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- PDB-4gba: DCNL complex with N-terminally acetylated NEDD8 E2 peptide -

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Basic information

Entry
Database: PDB / ID: 4gba
TitleDCNL complex with N-terminally acetylated NEDD8 E2 peptide
Components
  • DCN1-like protein 3
  • NEDD8-conjugating enzyme UBE2F
Keywordsligase/peptide / E3 ligase / ligase-peptide complex
Function / homology
Function and homology information


NEDD8 conjugating enzyme activity / ubiquitin-like protein binding / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / protein neddylation / ubiquitin conjugating enzyme binding / positive regulation of ubiquitin-protein transferase activity / NEDD8 ligase activity / response to UV-C / negative regulation of G1/S transition of mitotic cell cycle ...NEDD8 conjugating enzyme activity / ubiquitin-like protein binding / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / protein neddylation / ubiquitin conjugating enzyme binding / positive regulation of ubiquitin-protein transferase activity / NEDD8 ligase activity / response to UV-C / negative regulation of G1/S transition of mitotic cell cycle / cullin family protein binding / ubiquitin ligase complex / post-translational protein modification / response to gamma radiation / negative regulation of cell growth / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / positive regulation of apoptotic process / perinuclear region of cytoplasm / ATP binding / nucleus / plasma membrane / cytosol
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. / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 ...Cullin, PONY binding domain / Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / EF-hand / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DCN1-like protein 3 / NEDD8-conjugating enzyme UBE2F
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMonda, J.K. / Scott, D.C. / Miller, D.J. / Harper, J.W. / Bennett, E.J. / Schulman, B.A.
CitationJournal: Structure / Year: 2013
Title: Structural Conservation of Distinctive N-terminal Acetylation-Dependent Interactions across a Family of Mammalian NEDD8 Ligation Enzymes.
Authors: Monda, J.K. / Scott, D.C. / Miller, D.J. / Lydeard, J. / King, D. / Harper, J.W. / Bennett, E.J. / Schulman, B.A.
History
DepositionJul 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Jan 30, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DCN1-like protein 3
B: DCN1-like protein 3
F: NEDD8-conjugating enzyme UBE2F
G: NEDD8-conjugating enzyme UBE2F


Theoretical massNumber of molelcules
Total (without water)56,6524
Polymers56,6524
Non-polymers00
Water2,378132
1
A: DCN1-like protein 3
F: NEDD8-conjugating enzyme UBE2F


Theoretical massNumber of molelcules
Total (without water)28,3262
Polymers28,3262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-15 kcal/mol
Surface area10530 Å2
MethodPISA
2
B: DCN1-like protein 3
G: NEDD8-conjugating enzyme UBE2F


Theoretical massNumber of molelcules
Total (without water)28,3262
Polymers28,3262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-17 kcal/mol
Surface area11180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.465, 44.578, 101.216
Angle α, β, γ (deg.)90.00, 103.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DCN1-like protein 3 / DCUN1 domain-containing protein 3 / Defective in cullin neddylation protein 1-like protein 3


Mass: 25671.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCUN1D3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IWE4
#2: Protein/peptide NEDD8-conjugating enzyme UBE2F / NEDD8 carrier protein UBE2F / NEDD8 protein ligase UBE2F / NEDD8-conjugating enzyme 2 / Ubiquitin- ...NEDD8 carrier protein UBE2F / NEDD8 protein ligase UBE2F / NEDD8-conjugating enzyme 2 / Ubiquitin-conjugating enzyme E2 F


Mass: 2654.029 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q969M7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 3.23 Å3/Da / Density % sol: 61.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: crystals in 2.28M sodium malonate, seeded into 2.05M sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 14, 2011
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→29.1 Å / Num. all: 28832 / Num. obs: 28812 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.4-2.49197.9
2.49-2.59198.8
2.59-2.7199.9
2.7-2.851100
2.85-3.021100
3.02-3.261100
3.26-3.581100
3.58-4.11100
4.1-5.161100
5.16-301100

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.085 Å / SU ML: 0.54 / σ(F): 1.34 / Phase error: 23.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2273 1466 5.09 %random
Rwork0.1939 ---
obs0.1956 28812 99.44 %-
all-28832 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.838 Å2 / ksol: 0.403 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.1497 Å2-0 Å2-9.9209 Å2
2---10.8347 Å20 Å2
3----0.8215 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3403 0 0 132 3535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083481
X-RAY DIFFRACTIONf_angle_d1.0324701
X-RAY DIFFRACTIONf_dihedral_angle_d15.2851263
X-RAY DIFFRACTIONf_chiral_restr0.069499
X-RAY DIFFRACTIONf_plane_restr0.004613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.48280.311460.26742608X-RAY DIFFRACTION96
2.4828-2.58220.31131330.25532703X-RAY DIFFRACTION99
2.5822-2.69960.29441330.2362737X-RAY DIFFRACTION100
2.6996-2.84180.27081580.21362703X-RAY DIFFRACTION100
2.8418-3.01970.28691450.20782717X-RAY DIFFRACTION100
3.0197-3.25260.22321620.18912722X-RAY DIFFRACTION100
3.2526-3.57940.21691440.1872744X-RAY DIFFRACTION100
3.5794-4.09610.20211530.16712771X-RAY DIFFRACTION100
4.0961-5.1560.18121310.15932780X-RAY DIFFRACTION100
5.156-29.08710.20941610.20472861X-RAY DIFFRACTION100

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