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- PDB-2p63: Suprafacial orientation of the SCFCdc4 dimer accommodates multipl... -

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Basic information

Entry
Database: PDB / ID: 2p63
TitleSuprafacial orientation of the SCFCdc4 dimer accommodates multiple geometries for substrate ubiquitination
ComponentsCell division control protein 4
KeywordsCELL CYCLE / ubiquitination / helix bundle / scf complex
Function / homology
Function and homology information


nuclear SCF ubiquitin ligase complex / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / U3 snoRNA binding / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / sporulation resulting in formation of a cellular spore / phosphoserine residue binding / 90S preribosome / meiotic cell cycle ...nuclear SCF ubiquitin ligase complex / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / U3 snoRNA binding / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / sporulation resulting in formation of a cellular spore / phosphoserine residue binding / 90S preribosome / meiotic cell cycle / ubiquitin binding / nuclear matrix / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / ubiquitin-dependent protein catabolic process / protein ubiquitination / cell division / nucleolus / nucleus
Similarity search - Function
Cdc4 dimerisation domain-like / Cell division control protein 4, dimerisation domain / Cell division control protein 4 dimerisation domain / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / F-box domain / Helix non-globular ...Cdc4 dimerisation domain-like / Cell division control protein 4, dimerisation domain / Cell division control protein 4 dimerisation domain / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / F-box domain / Helix non-globular / Special / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Cell division control protein 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.67 Å
AuthorsOrlicky, S. / Neculai, D. / Ceccarelli, D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Suprafacial orientation of the SCFCdc4 dimer accommodates multiple geometries for substrate ubiquitination.
Authors: Tang, X. / Orlicky, S. / Lin, Z. / Willems, A. / Neculai, D. / Ceccarelli, D. / Mercurio, F. / Shilton, B.H. / Sicheri, F. / Tyers, M.
History
DepositionMar 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division control protein 4
B: Cell division control protein 4
C: Cell division control protein 4
D: Cell division control protein 4


Theoretical massNumber of molelcules
Total (without water)25,7204
Polymers25,7204
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: Cell division control protein 4
D: Cell division control protein 4


Theoretical massNumber of molelcules
Total (without water)12,8602
Polymers12,8602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-25 kcal/mol
Surface area7310 Å2
MethodPISA
3
A: Cell division control protein 4
B: Cell division control protein 4


Theoretical massNumber of molelcules
Total (without water)12,8602
Polymers12,8602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-24 kcal/mol
Surface area7300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.816, 37.816, 298.118
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Beg label comp-ID: SER / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 227 - 271 / Label seq-ID: 10 - 54

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CC
12BB
22DD

NCS ensembles :
ID
1
2

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Components

#1: Protein
Cell division control protein 4 / F-box protein CDC4 / E3 ubiquitin ligase complex SCF subunit CDC4


Mass: 6429.942 Da / Num. of mol.: 4 / Fragment: D Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CDC4 / Plasmid: PGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07834
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 50%MPD, 100 mM (NH4)H2PO4 ph 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9788 Å
DetectorType: SBC / Detector: CCD / Date: Jun 29, 2005
Details: Rosenbaum-Rock double-crystal monochromator: Water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.67→49.69 Å / Num. all: 6882 / Num. obs: 6756 / % possible obs: 99.3 % / Observed criterion σ(F): 8.4 / Observed criterion σ(I): 8.4 / Redundancy: 9.81 % / Rmerge(I) obs: 0.0702 / Rsym value: 0.0349 / Net I/σ(I): 21.15
Reflection shellResolution: 2.67→2.73 Å / Redundancy: 6.95 % / Rmerge(I) obs: 0.1712 / Mean I/σ(I) obs: 8.47 / Num. unique all: 383 / Rsym value: 0.1228 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
EPICS-basedbeamline controldata collection
dataacquisition systemsdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.67→49.69 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.871 / SU B: 25.966 / SU ML: 0.316 / Cross valid method: THROUGHOUT / σ(F): 8.47 / σ(I): 8.47 / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27851 472 7 %RANDOM
Rwork0.21974 ---
all0.22396 6284 --
obs0.22396 6284 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.025 Å2
Baniso -1Baniso -2Baniso -3
1-3.17 Å21.59 Å20 Å2
2--3.17 Å20 Å2
3----4.76 Å2
Refinement stepCycle: LAST / Resolution: 2.67→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1678 0 0 37 1715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221751
X-RAY DIFFRACTIONr_angle_refined_deg1.271.9732364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0455211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3824.51693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.59515315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9171512
X-RAY DIFFRACTIONr_chiral_restr0.0930.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021334
X-RAY DIFFRACTIONr_nbd_refined0.2210.2769
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21205
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.279
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.28
X-RAY DIFFRACTIONr_mcbond_it0.7751.51081
X-RAY DIFFRACTIONr_mcangle_it1.3221698
X-RAY DIFFRACTIONr_scbond_it1.2643733
X-RAY DIFFRACTIONr_scangle_it2.0444.5665
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A360tight positional0.020.05
2B377tight positional0.010.05
1A360tight thermal0.030.5
2B377tight thermal0.030.5
LS refinement shellResolution: 2.67→2.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 31 -
Rwork0.273 473 -
obs--98.63 %
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)
11.5798-2.65281.65785.3017-1.49273.70640.2998-0.0420.0395-0.2766-0.1512-0.12170.10040.0563-0.14860.23150.04010.08390.0249-0.040.168210.79721.970613.6394
20.6088-1.81571.487512.1532-2.14558.5283-0.1521-0.1531-0.06070.22970.6962-0.2269-0.16920.0891-0.54410.06850.11790.05870.0866-0.08790.1089.74080.736112.1976
32.06963.2161-1.465.0032-2.14373.86390.3210.0278-0.04610.237-0.1054-0.1133-0.10970.0523-0.21560.2212-0.0323-0.06350.0446-0.05540.174511.02-2.3219-13.7254
40.46781.4884-1.743913.2058-2.33678.8648-0.15690.23390.0695-0.12810.8252-0.25370.2360.012-0.66840.0772-0.0883-0.09030.0754-0.10560.13319.403-1.0331-11.7959
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA228 - 27211 - 55
2X-RAY DIFFRACTION2BB228 - 27211 - 55
3X-RAY DIFFRACTION3CC228 - 27311 - 56
4X-RAY DIFFRACTION4DD228 - 27311 - 56

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