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- PDB-9uv6: Encounter complex structure of E2N and Ubiquitin -

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Basic information

Entry
Database: PDB / ID: 9uv6
TitleEncounter complex structure of E2N and Ubiquitin
Components
  • Ubiquitin
  • Ubiquitin-conjugating enzyme E2 N
KeywordsPROTEIN BINDING / Enzyme / ubiquitin / encounter complex
Function / homology
Function and homology information


UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / DNA damage tolerance / Formation of the ternary complex, and subsequently, the 43S complex / E2 ubiquitin-conjugating enzyme / Ribosomal scanning and start codon recognition / Translation initiation complex formation ...UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / DNA damage tolerance / Formation of the ternary complex, and subsequently, the 43S complex / E2 ubiquitin-conjugating enzyme / Ribosomal scanning and start codon recognition / Translation initiation complex formation / positive regulation of double-strand break repair / ubiquitin conjugating enzyme activity / SARS-CoV-1 modulates host translation machinery / positive regulation of intracellular signal transduction / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / protein K63-linked ubiquitination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / protein monoubiquitination / GTP hydrolysis and joining of the 60S ribosomal subunit / ubiquitin ligase complex / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / regulation of DNA repair / negative regulation of TORC1 signaling / 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 / antiviral innate immune response / 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 / cytosolic ribosome / 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 / positive regulation of DNA repair / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / 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 / ubiquitin binding / 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
Similarity search - Function
Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a ...Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc-binding ribosomal protein / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
: / Ubiquitin-conjugating enzyme E2 N / Ubiquitin-ribosomal protein eS31 fusion protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsGong, Z. / Liu, M.L. / Zhang, X. / He, L.C. / Zhao, Q. / Zhang, L.H. / Zhang, B.R.
Funding support China, 7items
OrganizationGrant numberCountry
Other governmentXDB0540000
Other government2021YFA1301501
Other government2024YFC3405400
National Natural Science Foundation of China (NSFC)22322411 China
National Natural Science Foundation of China (NSFC)22374154 China
National Natural Science Foundation of China (NSFC)22393931 China
National Natural Science Foundation of China (NSFC)32088101 China
CitationJournal: To Be Published
Title: X-GAME: An Integrative Framework for Deciphering Protein-Protein Interactions in Living Cells
Authors: Gong, Z. / Zhang, B.R. / He, X.F. / Zhong, B.W. / Zhu, Y.L. / Tan, K.N. / Liu, Z. / Chen, J. / Liang, Z. / Zhang, X. / He, L.C. / Zhang, Y.K. / Zhang, L.H. / Liu, M.L. / Zhao, Q.
History
DepositionMay 9, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 N
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9913
Polymers25,5212
Non-polymers4691
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)3 / 240structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / ...Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


Mass: 16944.533 Da / Num. of mol.: 1 / Mutation: N123C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N, BLU / Production host: Escherichia coli (E. coli)
References: UniProt: P61088, E2 ubiquitin-conjugating enzyme
#2: Protein Ubiquitin / Donor Ub


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA80, UBCEP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62979
#3: Chemical ChemComp-A1EQF / (5~{S},16~{S})-16-[2-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]ethylamino]-2,11,12,17-tetraoxa-5,8-diaza-1$l^{4}-manganatricyclo[6.3.3.3^{1,5}]heptadecane-3,10,13-trione


Mass: 469.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H22MnN4O9 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: 2D PRE

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Sample preparation

DetailsType: solution
Contents: 0.6 mM [U-15N] Ubi, 0.2 mM E2N, 20 mM HEPES, 90 % H2O, 10 % [U-2H] D2O, 90% H2O/10% D2O
Label: sample_1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMUbi[U-15N]1
0.2 mME2Nnatural abundance1
20 mMHEPESnatural abundance1
90 %H2Onatural abundance1
10 %D2O[U-2H]1
Sample conditionsIonic strength: 0.02 M / Label: sample_conditions_1 / pH: 7.5 / PH err: 0.05 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.5

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz / Details: cryogenic probes

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2010Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 240 / Conformers submitted total number: 3

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