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- PDB-2mbe: Backbone 1H and 15N Chemical Shift Assignments for the first doma... -

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Basic information

Entry
Database: PDB / ID: 2mbe
TitleBackbone 1H and 15N Chemical Shift Assignments for the first domain of FAT10
ComponentsUbiquitin D
KeywordsPROTEIN BINDING / FAT10
Function / homology
Function and homology information


protein modification by small protein conjugation / myeloid dendritic cell differentiation / aggresome assembly / aggresome / regulation of mitotic cell cycle phase transition / proteasome binding / response to type II interferon / response to tumor necrosis factor / fibrillar center / Neddylation ...protein modification by small protein conjugation / myeloid dendritic cell differentiation / aggresome assembly / aggresome / regulation of mitotic cell cycle phase transition / proteasome binding / response to type II interferon / response to tumor necrosis factor / fibrillar center / Neddylation / ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination / positive regulation of apoptotic process / proteolysis / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin D / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, torsion angle dynamics, molecular dynamics
Model detailslowest energy, model1
AuthorsWang, W. / Lim, L. / Qin, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Disruption of FAT10-MAD2 binding inhibits tumor progression.
Authors: Theng, S.S. / Wang, W. / Mah, W.C. / Chan, C. / Zhuo, J. / Gao, Y. / Qin, H. / Lim, L. / Chong, S.S. / Song, J. / Lee, C.G.
History
DepositionJul 30, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin D


Theoretical massNumber of molelcules
Total (without water)8,6761
Polymers8,6761
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin D / Diubiquitin / Ubiquitin-like protein FAT10


Mass: 8676.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBD, FAT10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O15205

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N TOCSY
1313D 1H-15N NOESY

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Sample preparation

DetailsContents: 0.01 mM sodium phosphate-1, 0.01 mM DTT-2, 0.4 mM [U-100% 15N] entity-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.01 mMsodium phosphate-11
0.01 mMDTT-21
0.4 mMentity-3[U-100% 15N]1
Sample conditionsIonic strength: 0 / pH: 7.4 / Pressure: ambient / Temperature: 298.15 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
TopSpinGuntert, Mumenthaler and Wuthrichcollection
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: distance geometry, torsion angle dynamics, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 8 / Representative conformer: 1

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