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- PDB-2cwb: Solution Structure of the Ubiquitin-Associated Domain of Human BM... -

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Basic information

Entry
Database: PDB / ID: 2cwb
TitleSolution Structure of the Ubiquitin-Associated Domain of Human BMSC-UbP and its Complex with Ubiquitin
ComponentsImmunoglobulin G-binding protein G,Ubiquitin-like protein 7
KeywordsPROTEIN BINDING / HELICAL BUNDLE
Function / homology
Function and homology information


IgG binding / polyubiquitin modification-dependent protein binding / antiviral innate immune response / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / extracellular region / cytoplasm / cytosol
Similarity search - Function
: / : / : / IgG-binding B / B domain / M protein-type anchor domain / Ubiquitin-associated (UBA) domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily ...: / : / : / IgG-binding B / B domain / M protein-type anchor domain / Ubiquitin-associated (UBA) domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / YSIRK Gram-positive signal peptide / UBA-like superfamily / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Helicase, Ruva Protein; domain 3 / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Immunoglobulin G-binding protein G / Ubiquitin-like protein 7
Similarity search - Component
Biological speciesStreptococcus sp. group G (bacteria)
Homo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsChang, Y.G. / Song, A.X. / Gao, Y.G. / Shi, Y.H. / Lin, X.J. / Cao, X.T. / Lin, D.H. / Hu, H.Y.
CitationJournal: Protein Sci. / Year: 2006
Title: Solution structure of the ubiquitin-associated domain of human BMSC-UbP and its complex with ubiquitin.
Authors: Chang, Y.G. / Song, A.X. / Gao, Y.G. / Shi, Y.H. / Lin, X.J. / Cao, X.T. / Lin, D.H. / Hu, H.Y.
History
DepositionJun 17, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity.pdbx_fragment / _entity_name_com.name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G,Ubiquitin-like protein 7


Theoretical massNumber of molelcules
Total (without water)11,9081
Polymers11,9081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3240 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Antibody Immunoglobulin G-binding protein G,Ubiquitin-like protein 7 / IgG-binding protein G / Bone marrow stromal cell ubiquitin-like protein / BMSC-UbP / Ubiquitin-like ...IgG-binding protein G / Bone marrow stromal cell ubiquitin-like protein / BMSC-UbP / Ubiquitin-like protein SB132


Mass: 11908.023 Da / Num. of mol.: 1 / Fragment: C-TERMINAL UBA DOMAIN,C-TERMINAL UBA DOMAIN / Mutation: I12A
Source method: isolated from a genetically manipulated source
Details: A solubility-enhancement tag (SET) GB1, immunoglobulin G binding domain 1 of Streptococcal protein G, was used to enhance the solubility of the UBA domain of BMSC-UbP. The sequence of the ...Details: A solubility-enhancement tag (SET) GB1, immunoglobulin G binding domain 1 of Streptococcal protein G, was used to enhance the solubility of the UBA domain of BMSC-UbP. The sequence of the chimerical HGB1-UBA is as follows:MHHHHHHQYKLALNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSQWQPQLQQLRDMGIQDDELSLRALQATGGDIQAALELIFAGGAP.,A solubility-enhancement tag (SET) GB1, immunoglobulin G binding domain 1 of Streptococcal protein G, was used to enhance the solubility of the UBA domain of BMSC-UbP. The sequence of the chimerical HGB1-UBA is as follows:MHHHHHHQYKLALNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSQWQPQLQQLRDMGIQDDELSLRALQATGGDIQAALELIFAGGAP.
Source: (gene. exp.) Streptococcus sp. group G (bacteria), (gene. exp.) Homo sapiens (human)
Genus: Streptococcus, Homo / Species: , / Gene: spg, UBL7, BMSCUBP, SB132 / Plasmid: pHGB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06654, UniProt: Q96S82

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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
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1mM HGB1-UBA U-15N,13C; 20mM phosphate buffer; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeF.Delaglio, S.Grzesiek, G.W.Vuister, G.Zhu, J.Pfeifer, A.Baxprocessing
SparkyT.D.Goddard, D.G.Knellerdata analysis
ARIA1.2J.Linge, S.O.Donoghue, M.Nilgesstructure solution
ARIA1.2J.Linge, S.O.Donoghue, M.Nilgesrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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