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- PDB-1ldd: Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex -

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Basic information

Entry
Database: PDB / ID: 1ldd
TitleStructure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex
ComponentsAnaphase Promoting Complex
KeywordsLIGASE / ubiquitin / ubiquitination / RING finger / winged-helix
Function / homology
Function and homology information


positive regulation of mitotic actomyosin contractile ring contraction / anaphase-promoting complex / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / metaphase/anaphase transition of mitotic cell cycle / exit from mitosis / protein K11-linked ubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / regulation of mitotic cell cycle / protein ubiquitination ...positive regulation of mitotic actomyosin contractile ring contraction / anaphase-promoting complex / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / metaphase/anaphase transition of mitotic cell cycle / exit from mitosis / protein K11-linked ubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / regulation of mitotic cell cycle / protein ubiquitination / ubiquitin protein ligase binding / cytoplasm
Similarity search - Function
Anaphase-promoting complex subunit 2, C-terminal / Anaphase-promoting complex subunit 2 / Anaphase promoting complex (APC) subunit 2 / Anaphase promoting complex (APC) subunit 2 / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin alpha solenoid domain / Cullin family profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...Anaphase-promoting complex subunit 2, C-terminal / Anaphase-promoting complex subunit 2 / Anaphase promoting complex (APC) subunit 2 / Anaphase promoting complex (APC) subunit 2 / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin alpha solenoid domain / Cullin family profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Anaphase-promoting complex subunit 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsZheng, N. / Schulman, B.A. / Song, L. / Miller, J.J. / Jeffrey, P.D. / Wang, P. / Chu, C. / Koepp, D.M. / Elledge, S.J. / Pagano, M. ...Zheng, N. / Schulman, B.A. / Song, L. / Miller, J.J. / Jeffrey, P.D. / Wang, P. / Chu, C. / Koepp, D.M. / Elledge, S.J. / Pagano, M. / Conaway, R.C. / Conaway, J.W. / Harper, J.W. / Pavletich, N.P.
CitationJournal: Nature / Year: 2002
Title: Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF ubiquitin ligase complex.
Authors: Zheng, N. / Schulman, B.A. / Song, L. / Miller, J.J. / Jeffrey, P.D. / Wang, P. / Chu, C. / Koepp, D.M. / Elledge, S.J. / Pagano, M. / Conaway, R.C. / Conaway, J.W. / Harper, J.W. / Pavletich, N.P.
History
DepositionApr 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anaphase Promoting Complex
B: Anaphase Promoting Complex
C: Anaphase Promoting Complex
D: Anaphase Promoting Complex


Theoretical massNumber of molelcules
Total (without water)34,2724
Polymers34,2724
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.7, 72.9, 79.8
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Anaphase Promoting Complex / Apc2WHB


Mass: 8567.958 Da / Num. of mol.: 4 / Fragment: RESIDUES 773-846
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pGEX4T3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12440

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4K, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
180 mg/mlprotein1drop
218.5 %PEG40001reservoir
30.16 M1reservoirKSCN
40.1 MTris1reservoirpH8.5

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9747 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9747 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 40867 / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 2 Å / % possible obs: 97.9 % / Num. measured all: 120747 / Rmerge(I) obs: 0.052

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Processing

Software
NameVersionClassification
SHELXSphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→30 Å / σ(F): 0 /
RfactorNum. reflection
Rfree0.266 -
Rwork0.205 -
obs-40867
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2972 0 0 0 2972
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor obs: 0.205 / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.205 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.4

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