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- PDB-5afr: N-terminal fragment of dynein heavy chain -

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Basic information

Entry
Database: PDB / ID: 5afr
TitleN-terminal fragment of dynein heavy chain
ComponentsDYNEIN HEAVY CHAIN, CYTOPLASMIC
KeywordsMOTOR PROTEIN / DYNEIN / TAIL / HEAVY CHAIN
Function / homology
Function and homology information


karyogamy / astral microtubule / establishment of mitotic spindle localization / nuclear migration along 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 / astral microtubule / establishment of mitotic spindle localization / nuclear migration along 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 / mitotic sister chromatid segregation / cytoplasmic microtubule / cytoplasmic microtubule organization / Neutrophil degranulation / mitotic spindle organization / cell cortex / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
: / DYN1, AAA+ ATPase lid domain / : / Dynein heavy chain, ATPase lid 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 ...: / DYN1, AAA+ ATPase lid domain / : / Dynein heavy chain, ATPase lid 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Dynein heavy chain, cytoplasmic
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 5 Å
AuthorsUrnavicius, L. / Zhang, K. / Diamant, A.G. / Motz, C. / Schlager, M.A. / Yu, M. / Patel, N.A. / Robinson, C.V. / Carter, A.P.
CitationJournal: Science / Year: 2015
Title: The structure of the dynactin complex and its interaction with dynein.
Authors: Linas Urnavicius / Kai Zhang / Aristides G Diamant / Carina Motz / Max A Schlager / Minmin Yu / Nisha A Patel / Carol V Robinson / Andrew P Carter /
Abstract: Dynactin is an essential cofactor for the microtubule motor cytoplasmic dynein-1. We report the structure of the 23-subunit dynactin complex by cryo-electron microscopy to 4.0 angstroms. Our ...Dynactin is an essential cofactor for the microtubule motor cytoplasmic dynein-1. We report the structure of the 23-subunit dynactin complex by cryo-electron microscopy to 4.0 angstroms. Our reconstruction reveals how dynactin is built around a filament containing eight copies of the actin-related protein Arp1 and one of β-actin. The filament is capped at each end by distinct protein complexes, and its length is defined by elongated peptides that emerge from the α-helical shoulder domain. A further 8.2 angstrom structure of the complex between dynein, dynactin, and the motility-inducing cargo adaptor Bicaudal-D2 shows how the translational symmetry of the dynein tail matches that of the dynactin filament. The Bicaudal-D2 coiled coil runs between dynein and dynactin to stabilize the mutually dependent interactions between all three components.
History
DepositionJan 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Apr 25, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DYNEIN HEAVY CHAIN, CYTOPLASMIC
B: DYNEIN HEAVY CHAIN, CYTOPLASMIC


Theoretical massNumber of molelcules
Total (without water)128,7582
Polymers128,7582
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-17.9 kcal/mol
Surface area42080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.899, 148.861, 179.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ALAALAAA9 - 4109 - 410
2ARGARGBB7 - 4107 - 410

NCS oper: (Code: given
Matrix: (-0.597, -0.091, 0.797), (-0.113, -0.974, -0.196), (0.795, -0.207, 0.571)
Vector: 27.104, 125.06, 2.275)

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Components

#1: Protein DYNEIN HEAVY CHAIN, CYTOPLASMIC / DYN1 / DYNEIN HEAVY CHAIN\ / CYTOSOLIC / DYHC


Mass: 64379.160 Da / Num. of mol.: 2
Fragment: N-TERMINAL FRAGMENT OF TAIL DOMAIN, RESIDUES 1-557
Source method: isolated from a genetically manipulated source
Details: POLYALANINE MODEL WITH SELENOMETHIONINES
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P36022
Has protein modificationY

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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: 3.76 Å3/Da / Density % sol: 67.26 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Type: DIAMOND / Wavelength: 0.9763
DetectorDate: May 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 5→52.6 Å / Num. obs: 8866 / % possible obs: 100 % / Observed criterion σ(I): 10 / Redundancy: 11.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.8

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Processing

SoftwareName: REFMAC / Version: 5.8.0103 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 5→114.62 Å / Cor.coef. Fo:Fc: 0.805 / Cor.coef. Fo:Fc free: 0.832 / SU B: 156.924 / SU ML: 1.848 / Cross valid method: THROUGHOUT / ESU R Free: 1.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.43658 413 4.7 %RANDOM
Rwork0.39275 ---
obs0.39488 8387 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 202.593 Å2
Baniso -1Baniso -2Baniso -3
1-13.42 Å20 Å20 Å2
2---4.65 Å20 Å2
3----8.77 Å2
Refinement stepCycle: LAST / Resolution: 5→114.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 0 0 0 3318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193318
X-RAY DIFFRACTIONr_bond_other_d0.0060.023354
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.8584598
X-RAY DIFFRACTIONr_angle_other_deg1.25537370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3765640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0620.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024480
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02640
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_it17.51120.1072626
X-RAY DIFFRACTIONr_mcbond_other17.48620.12625
X-RAY DIFFRACTIONr_mcangle_it30.85830.0513244
X-RAY DIFFRACTIONr_mcangle_other30.85930.0623245
X-RAY DIFFRACTIONr_scbond_it11.23620.513692
X-RAY DIFFRACTIONr_scbond_other11.22820.55693
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other23.05930.4441355
X-RAY DIFFRACTIONr_long_range_B_refined62.82714223
X-RAY DIFFRACTIONr_long_range_B_other62.82514224
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17128 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 5→5.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 29 -
Rwork0.396 620 -
obs--99.54 %

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