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- PDB-1wx9: Solution Structure of the N-terminal Ubiquitin-like Domain in the... -

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Entry
Database: PDB / ID: 1wx9
TitleSolution Structure of the N-terminal Ubiquitin-like Domain in the Human BAT3 Protein
ComponentsHLA-B associated transcript-3 isoform b
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ubiquitin-like domain / BAT3 protein / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


BAT3 complex / immune response-activating cell surface receptor signaling pathway / NK T cell activation / maintenance of unfolded protein / tail-anchored membrane protein insertion into ER membrane / protein carrier chaperone / positive regulation of ERAD pathway / synaptonemal complex assembly / post-translational protein targeting to endoplasmic reticulum membrane / internal peptidyl-lysine acetylation ...BAT3 complex / immune response-activating cell surface receptor signaling pathway / NK T cell activation / maintenance of unfolded protein / tail-anchored membrane protein insertion into ER membrane / protein carrier chaperone / positive regulation of ERAD pathway / synaptonemal complex assembly / post-translational protein targeting to endoplasmic reticulum membrane / internal peptidyl-lysine acetylation / misfolded protein binding / endoplasmic reticulum stress-induced pre-emptive quality control / natural killer cell activation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / proteasome binding / ubiquitin-specific protease binding / regulation of embryonic development / polyubiquitin modification-dependent protein binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / proteasomal protein catabolic process / ERAD pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Hsp70 protein binding / molecular function activator activity / kidney development / negative regulation of proteolysis / lung development / brain development / regulation of protein stability / chromatin organization / ribosome binding / ubiquitin-dependent protein catabolic process / spermatogenesis / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / cell differentiation / protein stabilization / receptor ligand activity / signaling receptor binding / intracellular membrane-bounded organelle / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Large proline-rich protein BAG6 / : / BCL2-associated athanogene 6 / Bag6, BAG-similar domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues ...Large proline-rich protein BAG6 / : / BCL2-associated athanogene 6 / Bag6, BAG-similar domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Large proline-rich protein BAG6 / Large proline-rich protein BAG6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsZhao, C. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of the N-terminal Ubiquitin-like Domain in the Human BAT3 Protein
Authors: Zhao, C. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionJan 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX Determination method: Author determined
Remark 700SHEET Determination method: Author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA-B associated transcript-3 isoform b


Theoretical massNumber of molelcules
Total (without water)9,2971
Polymers9,2971
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)20 / 100target function,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein HLA-B associated transcript-3 isoform b / BAT3


Mass: 9296.517 Da / Num. of mol.: 1 / Fragment: ubiquitin-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: BAT3 / Plasmid: P040921-06 / References: UniProt: Q5STX1, UniProt: P46379*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.23mM protein U-15N, 13C, 20mM d-Tris-HCl, 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM / pH: 7 / Pressure: ambient / Temperature: 298.0 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.921Kobayashi, N.data analysis
CYANA1.0.8Guentert, P.structure solution
CYANA1.0.8Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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