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- PDB-6oq2: NMR Structure of Branched K11/K48-Linked Tri-Ubiquitin -

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Basic information

Entry
Database: PDB / ID: 6oq2
TitleNMR Structure of Branched K11/K48-Linked Tri-Ubiquitin
Components(Ubiquitin) x 3
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / seminiferous tubule development / female gonad development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / neuron projection morphogenesis ...hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / seminiferous tubule development / female gonad development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / neuron projection morphogenesis / energy homeostasis / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / 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 / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / 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 / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / regulation of neuron apoptotic process / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Pexophagy / Regulation of innate immune responses to cytosolic DNA / NRIF signals cell death from the nucleus / Downregulation of ERBB2:ERBB3 signaling / Regulation of PTEN localization / positive regulation of protein ubiquitination / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Regulation of BACH1 activity / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / regulation of mitochondrial membrane potential / Josephin domain DUBs / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of activated PAK-2p34 by proteasome mediated degradation / TNFR1-induced NF-kappa-B signaling pathway / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Regulation of signaling by CBL / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Ubiquitin-dependent degradation of Cyclin D / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Fanconi Anemia Pathway / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulation of FGFR3 signaling / Peroxisomal protein import / TNFR2 non-canonical NF-kB pathway / Deactivation of the beta-catenin transactivating complex / Stabilization of p53 / Assembly of the pre-replicative complex / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Vpu mediated degradation of CD4 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR1 signaling / Termination of translesion DNA synthesis
Similarity search - Function
: / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBoughton, A.J. / Fushman, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM065334 United States
CitationJournal: Structure / Year: 2020
Title: Branching via K11 and K48 Bestows Ubiquitin Chains with a Unique Interdomain Interface and Enhanced Affinity for Proteasomal Subunit Rpn1.
Authors: Boughton, A.J. / Krueger, S. / Fushman, D.
History
DepositionApr 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
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
B: Ubiquitin
D: Ubiquitin
E: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)25,9583
Polymers25,9583
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1860 Å2
ΔGint-2 kcal/mol
Surface area12810 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin


Mass: 8660.873 Da / Num. of mol.: 1 / Mutation: K11R, K48R, K63R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#2: Protein Ubiquitin


Mass: 8604.845 Da / Num. of mol.: 1 / Mutation: K48R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#3: Protein Ubiquitin


Mass: 8691.918 Da / Num. of mol.: 1 / Mutation: M77D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
122isotropic12D 1H-15N HSQC
133isotropic22D 1H-15N HSQC
144isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetails (eV)LabelSolvent system
solution1120 uM [U-15N-distal11] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2OThe distal K11-linked Ub was uniformly 15N-enriched, while the distal K48-linked Ub and the proximal Ub were not isotopically enriched.15N_distal1195% H2O/5% D2O
solution2100 uM [U-15N-distal48] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2OThe distal K48-linked Ub was uniformly 15N-enriched, while the distal K11-linked Ub and the proximal Ub were not isotopically enriched.15N_distal4895% H2O/5% D2O
solution360 uM [U-15N-distal11] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2OThe distal K11-linked Ub was uniformly 15N-enriched, while the distal K48-linked Ub and the proximal Ub were not isotopically enriched. MTSL was attached to residue C48 in the distal K48-linked Ub.15N_distal11_MTSL4895% H2O/5% D2O
solution4110 uM [U-15N-distal48] Branched K11/K48-Linked Tri-Ubiquitin, 95% H2O/5% D2OThe distal K48-linked Ub was uniformly 15N-enriched, while the distal K11-linked Ub and the proximal Ub were not isotopically enriched. MTSL was attached to residue C48 in the distal K11-linked Ub.15N_distal48_MTSL1195% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
120 uMBranched K11/K48-Linked Tri-Ubiquitin[U-15N-distal11]1
100 uMBranched K11/K48-Linked Tri-Ubiquitin[U-15N-distal48]2
60 uMBranched K11/K48-Linked Tri-Ubiquitin[U-15N-distal11]3
110 uMBranched K11/K48-Linked Tri-Ubiquitin[U-15N-distal48]4
Sample conditionsDetails: Buffer: 20 mM sodium phosphate, pH 6.8. / Ionic strength: 0 M / Label: sample_conditions / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
SparkyGoddardpeak picking
HADDOCKBonvinrefinement
HADDOCKBonvinstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
Details: THE INITIAL HADDOCK INPUT WAS THE CRYSTAL STRUCTURE OF BRANCHED K11/K48-LINKED TRI-UBIQUITIN (PDB ID 6OQ1). AMBIGUOUS DISTANCE RESTRAINTS WERE FROM CHEMICAL SHIFT PERTURBATIONS AND DISTANCE ...Details: THE INITIAL HADDOCK INPUT WAS THE CRYSTAL STRUCTURE OF BRANCHED K11/K48-LINKED TRI-UBIQUITIN (PDB ID 6OQ1). AMBIGUOUS DISTANCE RESTRAINTS WERE FROM CHEMICAL SHIFT PERTURBATIONS AND DISTANCE RESTRAINTS WERE BASED ON PRES.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 10

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