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- PDB-3vkg: X-ray structure of an MTBD truncation mutant of dynein motor domain -

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Basic information

Entry
Database: PDB / ID: 3vkg
TitleX-ray structure of an MTBD truncation mutant of dynein motor domain
ComponentsDynein heavy chain, cytoplasmic
KeywordsMOTOR PROTEIN / AAA+ protein / molecular motor / microtubles
Function / homology
Function and homology information


minus-end-directed vesicle transport along microtubule / early phagosome membrane / COPI-mediated anterograde transport / phagolysosome membrane / CTPase activity / Neutrophil degranulation / phagosome maturation / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding ...minus-end-directed vesicle transport along microtubule / early phagosome membrane / COPI-mediated anterograde transport / phagolysosome membrane / CTPase activity / Neutrophil degranulation / phagosome maturation / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / nuclear migration / microtubule motor activity / dynein intermediate chain binding / ATPase complex / endocytic vesicle / mitotic spindle assembly / cytoplasmic microtubule / cytoplasmic microtubule organization / tubulin binding / mitotic spindle organization / cell cortex / microtubule binding / microtubule / centrosome / ATP hydrolysis activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Helix Hairpins - #2610 / Helicase, Ruva Protein; domain 3 - #1220 / Dynein motor C sequence, barrel region / Helix Hairpins - #1060 / Dynein motor, AAA2 domain, small subdomain / Dynein motor, AAA1 domain, small subdomain / Region D6 of dynein motor / Dynein motor heavy chain, linker domain, N-terminal subdomain / Dynein motor heavy chain, linker domain, subdomain 4 / Histone Acetyltransferase; Chain A - #20 ...Helix Hairpins - #2610 / Helicase, Ruva Protein; domain 3 - #1220 / Dynein motor C sequence, barrel region / Helix Hairpins - #1060 / Dynein motor, AAA2 domain, small subdomain / Dynein motor, AAA1 domain, small subdomain / Region D6 of dynein motor / Dynein motor heavy chain, linker domain, N-terminal subdomain / Dynein motor heavy chain, linker domain, subdomain 4 / Histone Acetyltransferase; Chain A - #20 / Histone Acetyltransferase; Chain A - #30 / Dynein motor heavy chain, linker domain, subdomain 3 / Split barrel-like / Hypothetical upf0131 protein ytfp / Dynein heavy chain, AAA 5 extension domain / Dynein heavy chain AAA lid domain / Dynein heavy chain 3, AAA+ lid domain / 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 / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Cyclin A; domain 1 / Helix Hairpins / Helicase, Ruva Protein; domain 3 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix non-globular / Histone Acetyltransferase; Chain A / Special / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / Alpha-Beta Barrel / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / SPERMINE / Dynein heavy chain, cytoplasmic
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.81 Å
AuthorsKon, T. / Oyama, T. / Shimo-Kon, R. / Suto, K. / Kurisu, G.
CitationJournal: Nature / Year: 2012
Title: The 2.8 A crystal structure of the dynein motor domain
Authors: Kon, T. / Oyama, T. / Shimo-Kon, R. / Imamula, K. / Shima, T. / Sutoh, K. / Kurisu, G.
History
DepositionNov 16, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references / Structure summary
Revision 1.2Jun 7, 2017Group: Source and taxonomy
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.value / _struct_conn.pdbx_dist_value / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynein heavy chain, cytoplasmic
B: Dynein heavy chain, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)745,15317
Polymers740,8532
Non-polymers4,30015
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Dynein heavy chain, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)372,5648
Polymers370,4271
Non-polymers2,1387
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Dynein heavy chain, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)372,5899
Polymers370,4271
Non-polymers2,1628
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)204.256, 221.806, 192.898
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dynein heavy chain, cytoplasmic / Dynein heavy chain / cytosolic / DYHC


Mass: 370426.656 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1388-3371, 3496-4730
Source method: isolated from a genetically manipulated source
Details: The fusion protein of residues 1388-3371, artificial linker (TG), and residues 3496-4730
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: DDB_G0276355, dhcA, slime mold / Plasmid: PHSG3MB38HFG380 / Production host: Dictyostelium discoideum (eukaryote) / Strain (production host): slime mold / References: UniProt: P34036
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H26N4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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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: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 3.0-6.0% PEG 8000, 10MM SPERMINE-HCL, 3MM ADP, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-225 / Date: Apr 25, 2011 / Details: mirror
RadiationMonochromator: SI 111 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→150 Å / Num. obs: 209488 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 17.6

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.81→96.45 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 4330412.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.319 10425 5 %RANDOM
Rwork0.262 ---
obs0.262 209311 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.2067 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 52.8 Å2
Baniso -1Baniso -2Baniso -3
1-7.73 Å20 Å20 Å2
2---3.74 Å20 Å2
3----4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.81→96.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44967 0 275 42 45284
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it11.5
X-RAY DIFFRACTIONc_mcangle_it1.712
X-RAY DIFFRACTIONc_scbond_it1.42
X-RAY DIFFRACTIONc_scangle_it2.142.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.427 1542 5.1 %
Rwork0.37 28490 -
obs--84.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6ADP_paramADP_top
X-RAY DIFFRACTION7spm_xplor_paramspm_xplor_top

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