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- PDB-1ur6: NMR based structural model of the UbcH5B-CNOT4 complex -

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Basic information

Entry
Database: PDB / ID: 1ur6
TitleNMR based structural model of the UbcH5B-CNOT4 complex
Components
  • POTENTIAL TRANSCRIPTIONAL REPRESSOR NOT4HP
  • UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2
KeywordsLIGASE / UBIQUITIN CONJUGATING ENZYME / UBIQUITIN LIGASE / RING FINGER PROTEIN / CCR4-NOT COMPLEX / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / Inactivation of CSF3 (G-CSF) signaling / IKK complex recruitment mediated by RIP1 / CCR4-NOT complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / FCERI mediated NF-kB activation / nuclear-transcribed mRNA poly(A) tail shortening / CLEC7A (Dectin-1) signaling / Downstream TCR signaling ...Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / Inactivation of CSF3 (G-CSF) signaling / IKK complex recruitment mediated by RIP1 / CCR4-NOT complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / FCERI mediated NF-kB activation / nuclear-transcribed mRNA poly(A) tail shortening / CLEC7A (Dectin-1) signaling / Downstream TCR signaling / Peroxisomal protein import / regulation of megakaryocyte differentiation / (E3-independent) E2 ubiquitin-conjugating enzyme / Deadenylation of mRNA / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / M-decay: degradation of maternal mRNAs by maternally stored factors / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / protein modification process / RING-type E3 ubiquitin transferase / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / protein ubiquitination / ubiquitin protein ligase binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
RING/Ubox like zinc-binding domain / CNOT4, RNA recognition motif / NOT4, modified RING finger, HC subclass (C4C4-type) / CCR4-NOT transcription complex subunit 4 / RNA recognition motif domain, eukaryote / RNA recognition motif / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. ...RING/Ubox like zinc-binding domain / CNOT4, RNA recognition motif / NOT4, modified RING finger, HC subclass (C4C4-type) / CCR4-NOT transcription complex subunit 4 / RNA recognition motif domain, eukaryote / RNA recognition motif / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 4 / Ubiquitin-conjugating enzyme E2 D2 / Ubiquitin-conjugating enzyme E2 D2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / THEORETICAL MODEL
AuthorsDominguez, C. / Bonvin, A.M.J.J. / Winkler, G.S. / Van Schaik, F.M.A. / Timmers, H.Th.M. / Boelens, R.
CitationJournal: Structure / Year: 2004
Title: Structural Model of the Ubch5B/Cnot4 Complex Revealed by Combining NMR, Mutagenesis, and Docking Approaches.
Authors: Dominguez, C. / Bonvin, A.M.J.J. / Winkler, G.S. / Van Schaik, F.M.A. / Timmers, H.T.M. / Boelens, R.
History
DepositionOct 27, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2
B: POTENTIAL TRANSCRIPTIONAL REPRESSOR NOT4HP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0344
Polymers22,9032
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / -
Representative

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Components

#1: Protein UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2 / UBCH5B / UBIQUITIN CARRIER PROTEIN / E2(17)KB 2


Mass: 16755.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human)
References: UniProt: P51669, UniProt: P62837*PLUS, ubiquitin-protein ligase
#2: Protein POTENTIAL TRANSCRIPTIONAL REPRESSOR NOT4HP / CNOT4 / NOT4H


Mass: 6148.101 Da / Num. of mol.: 1 / Fragment: RING FINGER, RESIDUES 12-63 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: O95628
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Compound detailsCATALYZES THE COVALENT ATTACHMENT OF UBIQUITIN TO OTHER PROTEINS ATP + UBIQUITIN + PROTEIN LYSINE = ...CATALYZES THE COVALENT ATTACHMENT OF UBIQUITIN TO OTHER PROTEINS ATP + UBIQUITIN + PROTEIN LYSINE = AMP + DIPHOSPHATE + PROTEIN N-UBIQUITYLLYSINE.

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
THEORETICAL MODEL
NMR detailsText: NONE

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Processing

NMR softwareName: CNS
Developer: BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARREN
Classification: refinement
RefinementSoftware ordinal: 1
Details: REFINEMENT DETAILS AS DESCIRIBED IN C. DOMINGUEZ ET AL. (2003), J.AM.CHEM.SOC, 125, P1731
NMR ensembleConformers submitted total number: 5

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