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- PDB-2kr4: U-box domain of the E3 Ubiquitin Ligase E4B -

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Basic information

Entry
Database: PDB / ID: 2kr4
TitleU-box domain of the E3 Ubiquitin Ligase E4B
ComponentsUbiquitin conjugation factor E4 B
KeywordsLIGASE / U-box / E4B / Ufd2 / RING / Ubiquitin / E3 Ligase / Ubl conjugation pathway
Function / homology
Function and homology information


granzyme-mediated apoptotic signaling pathway / protein catabolic process => GO:0030163 / ventricular trabecula myocardium morphogenesis / ubiquitin-ubiquitin ligase activity / protein monoubiquitination / protein autoubiquitination / ubiquitin ligase complex / : / response to UV / response to endoplasmic reticulum stress ...granzyme-mediated apoptotic signaling pathway / protein catabolic process => GO:0030163 / ventricular trabecula myocardium morphogenesis / ubiquitin-ubiquitin ligase activity / protein monoubiquitination / protein autoubiquitination / ubiquitin ligase complex / : / response to UV / response to endoplasmic reticulum stress / RING-type E3 ubiquitin transferase / protein polyubiquitination / neuron projection development / ubiquitin protein ligase activity / unfolded protein binding / protein folding / ATPase binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / enzyme binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
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
Ubiquitin conjugation factor E4 B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsclosest to the average, model 1
AuthorsNordquist, K. / Soss, S. / Chazin, W.
CitationJournal: Biochemistry / Year: 2010
Title: Structural and functional characterization of the monomeric U-box domain from E4B.
Authors: Nordquist, K.A. / Dimitrova, Y.N. / Brzovic, P.S. / Ridenour, W.B. / Munro, K.A. / Soss, S.E. / Caprioli, R.M. / Klevit, R.E. / Chazin, W.J.
History
DepositionDec 3, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin conjugation factor E4 B


Theoretical massNumber of molelcules
Total (without water)9,7791
Polymers9,7791
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Ubiquitin conjugation factor E4 B / Ubiquitin fusion degradation protein 2 / Ufd2a


Mass: 9778.996 Da / Num. of mol.: 1 / Fragment: U-Box Domain (UNP residues 1092-1173)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: 6xHIS-SUMO tag with H3C protease cleavage site / Gene: Ube4b, Ufd2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ES00

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D DQF-COSY
1422D 1H-1H NOESY
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D HN(CO)CA
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11213D (H)CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
1750 uM [U-100% 13C; U-100% 15N] U-box domain of E4B, 90% H2O/10% D2O90% H2O/10% D2O
21 mM U-box domain of E4B, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
750 uMU-box domain of E4B-1[U-100% 13C; U-100% 15N]1
1 mMU-box domain of E4B-22
Sample conditionsIonic strength: 25 / pH: 6.5 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2009.015.15.35Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddardpeak picking
CYANA2..1Guntert, Mumenthaler and Wuthrichstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: Computed through AMBER9 in water, Computed through AMBER9 in water. Single residues in some models have phi-psi angle combinations that are outside the norm. These are found only for ...Details: Computed through AMBER9 in water, Computed through AMBER9 in water. Single residues in some models have phi-psi angle combinations that are outside the norm. These are found only for residues that lack experimental constraints and which are therefore poorly defined in the structure.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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