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- PDB-5ayh: Structure of the entire dynein stalk region -

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Basic information

Entry
Database: PDB / ID: 5ayh
TitleStructure of the entire dynein stalk region
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 / regulation of metaphase plate congression ...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 / regulation of metaphase plate congression / Resolution of Sister Chromatid Cohesion / establishment of spindle localization / positive regulation of spindle assembly / RHO GTPases Activate Formins / 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 / Regulation of PLK1 Activity at G2/M Transition / manchette / 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 / cytoplasmic microtubule organization / stress granule assembly / regulation of mitotic spindle organization / axon cytoplasm / Neutrophil degranulation / mitotic spindle organization / filopodium / nuclear envelope / positive regulation of cold-induced thermogenesis / cell cortex / microtubule / axon / cell division / 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 / MOLECULAR REPLACEMENT / Resolution: 3.011 Å
AuthorsKurisu, G. / Nishikawa, Y. / Inatomi, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS26291014 Japan
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structural Change in the Dynein Stalk Region Associated with Two Different Affinities for the Microtubule
Authors: Nishikawa, Y. / Inatomi, M. / Iwasaki, H. / Kurisu, G.
History
DepositionAug 21, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)31,7161
Polymers31,7161
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15670 Å2
Unit cell
Length a, b, c (Å)103.325, 103.325, 69.709
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: 31716.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dync1h1, Dhc1, Dnch1, Dnchc1, Dyhc / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JHU4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.82 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. all: 14221 / Num. obs: 14221 / % possible obs: 96.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 36.3
Reflection shellResolution: 3→3.05 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.704 / Mean I/σ(I) obs: 3.6 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WUQ

3wuq


Resolution: 3.011→23.38 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 2.5 / Phase error: 32.52 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2951 1412 9.93 %
Rwork0.2549 --
obs0.259 14221 86.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.011→23.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 0 0 1924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021944
X-RAY DIFFRACTIONf_angle_d0.5922625
X-RAY DIFFRACTIONf_dihedral_angle_d12.186735
X-RAY DIFFRACTIONf_chiral_restr0.023306
X-RAY DIFFRACTIONf_plane_restr0.002345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0113-3.11870.3678970.3466939X-RAY DIFFRACTION62
3.1187-3.24330.3781330.34961110X-RAY DIFFRACTION76
3.2433-3.39040.38191260.32041229X-RAY DIFFRACTION84
3.3904-3.56860.33861330.33511348X-RAY DIFFRACTION88
3.5686-3.79130.26971440.28341340X-RAY DIFFRACTION91
3.7913-4.08260.291650.26631322X-RAY DIFFRACTION91
4.0826-4.49090.3071560.23151420X-RAY DIFFRACTION96
4.4909-5.13470.29771680.23511407X-RAY DIFFRACTION95
5.1347-6.44660.3811540.2811414X-RAY DIFFRACTION95
6.4466-23.3810.20931360.18781280X-RAY DIFFRACTION86
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)
11.0811-0.89771.24541.9932-0.69921.52240.08241.5120.7479-0.66660.449-1.12740.46591.51930.33560.10640.1180.15452.5618-0.63151.93182.396363.612572.382
28.6913-5.2166-3.08063.44141.74966.39330.2628-2.07430.56410.23430.64380.1443-1.14320.5218-0.68770.7173-0.06530.13210.6993-0.05840.5903141.745377.758782.7482
39.91741.5418-0.01912.55510.733.496-0.30811.0371-0.6124-0.55690.0878-0.31310.41460.07170.30240.5853-0.01330.15450.7283-0.05780.790289.559187.313773.1052
43.1065-0.2454-2.57870.76420.9672.6253-0.7061-0.94731.47540.19150.53490.21340.26410.01450.11320.67780.19640.07781.01070.00920.85499.08491.152380.8969
54.1709-2.50521.71467.01550.06756.18361.00770.6634-0.4557-0.457-0.0123-0.0292-0.21360.9364-0.45340.31-0.10440.0260.5924-0.12930.346150.668669.474875.0761
61.16691.7508-0.71812.654-1.07540.4424-0.8798-1.4486-1.2741-0.0581-0.9174-0.69671.47581.58290.0231.47381.220.13073.5986-0.09681.1885187.631951.502479.9325
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3219 through 3237 )
2X-RAY DIFFRACTION2chain 'A' and (resid 3238 through 3277 )
3X-RAY DIFFRACTION3chain 'A' and (resid 3278 through 3357 )
4X-RAY DIFFRACTION4chain 'A' and (resid 3358 through 3417 )
5X-RAY DIFFRACTION5chain 'A' and (resid 3418 through 3453 )
6X-RAY DIFFRACTION6chain 'A' and (resid 3454 through 3472 )

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