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- PDB-2qj0: Structure of the yeast U-box-containing ubiquitin ligase Ufd2p -

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Basic information

Entry
Database: PDB / ID: 2qj0
TitleStructure of the yeast U-box-containing ubiquitin ligase Ufd2p
ComponentsUbiquitin conjugation factor E4
KeywordsLIGASE / helical hairpin
Function / homology
Function and homology information


Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-ubiquitin ligase activity / protein K48-linked ubiquitination / ubiquitin ligase complex / : / positive regulation of protein ubiquitination / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-dependent protein catabolic process / protein ubiquitination ...Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-ubiquitin ligase activity / protein K48-linked ubiquitination / ubiquitin ligase complex / : / positive regulation of protein ubiquitination / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-dependent protein catabolic process / protein ubiquitination / nucleus / cytoplasm
Similarity search - Function
Ubiquitin conjugation factor E4 / Ubiquitin conjugation factor E4, core / Ubiquitin elongating factor core / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING/FYVE/PHD-type ...Ubiquitin conjugation factor E4 / Ubiquitin conjugation factor E4, core / Ubiquitin elongating factor core / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E4 ubiquitin-protein ligase UFD2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.65 Å
AuthorsTu, D. / Brunger, A.T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Inaugural Article: Structure and function of the yeast U-box-containing ubiquitin ligase Ufd2p.
Authors: Tu, D. / Li, W. / Ye, Y. / Brunger, A.T.
History
DepositionJul 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin conjugation factor E4


Theoretical massNumber of molelcules
Total (without water)113,2141
Polymers113,2141
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.795, 122.798, 178.856
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin conjugation factor E4 / Ubiquitin fusion degradation protein 2 / UB fusion protein 2


Mass: 113213.789 Da / Num. of mol.: 1 / Mutation: S102L, D677V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UFD2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P54860
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 3.19 Å3/Da / Density % sol: 61.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 20% PEG 3350, 0.3M tri-ammonium citrate (pH 7.2), 0.1M sodium chloride, 10mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.211
SYNCHROTRONSSRL BL11-120.97920, 0.97895, 0.91837
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 19, 2006
ADSC QUANTUM 3152CCDJul 9, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal, Si(111)SINGLE WAVELENGTHMx-ray1
2flat mirror (vertical focusing), single crystal Si(111) bent monochromator (horizontal focusing)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97921
30.978951
40.918371
ReflectionResolution: 2.74→50 Å / Num. all: 37483 / Num. obs: 37483 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.056 / Net I/σ(I): 19
Reflection shellResolution: 2.74→2.84 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 2834 / Rsym value: 0.398 / % possible all: 74.2

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.65→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The native data was really collected to 2.65 A. But in order to have a cutoff of I/sigma >= 2.0, the authors chose to report only to 2.74 A in the paper. However during refinement, all data were used.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 3396 -random
Rwork0.234 ---
obs0.237 34316 87.4 %-
all-39248 --
Displacement parametersBiso mean: 77.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7567 0 0 94 7661
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 2.65→2.74 Å
RfactorNum. reflection% reflection
Rfree0.422 146 -
Rwork0.341 --
obs-1372 32.4 %

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