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- PDB-3o6b: A Dual E3 Mechanism for Rub1 Ligation to Cdc53: Dcn1(P)-Cdc53(WHB... -

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Basic information

Entry
Database: PDB / ID: 3o6b
TitleA Dual E3 Mechanism for Rub1 Ligation to Cdc53: Dcn1(P)-Cdc53(WHB) low resolution
Components
  • Cell division control protein 53
  • Defective in cullin neddylation protein 1
KeywordsLigase / Cell Cycle
Function / homology
Function and homology information


Iron uptake and transport / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / ubiquitin-like protein binding / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Antigen processing: Ubiquitination & Proteasome degradation / regulation of metabolic process / positive regulation of glucose transmembrane transport / protein neddylation ...Iron uptake and transport / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / ubiquitin-like protein binding / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Antigen processing: Ubiquitination & Proteasome degradation / regulation of metabolic process / positive regulation of glucose transmembrane transport / protein neddylation / ubiquitin conjugating enzyme binding / mitotic intra-S DNA damage checkpoint signaling / silent mating-type cassette heterochromatin formation / mitochondrial fusion / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / DNA replication origin binding / cullin family protein binding / subtelomeric heterochromatin formation / ubiquitin ligase complex / regulation of mitotic cell cycle / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / chromosome, telomeric region / protein ubiquitination / cell division / ubiquitin protein ligase binding / nucleus / cytoplasm
Similarity search - Function
Cullin, PONY binding domain / Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like domain / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. ...Cullin, PONY binding domain / Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / UBA-like domain / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / UBA-like superfamily / EF-hand / Recoverin; domain 1 / 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
Cell division control protein 53 / Defective in cullin neddylation protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsScott, D.C. / Monda, J.K. / Grace, C.R.R. / Duda, D.M. / Kriwacki, R.W. / Kurz, T. / Schulman, B.A.
CitationJournal: Mol.Cell / Year: 2010
Title: A dual E3 mechanism for Rub1 ligation to Cdc53.
Authors: Scott, D.C. / Monda, J.K. / Grace, C.R. / Duda, D.M. / Kriwacki, R.W. / Kurz, T. / Schulman, B.A.
History
DepositionJul 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Defective in cullin neddylation protein 1
B: Cell division control protein 53
C: Defective in cullin neddylation protein 1
D: Cell division control protein 53
E: Defective in cullin neddylation protein 1
F: Cell division control protein 53
G: Defective in cullin neddylation protein 1
H: Cell division control protein 53
I: Defective in cullin neddylation protein 1
J: Cell division control protein 53


Theoretical massNumber of molelcules
Total (without water)165,03310
Polymers165,03310
Non-polymers00
Water0
1
A: Defective in cullin neddylation protein 1
B: Cell division control protein 53


Theoretical massNumber of molelcules
Total (without water)33,0072
Polymers33,0072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Defective in cullin neddylation protein 1
D: Cell division control protein 53


Theoretical massNumber of molelcules
Total (without water)33,0072
Polymers33,0072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Defective in cullin neddylation protein 1
F: Cell division control protein 53


Theoretical massNumber of molelcules
Total (without water)33,0072
Polymers33,0072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Defective in cullin neddylation protein 1
H: Cell division control protein 53


Theoretical massNumber of molelcules
Total (without water)33,0072
Polymers33,0072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Defective in cullin neddylation protein 1
J: Cell division control protein 53


Theoretical massNumber of molelcules
Total (without water)33,0072
Polymers33,0072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.914, 123.914, 192.558
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Defective in cullin neddylation protein 1


Mass: 24353.648 Da / Num. of mol.: 5 / Fragment: DCUN1 domain, residues 70-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DCN1, YLR128W, L3111 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12395
#2: Protein
Cell division control protein 53 / Cullin-A / E3 ubiquitin ligase complex SCF subunit CDC53


Mass: 8652.943 Da / Num. of mol.: 5 / Fragment: residues 742-815
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CDC53, YDL132W, D2190 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12018

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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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 21% PEG 3350, 0.1M Bis-Tris-Propane, 0.2M NaF, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. all: 30487 / Num. obs: 30204 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.1-3.21199.1
3.21-3.34199.6
3.34-3.49199.7
3.49-3.68199.7
3.68-3.91199.7
3.91-4.25199.5

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Processing

Software
NameVersionClassification
NecatID-C softwaredata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→40 Å / σ(F): 0 / Stereochemistry target values: energy minimization
RfactorNum. reflectionSelection details
Rfree0.3083 1529 Random
Rwork0.2578 --
all0.2578 30487 -
obs0.2578 30204 -
Refinement stepCycle: LAST / Resolution: 3.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10662 0 0 0 10662

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