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- PDB-2pg1: Structural analysis of a cytoplasmic dynein Light Chain-Intermedi... -

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Basic information

Entry
Database: PDB / ID: 2pg1
TitleStructural analysis of a cytoplasmic dynein Light Chain-Intermediate Chain complex
Components
  • Cytoplasmic dynein 1 intermediate chain 2
  • Dynein light chain 1, cytoplasmic
  • Dynein light chain Tctex-type
KeywordsSTRUCTURAL PROTEIN / Dynein intermediate chain / dynein light chain / LC8 / PIN / TcTex1
Function / homology
Function and homology information


Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / COPI-independent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Aggrephagy / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome ...Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / COPI-independent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Aggrephagy / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / spermatid nucleus elongation / Regulation of PLK1 Activity at G2/M Transition / chaeta morphogenesis / Separation of Sister Chromatids / Macroautophagy / Aggrephagy / positive regulation of neuron remodeling / wing disc development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / outer dynein arm / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / chaeta development / sperm individualization / imaginal disc-derived wing morphogenesis / COPI-mediated anterograde transport / transposable element silencing by piRNA-mediated heterochromatin formation / transport along microtubule / RNA polymerase II transcription repressor complex / microtubule anchoring at centrosome / dynein light chain binding / MHC class II antigen presentation / dynein heavy chain binding / Neutrophil degranulation / dynein complex / retrograde axonal transport / cytoplasmic dynein complex / dynein light intermediate chain binding / oogenesis / microtubule-based movement / dynein intermediate chain binding / establishment of mitotic spindle orientation / actin filament bundle assembly / spermatid development / axon cytoplasm / centriole / determination of adult lifespan / cellular response to nerve growth factor stimulus / disordered domain specific binding / transcription corepressor activity / mitotic cell cycle / negative regulation of neuron projection development / spermatogenesis / vesicle / microtubule / centrosome / protein-containing complex binding / protein homodimerization activity / protein-containing complex / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Tctex-1 / Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. ...Tctex-1 / Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / : / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / Ribosomal protein S3 C-terminal domain / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Dynein light chain 1, cytoplasmic / Cytoplasmic dynein 1 intermediate chain 2 / Dynein light chain Tctex-type
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsWilliams, J.C. / Hendrickson, W.A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural and thermodynamic characterization of a cytoplasmic dynein light chain-intermediate chain complex
Authors: Williams, J.C. / Roulhac, P.L. / Roy, A.G. / Vallee, R.B. / Fitzgerald, M.C. / Hendrickson, W.A.
History
DepositionApr 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: Dynein light chain 1, cytoplasmic
B: Dynein light chain 1, cytoplasmic
C: Dynein light chain 1, cytoplasmic
D: Dynein light chain 1, cytoplasmic
E: Dynein light chain Tctex-type
F: Dynein light chain Tctex-type
G: Dynein light chain Tctex-type
H: Dynein light chain Tctex-type
I: Cytoplasmic dynein 1 intermediate chain 2
J: Cytoplasmic dynein 1 intermediate chain 2
K: Cytoplasmic dynein 1 intermediate chain 2
L: Cytoplasmic dynein 1 intermediate chain 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,25717
Polymers107,77712
Non-polymers4805
Water43224
1
A: Dynein light chain 1, cytoplasmic
B: Dynein light chain 1, cytoplasmic
F: Dynein light chain Tctex-type
G: Dynein light chain Tctex-type
I: Cytoplasmic dynein 1 intermediate chain 2
L: Cytoplasmic dynein 1 intermediate chain 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9847
Polymers53,8886
Non-polymers961
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12760 Å2
ΔGint-78 kcal/mol
Surface area19560 Å2
MethodPISA
2
C: Dynein light chain 1, cytoplasmic
D: Dynein light chain 1, cytoplasmic
E: Dynein light chain Tctex-type
H: Dynein light chain Tctex-type
J: Cytoplasmic dynein 1 intermediate chain 2
K: Cytoplasmic dynein 1 intermediate chain 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,27310
Polymers53,8886
Non-polymers3844
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13070 Å2
ΔGint-106 kcal/mol
Surface area20120 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28030 Å2
ΔGint-198 kcal/mol
Surface area37470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.969, 119.870, 211.702
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Dynein light chain 1, cytoplasmic / 8 kDa dynein light chain / Cut up protein


Mass: 10635.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: ctp, Cdlc1, ddlc1 / Plasmid: pET21D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q24117
#2: Protein
Dynein light chain Tctex-type / TCTEX-1 protein homolog


Mass: 12631.708 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dlc90F, Tctex / Plasmid: pET24D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q94524
#3: Protein/peptide
Cytoplasmic dynein 1 intermediate chain 2 / Dynein intermediate chain 2 / cytosolic / DH IC-2 / Cytoplasmic dynein intermediate chain 2


Mass: 3677.293 Da / Num. of mol.: 4
Fragment: LC binding site, sequence database residues 132-164
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dync1i2, Dnci2, Dncic2 / Plasmid: pET28-SMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q62871
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
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: 3.44 Å3/Da / Density % sol: 64.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.8 M - 2.2 M Ammonium Sulfate, 0 - 20 % glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 14, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 13.9 / Number: 411870 / Rmerge(I) obs: 0.085 / Χ2: 1.27 / D res high: 2.8 Å / D res low: 30 Å / Num. obs: 36881 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
6.023098.810.0621.497
4.786.0210010.0651.446
4.184.7810010.0621.497
3.84.1810010.0731.406
3.533.810010.0861.342
3.323.5310010.1041.328
3.153.3210010.1411.182
3.023.1510010.1931.081
2.93.0210010.2710.978
2.82.910010.3620.94
ReflectionResolution: 2.8→30 Å / Num. obs: 36881 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.085 / Rsym value: 0.071 / Net I/σ(I): 31
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 6.7 / Rsym value: 0.362 / % possible all: 100

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.4410.50.0830.441
2Se47.5610.0190.1030.1820.382
3Se54.4650.9950.2070.180.395
4Se44.5920.9580.2880.1950.348
5Se600.7520.0440.0560.398
6Se42.6310.9430.1950.1830.21
7Se600.8520.0080.0650.395
8Se57.4440.950.170.1920.312
9Se34.5150.0030.190.1930.29
10Se600.8590.0670.0660.451

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Processing

Software
NameVersionClassificationNB
SOLVE2.03phasing
RESOLVEphasing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→19.98 Å / FOM work R set: 0.831 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.253 1815 4.9 %
Rwork0.208 --
obs-36416 98.4 %
Solvent computationBsol: 21.882 Å2
Displacement parametersBiso mean: 46.024 Å2
Baniso -1Baniso -2Baniso -3
1--8.829 Å20 Å20 Å2
2---2.817 Å20 Å2
3---11.646 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6902 0 25 24 6951
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 36

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.8-2.830.35560.319780836
2.83-2.850.416470.3129541001
2.85-2.880.35510.299591010
2.88-2.910.35560.296925981
2.91-2.940.348540.271925979
2.94-2.980.304590.28936995
2.98-3.010.352470.2719561003
3.01-3.040.35530.2489491002
3.04-3.080.265530.2569631016
3.08-3.120.273530.255935988
3.12-3.160.304440.244955999
3.16-3.210.304390.249761015
3.21-3.250.31470.2449731020
3.25-3.30.298480.229938986
3.3-3.350.292480.2279801028
3.35-3.410.269530.212939992
3.41-3.460.241400.1979821022
3.46-3.530.249500.2099661016
3.53-3.60.235490.2029621011
3.6-3.670.319510.219851036
3.67-3.750.205470.1749591006
3.75-3.840.227480.2089791027
3.84-3.930.285510.2199651016
3.93-4.040.297470.2059751022
4.04-4.160.22600.189661026
4.16-4.290.204450.1779731018
4.29-4.440.191450.179841029
4.44-4.620.211570.1629831040
4.62-4.830.231570.1679631020
4.83-5.090.21430.159881031
5.09-5.410.247470.1819911038
5.41-5.820.182620.2189761038
5.82-6.410.293470.23710061053
6.41-7.340.293640.2349851049
7.34-9.250.181430.16610261069
9.25-500.010.183540.189944998
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2sul_xplor.par
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5mse_xplor.par

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