[English] 日本語
Yorodumi
- PDB-2den: Solution Structure of the Ubiquitin-Associated Domain of Human BM... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2den
TitleSolution Structure of the Ubiquitin-Associated Domain of Human BMSC-UbP and its Complex with Ubiquitin
Components
  • Immunoglobulin G-binding protein G,Ubiquitin-like protein 7
  • Polyubiquitin-B
KeywordsPROTEIN BINDING / A:alpha-alpha-alpha / B:beta-beta-helix-helix-beta-beta-helix-beta
Function / homology
Function and homology information


IgG binding / polyubiquitin modification-dependent protein binding / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway ...IgG binding / polyubiquitin modification-dependent protein binding / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / antiviral innate immune response / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53 / Negative regulation of FGFR4 signaling / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Regulation of TNFR1 signaling / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / EGFR downregulation / Termination of translesion DNA synthesis / Degradation of GLI1 by the proteasome / G2/M Checkpoints / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Iron uptake and transport
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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ubiquitin B / Immunoglobulin G-binding protein G / Polyubiquitin-C / Ubiquitin-like protein 7
Similarity search - Component
Biological speciesStreptococcus sp. group G (bacteria)
Homo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsHu, H.Y. / Lin, D.H. / Chang, Y.G.
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
DepositionFeb 14, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 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 / _struct_ref_seq_dif.pdbx_seq_db_accession_code
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,4852
Polymers20,4852
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1570 Å2
ΔGint-6 kcal/mol
Surface area6530 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
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: UBA domain,UBA domain / Mutation: I12A
Source method: isolated from a genetically manipulated source
Details: HGB1-UBA is a chimeric protein. The N-terminal HisTag is for ease of purification. The GB1 domain is used for solubility enhancement. The GB1 domain sequence refers to the protein with ...Details: HGB1-UBA is a chimeric protein. The N-terminal HisTag is for ease of purification. The GB1 domain is used for solubility enhancement. The GB1 domain sequence refers to the protein with accession code P06654.,HGB1-UBA is a chimeric protein. The N-terminal HisTag is for ease of purification. The GB1 domain is used for solubility enhancement. The GB1 domain sequence refers to the protein with accession code P06654.
Source: (gene. exp.) Streptococcus sp. group G (bacteria), (gene. exp.) Homo sapiens (human)
Genus: Streptococcus, Homo / Species: , / Gene: spg, UBL7, BMSCUBP, SB132 / Plasmid: pHGB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus / References: UniProt: P06654, UniProt: Q96S82
#2: Protein Polyubiquitin-B


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pET-3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: J3QS39, UniProt: P0CG48*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111titration of sample 1 with sample 2
122titration of sample 2 with sample 1
NMR detailsText: This complex model is constructed by using the HADDOCK program which employs the Ambiguous Interaction Restraints (AIR) that are obtained from the reciprocal NMR titration of the two samples.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM HGB1-UBA20mM phosphate, 100mM NaCl, pH6.5
21mM Ubiquitin20mM phosphate, 100mM NaCl, pH6.5
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

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

-
Processing

NMR software
NameVersionDeveloperClassification
HADDOCK1.3Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvinrefinement
HADDOCK1.3Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvinstructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: Based on NMR titration data, the complex structrue is constructed using the HADDOCK program.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more