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- PDB-3tdi: yeast Cul1WHB-Dcn1P acetylated Ubc12N complex -

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Basic information

Entry
Database: PDB / ID: 3tdi
Titleyeast Cul1WHB-Dcn1P acetylated Ubc12N complex
Components
  • Defective in cullin neddylation protein 1
  • NEDD8-conjugating enzyme UBC12
KeywordsLigase/protein binding / E2:E3 / Ligase-protein binding complex
Function / homology
Function and homology information


E2 NEDD8-conjugating enzyme / NEDD8 conjugating enzyme activity / ubiquitin-like protein binding / NEDD8 transferase activity / protein neddylation / ubiquitin conjugating enzyme binding / Neddylation / cullin family protein binding / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin ligase complex ...E2 NEDD8-conjugating enzyme / NEDD8 conjugating enzyme activity / ubiquitin-like protein binding / NEDD8 transferase activity / protein neddylation / ubiquitin conjugating enzyme binding / Neddylation / cullin family protein binding / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin ligase complex / protein-macromolecule adaptor activity / ATP binding / nucleus
Similarity search - Function
Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / : / UBA-like domain / : / UBA-like superfamily / Ubiquitin-conjugating enzyme, active site ...Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / : / UBA-like domain / : / UBA-like superfamily / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / EF-hand / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NEDD8-conjugating enzyme UBC12 / Defective in cullin neddylation protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsScott, D.C. / Monda, J.K. / Bennett, E.J. / Harper, J.W. / Schulman, B.A.
CitationJournal: Science / Year: 2011
Title: N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex.
Authors: Scott, D.C. / Monda, J.K. / Bennett, E.J. / Harper, J.W. / Schulman, B.A.
History
DepositionAug 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Defective in cullin neddylation protein 1
A: Defective in cullin neddylation protein 1
C: NEDD8-conjugating enzyme UBC12
D: NEDD8-conjugating enzyme UBC12


Theoretical massNumber of molelcules
Total (without water)54,5124
Polymers54,5124
Non-polymers00
Water2,468137
1
B: Defective in cullin neddylation protein 1
A: Defective in cullin neddylation protein 1
D: NEDD8-conjugating enzyme UBC12


Theoretical massNumber of molelcules
Total (without water)51,6103
Polymers51,6103
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-10 kcal/mol
Surface area11360 Å2
MethodPISA
2
B: Defective in cullin neddylation protein 1
A: Defective in cullin neddylation protein 1
C: NEDD8-conjugating enzyme UBC12


Theoretical massNumber of molelcules
Total (without water)51,6103
Polymers51,6103
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-8 kcal/mol
Surface area11260 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-28 kcal/mol
Surface area20770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.906, 98.421, 143.923
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Defective in cullin neddylation protein 1


Mass: 24353.648 Da / Num. of mol.: 2 / Fragment: unp residues 70-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: DCN1, YLR128W, L3111 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / References: UniProt: Q12395
#2: Protein/peptide NEDD8-conjugating enzyme UBC12 / RUB1-conjugating enzyme / RUB1-protein ligase / Ubiquitin carrier protein 12


Mass: 2902.372 Da / Num. of mol.: 2 / Fragment: unp residues 2-24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: L2142.3, UBC12, YLR306W / Plasmid: pGEX / Production host: Escherichia coli (E. coli)
References: UniProt: P52491, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: 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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 20% PEG3350, 0.1M Bis-Tris Propane, 0.2M Na/K tartrate, 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-E / Wavelength: 0.91917 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2010
RadiationMonochromator: Cryogenically-cooled single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91917 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 21323 / % possible obs: 96.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2.8 / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 13.5
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.3-2.380.372.60.37165.8
2.38-2.48176.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CCP4model building
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→37 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.891 / SU B: 12.819 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26614 1092 5.2 %RANDOM
Rwork0.20271 ---
obs0.20583 19970 90.05 %-
all-23736 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.054 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å2-0 Å20 Å2
2---0.34 Å20 Å2
3---2.13 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3639 0 0 137 3776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223747
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0281.975061
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9325427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46724.899198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57415687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5061516
X-RAY DIFFRACTIONr_chiral_restr0.0720.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212837
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6861.52148
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40723488
X-RAY DIFFRACTIONr_scbond_it3.76931597
X-RAY DIFFRACTIONr_scangle_it5.6984.51570
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 61 -
Rwork0.248 1050 -
obs--64.78 %
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)
12.4536-0.26070.33160.4238-0.15830.11890.0128-0.00360.03080.037-0.00590.0418-0.0554-0.0115-0.00690.06170.0235-0.00150.0625-0.02230.1147-9.1179-10.86-17.0884
21.83790.0152-0.17210.2420.06530.05880.00390.0335-0.0504-0.0004-0.019-0.01750.0129-0.00070.01510.05270.00960.00490.0597-0.00780.1175-14.0691-36.8944-12.0903
312.2389-7.6566-2.989911.831116.535233.43710.2860.2629-0.59180.3389-0.49430.06511.0416-1.18990.20830.0593-0.0354-0.01620.0972-0.12150.2543-9.7624-49.4532-20.4596
44.7133-5.12695.39535.6832-5.88546.17960.11960.51410.4204-0.1742-0.5945-0.36520.11530.59490.47490.11690.0590.0520.1660.06750.2892-7.8031-0.6717-23.2059
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A68 - 150
2X-RAY DIFFRACTION1A151 - 228
3X-RAY DIFFRACTION2B69 - 153
4X-RAY DIFFRACTION2B154 - 248
5X-RAY DIFFRACTION3C1 - 13
6X-RAY DIFFRACTION4D1 - 11

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