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- PDB-5owo: Human cytoplasmic Dynein N-Terminus dimerization domain at 1.8 An... -

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Entry
Database: PDB / ID: 5owo
TitleHuman cytoplasmic Dynein N-Terminus dimerization domain at 1.8 Angstrom resolution
ComponentsCytoplasmic dynein 1 heavy chain 1
KeywordsMOTOR PROTEIN / Dynein / Heavy chain / Dimerization domain
Function / homology
Function and homology information


positive regulation of intracellular transport / regulation of metaphase plate congression / positive regulation of spindle assembly / establishment of spindle localization / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / retrograde axonal transport / P-body assembly / minus-end-directed microtubule motor activity / dynein light intermediate chain binding ...positive regulation of intracellular transport / regulation of metaphase plate congression / positive regulation of spindle assembly / establishment of spindle localization / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / retrograde axonal transport / P-body assembly / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / nuclear migration / dynein intermediate chain binding / COPI-mediated anterograde transport / cytoplasmic microtubule / cytoplasmic microtubule organization / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / axon cytoplasm / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Mitotic Prometaphase / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / EML4 and NUDC in mitotic spindle formation / stress granule assembly / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / regulation of mitotic spindle organization / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / mitotic spindle organization / filopodium / RHO GTPases Activate Formins / HCMV Early Events / Aggrephagy / azurophil granule lumen / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / positive regulation of cold-induced thermogenesis / cell cortex / microtubule / cell division / Neutrophil degranulation / centrosome / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / membrane / cytosol
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 / : / 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, 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 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.79 Å
AuthorsUrnavicius, L. / Lau, C.K. / Elshenawy, M.M. / Morales-Rios, E. / Motz, C. / Yildiz, A. / Carter, A.P.
Funding support United Kingdom, United States, 5items
OrganizationGrant numberCountry
Wellcome TrustWT100387 United Kingdom
Medical Research Council (United Kingdom)MC_UP_A025_1011 United Kingdom
National Institutes of HealthGM094522 United States
National Science Foundation (NSF, United States)MCB-1055017 United States
National Science Foundation (NSF, United States)MCB- 1617028 United States
CitationJournal: Nature / Year: 2018
Title: Cryo-EM shows how dynactin recruits two dyneins for faster movement.
Authors: Linas Urnavicius / Clinton K Lau / Mohamed M Elshenawy / Edgar Morales-Rios / Carina Motz / Ahmet Yildiz / Andrew P Carter /
Abstract: Dynein and its cofactor dynactin form a highly processive microtubule motor in the presence of an activating adaptor, such as BICD2. Different adaptors link dynein and dynactin to distinct cargoes. ...Dynein and its cofactor dynactin form a highly processive microtubule motor in the presence of an activating adaptor, such as BICD2. Different adaptors link dynein and dynactin to distinct cargoes. Here we use electron microscopy and single-molecule studies to show that adaptors can recruit a second dynein to dynactin. Whereas BICD2 is biased towards recruiting a single dynein, the adaptors BICDR1 and HOOK3 predominantly recruit two dyneins. We find that the shift towards a double dynein complex increases both the force and speed of the microtubule motor. Our 3.5 Å resolution cryo-electron microscopy reconstruction of a dynein tail-dynactin-BICDR1 complex reveals how dynactin can act as a scaffold to coordinate two dyneins side-by-side. Our work provides a structural basis for understanding how diverse adaptors recruit different numbers of dyneins and regulate the motile properties of the dynein-dynactin transport machine.
History
DepositionSep 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_wavelength_list / _diffrn_source.type
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytoplasmic dynein 1 heavy chain 1
B: Cytoplasmic dynein 1 heavy chain 1
C: Cytoplasmic dynein 1 heavy chain 1
D: Cytoplasmic dynein 1 heavy chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,19243
Polymers88,5894
Non-polymers1,60339
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17490 Å2
ΔGint-325 kcal/mol
Surface area27490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.242, 175.560, 50.444
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-312-

NA

21D-305-

CA

31D-306-

K

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 22147.223 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Selenomethionine labeled protein. / Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1H1, DHC1, DNCH1, DNCL, DNECL, DYHC, KIAA0325 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14204

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Non-polymers , 6 types, 313 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100mM Sodium acetate, pH 5.5, 10% Glycerol, 50mM Calcium acetate, 20% PEG 2,000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793, 0.9792
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 6, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97921
ReflectionResolution: 1.6→44.29 Å / Num. obs: 119216 / % possible obs: 98.5 % / Redundancy: 3.07 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 3.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 1.79→87.78 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.18 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22924 4245 5 %RANDOM
Rwork0.19647 ---
obs0.19811 81221 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.823 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2---0.85 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.79→87.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5022 0 84 274 5380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0195254
X-RAY DIFFRACTIONr_bond_other_d0.0020.025077
X-RAY DIFFRACTIONr_angle_refined_deg2.03527082
X-RAY DIFFRACTIONr_angle_other_deg1.068311819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1385640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.65725.221226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55815935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7941524
X-RAY DIFFRACTIONr_chiral_restr0.1260.2843
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02928
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1662.8012596
X-RAY DIFFRACTIONr_mcbond_other3.1612.7992595
X-RAY DIFFRACTIONr_mcangle_it4.7854.1463224
X-RAY DIFFRACTIONr_mcangle_other4.7864.1483225
X-RAY DIFFRACTIONr_scbond_it4.7523.4312658
X-RAY DIFFRACTIONr_scbond_other4.753.4312658
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2864.8593859
X-RAY DIFFRACTIONr_long_range_B_refined9.02534.2935640
X-RAY DIFFRACTIONr_long_range_B_other9.02534.35641
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 300 -
Rwork0.385 5866 -
obs--99.05 %

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