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- PDB-4ds1: The Structure of a Yeast Dyn2-Nup159 Complex and the Molecular Ba... -

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Basic information

Entry
Database: PDB / ID: 4ds1
TitleThe Structure of a Yeast Dyn2-Nup159 Complex and the Molecular Basis for the Dynein Light Chain - Nuclear Pore Interaction
Components
  • Dynein light chain 1, cytoplasmic
  • Nucleoporin NUP159
KeywordsSTRUCTURAL PROTEIN/TRANSPORT PROTEIN / nucleoporin / Dynein Light Chain fold / Peptide Binding / Nuclear Pore / STRUCTURAL PROTEIN-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


: / peroxisomal importomer complex / adenyl-nucleotide exchange factor activity / nuclear pore localization / nuclear pore central transport channel / establishment of mitotic spindle localization / nuclear migration along microtubule / nuclear pore complex assembly / nuclear pore cytoplasmic filaments / cytoplasmic dynein complex ...: / peroxisomal importomer complex / adenyl-nucleotide exchange factor activity / nuclear pore localization / nuclear pore central transport channel / establishment of mitotic spindle localization / nuclear migration along microtubule / nuclear pore complex assembly / nuclear pore cytoplasmic filaments / cytoplasmic dynein complex / structural constituent of nuclear pore / poly(A)+ mRNA export from nucleus / nucleocytoplasmic transport / NLS-bearing protein import into nucleus / dynein intermediate chain binding / establishment of mitotic spindle orientation / ribosomal small subunit export from nucleus / ribosomal large subunit export from nucleus / mRNA transport / cytoplasmic microtubule / nuclear pore / Neutrophil degranulation / protein export from nucleus / nuclear periphery / transcription corepressor activity / protein transport / nuclear envelope / nuclear membrane / molecular adaptor activity / protein-containing complex binding / nucleus / cytoplasm
Similarity search - Function
Nucleoporin Nup159/Nup146, N-terminal / Nucleoporin or Nuclear pore complex subunit NUP214=Nup159 / 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 ...Nucleoporin Nup159/Nup146, N-terminal / Nucleoporin or Nuclear pore complex subunit NUP214=Nup159 / 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/YVTN repeat-like-containing domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoporin NUP159 / Dynein light chain 1, cytoplasmic
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.851 Å
AuthorsSlep, K.C. / Romes, E.M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure of a yeast Dyn2-Nup159 complex and molecular basis for dynein light chain-nuclear pore interaction.
Authors: Romes, E.M. / Tripathy, A. / Slep, K.C.
History
DepositionFeb 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Jul 25, 2012Group: Database references
Revision 1.3Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Dynein light chain 1, cytoplasmic
B: Nucleoporin NUP159
C: Dynein light chain 1, cytoplasmic
D: Nucleoporin NUP159


Theoretical massNumber of molelcules
Total (without water)24,1574
Polymers24,1574
Non-polymers00
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-21 kcal/mol
Surface area8380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.869, 47.971, 110.703
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 light chain 1, cytoplasmic


Mass: 10868.436 Da / Num. of mol.: 2
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 Nucleoporin NUP159 / Nuclear pore protein NUP159


Mass: 1210.249 Da / Num. of mol.: 2 / Fragment: UNP residues 1116-1126 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40477
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 1.86 Å3/Da / Density % sol: 33.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.3 M Ammonium acetate, 5% methyl pentanediol (v/v), 35% PEG 4000 (w/v), pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 25, 2010 / Details: Osmic Mirrors
RadiationMonochromator: copper Kalpha / Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→29.2 Å / Num. obs: 15081 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 15.71 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 24.8
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 5.9 / Rsym value: 0.15 / % possible all: 62.7

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Processing

Software
NameVersionClassification
HKL-2000data 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 2PG1 lacking bound peptide

2pg1


Resolution: 1.851→29.249 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 16.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1869 1490 9.99 %Random 10%
Rwork0.1514 ---
all0.1548 16062 --
obs0.1548 14920 92.89 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.9 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.641 Å20 Å2-0 Å2
2--3.4708 Å20 Å2
3----2.8298 Å2
Refinement stepCycle: LAST / Resolution: 1.851→29.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1541 0 0 217 1758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061573
X-RAY DIFFRACTIONf_angle_d1.022127
X-RAY DIFFRACTIONf_dihedral_angle_d12.475563
X-RAY DIFFRACTIONf_chiral_restr0.071243
X-RAY DIFFRACTIONf_plane_restr0.003263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8505-1.91660.2472940.1801847X-RAY DIFFRACTION60
1.9166-1.99340.18931230.1441109X-RAY DIFFRACTION78
1.9934-2.08410.17791480.1451316X-RAY DIFFRACTION93
2.0841-2.19390.18241570.14111408X-RAY DIFFRACTION99
2.1939-2.33130.19631540.14371407X-RAY DIFFRACTION99
2.3313-2.51120.2071590.1511437X-RAY DIFFRACTION100
2.5112-2.76380.21931580.16381428X-RAY DIFFRACTION100
2.7638-3.16330.18581600.15891447X-RAY DIFFRACTION100
3.1633-3.98380.15891630.14851471X-RAY DIFFRACTION100
3.9838-29.25220.18341740.14971560X-RAY DIFFRACTION100

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