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- PDB-3o2p: A Dual E3 Mechanism for Rub1 Ligation to Cdc53: Dcn1(P)-Cdc53(WHB) -

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Basic information

Entry
Database: PDB / ID: 3o2p
TitleA Dual E3 Mechanism for Rub1 Ligation to Cdc53: Dcn1(P)-Cdc53(WHB)
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 / positive regulation of D-glucose transmembrane transport / protein neddylation / regulation of metabolic process / ubiquitin conjugating enzyme binding / mitochondrial fusion ...Iron uptake and transport / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / ubiquitin-like protein binding / positive regulation of D-glucose transmembrane transport / protein neddylation / regulation of metabolic process / ubiquitin conjugating enzyme binding / mitochondrial fusion / mitotic intra-S DNA damage checkpoint signaling / silent mating-type cassette heterochromatin formation / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / DNA replication origin binding / cullin family protein binding / Antigen processing: Ubiquitination & Proteasome degradation / 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, 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 repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / 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: 2.233 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 22, 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 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Defective in cullin neddylation protein 1
E: Cell division control protein 53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8005
Polymers34,5232
Non-polymers2763
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Defective in cullin neddylation protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5383
Polymers24,3541
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: Cell division control protein 53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2622
Polymers10,1701
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.157, 57.157, 177.725
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.: 1 / 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: 10169.643 Da / Num. of mol.: 1 / Fragment: residues 730-815
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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 27% PEG 3000, 0.1M Tris, 0.2M Lithium Sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. all: 15991 / Num. obs: 15730 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BQ3

3bq3


Resolution: 2.233→33.065 Å / SU ML: 0.27 / σ(F): 0.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 1572 9.99 %Random
Rwork0.1687 ---
all0.1745 15991 --
obs0.1745 15730 98.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.759 Å2 / ksol: 0.381 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5429 Å20 Å2-0 Å2
2--2.5429 Å20 Å2
3----5.0858 Å2
Refinement stepCycle: LAST / Resolution: 2.233→33.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2384 0 18 137 2539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072453
X-RAY DIFFRACTIONf_angle_d0.9533310
X-RAY DIFFRACTIONf_dihedral_angle_d16.685905
X-RAY DIFFRACTIONf_chiral_restr0.068357
X-RAY DIFFRACTIONf_plane_restr0.004421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.233-2.31330.23011530.16871392X-RAY DIFFRACTION97
2.3133-2.40590.29791550.17651388X-RAY DIFFRACTION98
2.4059-2.51530.24821540.18271396X-RAY DIFFRACTION97
2.5153-2.64790.28581540.17731408X-RAY DIFFRACTION99
2.6479-2.81370.26891610.1821417X-RAY DIFFRACTION99
2.8137-3.03080.23571670.18141433X-RAY DIFFRACTION100
3.0308-3.33550.22711550.16311430X-RAY DIFFRACTION100
3.3355-3.81760.19171580.15411432X-RAY DIFFRACTION100
3.8176-4.80740.19761570.13571426X-RAY DIFFRACTION100
4.8074-33.06830.18611580.17171436X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5515-0.0776-0.31980.2285-0.04810.29430.031-0.0476-0.04510.02480.0475-0.0010.0706-0.05120.00130.08090.00570.03880.09340.02710.079323.7192-24.168113.878
20.4267-0.0058-0.32280.7312-0.58520.82390.0295-0.0003-0.04460.0540.03030.0079-0.0909-0.06980.00050.05840.01350.0070.08270.00460.079726.8735-3.435-8.4776
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'E'E0
2X-RAY DIFFRACTION2chain 'A'A0

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