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- PDB-7f7x: Protein complex between phosphorylated ubiquitin and Ubqln2 UBA -

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Basic information

Entry
Database: PDB / ID: 7f7x
TitleProtein complex between phosphorylated ubiquitin and Ubqln2 UBA
Components
  • Polyubiquitin-B
  • Ubiquilin-2
KeywordsPROTEIN BINDING / protein-protein interaction / phosphorylation / proteasomal shuttle factor / ubiquitin-associated domain / induced fit
Function / homology
Function and homology information


negative regulation of G protein-coupled receptor internalization / negative regulation of clathrin-dependent endocytosis / positive regulation of ERAD pathway / regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of autophagosome assembly / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development ...negative regulation of G protein-coupled receptor internalization / negative regulation of clathrin-dependent endocytosis / positive regulation of ERAD pathway / regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of autophagosome assembly / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / autophagosome assembly / autophagosome / polyubiquitin modification-dependent protein binding / regulation of macroautophagy / regulation of neuron apoptotic process / energy homeostasis / regulation of proteasomal protein catabolic process / ERAD pathway / 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 / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / neuron projection morphogenesis / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / molecular condensate scaffold activity / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL
Similarity search - Function
: / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Ubiquitin domain signature. / Ubiquitin conserved site ...: / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Armadillo-type fold / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-B / Ubiquilin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsQin, L.Y. / Dong, X. / Tang, C.
Funding support China, 6items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0507700 China
Ministry of Science and Technology (MoST, China)2017YFA0505400 China
Ministry of Science and Technology (MoST, China)2016YFA0501200 China
National Natural Science Foundation of China (NSFC)31770799 China
National Natural Science Foundation of China (NSFC)21921004 China
National Natural Science Foundation of China (NSFC)31971155 China
CitationJournal: Biomolecules / Year: 2021
Title: Kinetic Constraints in the Specific Interaction between Phosphorylated Ubiquitin and Proteasomal Shuttle Factors.
Authors: Qin, L.Y. / Gong, Z. / Liu, K. / Dong, X. / Tang, C.
History
DepositionJun 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyubiquitin-B
B: Ubiquilin-2


Theoretical massNumber of molelcules
Total (without water)13,5282
Polymers13,5282
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area840 Å2
ΔGint-7 kcal/mol
Surface area7520 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 128structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Polyubiquitin-B


Mass: 8656.811 Da / Num. of mol.: 1
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/peptide Ubiquilin-2 / Chap1 / DSK2 homolog / Protein linking IAP with cytoskeleton 2 / PLIC-2 / hPLIC-2 / Ubiquitin-like ...Chap1 / DSK2 homolog / Protein linking IAP with cytoskeleton 2 / PLIC-2 / hPLIC-2 / Ubiquitin-like product Chap1/Dsk2


Mass: 4871.468 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBQLN2, N4BP4, PLIC2, HRIHFB2157 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHD9
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-13C NOESY
121isotropic2filtered NOE
131isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 20 mM HEPES, 0.15 M sodium chloride, 90% H2O/10% D2O
Label: 15N sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMHEPESnatural abundance1
0.15 Msodium chloridenatural abundance1
Sample conditionsIonic strength: 150 mM / Label: condition1 / pH: 7.4 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD6001
Bruker AVANCE IIIBrukerAVANCE III8502

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 128 / Conformers submitted total number: 20

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