / regulation of metaphase plate congression / establishment of spindle localization / RHO GTPases Activate Formins / positive regulation of spindle assembly / Separation of Sister Chromatids / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / manchette / Regulation of PLK1 Activity at G2/M Transition / P-body assembly / dynein complex / MHC class II antigen presentation / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / retrograde axonal transport / dynein light intermediate chain binding / nuclear migration / dynein intermediate chain binding / cytoplasmic microtubule / stress granule assembly / cytoplasmic microtubule organization / regulation of mitotic spindle organization / axon cytoplasm / Neutrophil degranulation / mitotic spindle organization / filopodium / nuclear envelope / positive regulation of cold-induced thermogenesis / cell cortex / microtubule / cell division / axon / centrosome / neuronal cell body / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
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 / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain / Dynein heavy chain region D6 P-loop 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 / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain / 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, 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Cytoplasmic dynein 1 heavy chain 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å
AuthorsNishikawa, Y. / Oyama, T. / Kamiya, N. / Kon, T. / Toyoshima, Y.Y. / Nakamura, H. / Kurisu, G.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structure of the entire stalk region of the Dynein motor domain
Authors: Nishikawa, Y. / Oyama, T. / Kamiya, N. / Kon, T. / Toyoshima, Y.Y. / Nakamura, H. / Kurisu, G.
History
DepositionMay 1, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytoplasmic dynein 1 heavy chain 1


Theoretical massNumber of molelcules
Total (without water)32,4281
Polymers32,4281
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.939, 102.939, 69.069
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Cytoplasmic dynein 1 heavy chain 1 / Cytoplasmic dynein heavy chain 1 / Dynein heavy chain / cytosolic


Mass: 32428.154 Da / Num. of mol.: 1 / Fragment: STALK DOMAIN, UNP residues 3207-3483
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dync1h1, Dhc1, Dnch1, Dnchc1, Dyhc / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JHU4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 20% PEG3350, 0.2M ammonium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 5560 / Num. obs: 5560 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.078 / Net I/σ(I): 29.2
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 3.3 / Num. unique all: 276 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.Autosol)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.5→44.574 Å / SU ML: 0.57 / σ(F): 1.33 / Phase error: 37.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3049 547 9.89 %RANDOM
Rwork0.2788 ---
obs0.2801 5530 99.6 %-
all-5530 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→44.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 0 0 0 1962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061983
X-RAY DIFFRACTIONf_angle_d1.1212680
X-RAY DIFFRACTIONf_dihedral_angle_d15.954743
X-RAY DIFFRACTIONf_chiral_restr0.082316
X-RAY DIFFRACTIONf_plane_restr0.005353
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.5-3.8520.39151350.3538121299
3.852-4.4090.35951380.29351229100
4.409-5.55320.35621350.30311241100
5.5532-44.57750.23931390.2373130199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.88114.3015-1.07945.4072-1.96061.37021.1373-0.1772-0.21110.8738-0.01360.3213-1.399-0.1781.53350.7567-0.29240.17370.429-0.2920.515762.915675.537720.7976
21.9212-3.06582.41745.2618-3.80293.06150.9894-1.001-1.45640.23580.43070.18031.35090.3596-0.53951.01640.01930.40341.2504-0.00681.525520.440718.815814.8165
35.21734.00520.30557.5117-1.00351.9028-0.6720.75860.6208-1.65420.88290.9693-0.274-0.14110.08841.2283-0.32960.07660.88670.01420.855416.388534.891214.976
43.56084.2203-0.69945.6815-0.00140.72770.5294-0.56060.24320.32-0.28990.2675-0.20250.0601-0.07640.7-0.04260.07590.46620.09880.434550.159161.895719.6939
50.0385-0.0402-0.16970.03890.16730.7139-0.18750.62360.239-0.52480.09060.0861-0.05990.38830.01334.8412-0.08262.67015.82860.1164.1682104.569107.352922.495
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3209 through 3296 )
2X-RAY DIFFRACTION2chain 'A' and (resid 3297 through 3306 )
3X-RAY DIFFRACTION3chain 'A' and (resid 3307 through 3376 )
4X-RAY DIFFRACTION4chain 'A' and (resid 3377 through 3464 )
5X-RAY DIFFRACTION5chain 'A' and (resid 3465 through 3471 )

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