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- PDB-4ht6: The Structure of a Yeast Dynein Dyn2-Pac11 Complex and Effect on ... -

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Basic information

Entry
Database: PDB / ID: 4ht6
TitleThe Structure of a Yeast Dynein Dyn2-Pac11 Complex and Effect on Single Molecule Dynein Motor Activity
Components
  • Dynein light chain 1, cytoplasmic
  • WD repeat-containing protein PAC11
KeywordsMOTOR PROTEIN / Dimerization / Dynein / Intermediate Chain / Light Chain / Dynein Intermediate Chain Dynein Heavy Chain
Function / homology
Function and homology information


: / peroxisomal importomer complex / dynein light chain binding / dynein heavy chain binding / establishment of mitotic spindle localization / nuclear migration along microtubule / nuclear pore complex assembly / cytoplasmic dynein complex / nucleocytoplasmic transport / dynein intermediate chain binding ...: / peroxisomal importomer complex / dynein light chain binding / dynein heavy chain binding / establishment of mitotic spindle localization / nuclear migration along microtubule / nuclear pore complex assembly / cytoplasmic dynein complex / nucleocytoplasmic transport / dynein intermediate chain binding / microtubule-based movement / establishment of mitotic spindle orientation / mRNA transport / cytoplasmic microtubule / nuclear pore / Neutrophil degranulation / nuclear periphery / protein transport / nuclear envelope / protein-containing complex binding / cytoplasm
Similarity search - Function
Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Dynein light chain type 1 / Dynein light chain, type 1/2 / Dynein light chain superfamily / Dynein light chain type 1 / : / WD40 repeat, conserved site ...Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Dynein light chain type 1 / Dynein light chain, type 1/2 / Dynein light chain superfamily / Dynein light chain type 1 / : / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
WD repeat-containing protein PAC11 / Dynein light chain 1, cytoplasmic
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSlep, K.C. / Romes, E.R.
CitationJournal: Mol Biol Cell / Year: 2013
Title: The yeast dynein Dyn2-Pac11 complex is a dynein dimerization/processivity factor: structural and single-molecule characterization.
Authors: Rao, L. / Romes, E.M. / Nicholas, M.P. / Brenner, S. / Tripathy, A. / Gennerich, A. / Slep, K.C.
History
DepositionOct 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / 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: Dynein light chain 1, cytoplasmic
B: WD repeat-containing protein PAC11
C: Dynein light chain 1, cytoplasmic
D: WD repeat-containing protein PAC11
E: Dynein light chain 1, cytoplasmic
F: WD repeat-containing protein PAC11


Theoretical massNumber of molelcules
Total (without water)36,4526
Polymers36,4526
Non-polymers00
Water4,936274
1
A: Dynein light chain 1, cytoplasmic
B: WD repeat-containing protein PAC11


Theoretical massNumber of molelcules
Total (without water)12,1512
Polymers12,1512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-6 kcal/mol
Surface area5490 Å2
MethodPISA
2
C: Dynein light chain 1, cytoplasmic
D: WD repeat-containing protein PAC11


Theoretical massNumber of molelcules
Total (without water)12,1512
Polymers12,1512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-5 kcal/mol
Surface area5500 Å2
MethodPISA
3
E: Dynein light chain 1, cytoplasmic
F: WD repeat-containing protein PAC11


Theoretical massNumber of molelcules
Total (without water)12,1512
Polymers12,1512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-5 kcal/mol
Surface area5570 Å2
MethodPISA
4
E: Dynein light chain 1, cytoplasmic
F: WD repeat-containing protein PAC11

E: Dynein light chain 1, cytoplasmic
F: WD repeat-containing protein PAC11


Theoretical massNumber of molelcules
Total (without water)24,3024
Polymers24,3024
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Buried area5210 Å2
ΔGint-20 kcal/mol
Surface area8700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.506, 112.747, 56.369
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-125-

HOH

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Components

#1: Protein Dynein light chain 1, cytoplasmic


Mass: 10868.436 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: DYN2, SLC1, YDR424C / Plasmid: pGEX-6P2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 (pLysS) / References: UniProt: Q02647
#2: Protein/peptide WD repeat-containing protein PAC11


Mass: 1282.377 Da / Num. of mol.: 3 / Fragment: residues 75-85 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40960
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.4M sodium phosphate monobasic, 0.1M 1,6-hexanediol, 25% PEG 3350 (w/v), pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9792 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 13, 2012
RadiationMonochromator: APS ID22 Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 25879 / Num. obs: 25589 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rsym value: 0.087 / Net I/σ(I): 15.5
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.9-1.97188.8
1.97-2.05198.9
2.05-2.14199.8
2.14-2.25199.8
2.25-2.39199.7
2.39-2.58199.7
2.58-2.84199.7
2.84-3.25199.8
3.25-4.09199.6
4.09-50199.4

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4DS1

4ds1


Resolution: 1.9→37.717 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 18.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 2000 7.79 %Random
Rwork0.1596 ---
all0.1698 25965 --
obs0.1698 25575 98.5 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.561 Å2 / ksol: 0.406 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9111 Å20 Å20 Å2
2--0.7736 Å2-0 Å2
3---0.1375 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2343 0 0 274 2617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072391
X-RAY DIFFRACTIONf_angle_d1.0353231
X-RAY DIFFRACTIONf_dihedral_angle_d12.118864
X-RAY DIFFRACTIONf_chiral_restr0.078369
X-RAY DIFFRACTIONf_plane_restr0.004399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8987-1.94620.26971070.19871297X-RAY DIFFRACTION77
1.9462-1.99880.23081250.17921512X-RAY DIFFRACTION89
1.9988-2.05760.24141320.1621532X-RAY DIFFRACTION92
2.0576-2.1240.19781310.15611589X-RAY DIFFRACTION95
2.124-2.19990.17991400.1421622X-RAY DIFFRACTION96
2.1999-2.2880.19751380.1461639X-RAY DIFFRACTION97
2.288-2.39210.22251420.15211647X-RAY DIFFRACTION98
2.3921-2.51820.26991410.16481658X-RAY DIFFRACTION98
2.5182-2.67590.25111400.17821675X-RAY DIFFRACTION98
2.6759-2.88250.24291400.1611663X-RAY DIFFRACTION98
2.8825-3.17240.22751470.15861721X-RAY DIFFRACTION99
3.1724-3.63120.18221450.14681714X-RAY DIFFRACTION99
3.6312-4.57360.17621460.14081725X-RAY DIFFRACTION100
4.5736-37.72490.2061540.18311814X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 18.7782 Å / Origin y: 128.8921 Å / Origin z: 56.7859 Å
111213212223313233
T0.0816 Å2-0.0099 Å20.0136 Å2-0.0389 Å20.0046 Å2--0.0356 Å2
L1.2275 °2-0.2065 °20.4311 °2-0.3108 °2-0.1003 °2--0.4666 °2
S-0.0094 Å °-0.1244 Å °-0.009 Å °0.0504 Å °0.0128 Å °0.0131 Å °-0.0355 Å °-0.0212 Å °-0.0079 Å °
Refinement TLS groupSelection details: all

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