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- PDB-1e4u: N-terminal RING finger domain of human NOT-4 -

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Basic information

Entry
Database: PDB / ID: 1e4u
TitleN-terminal RING finger domain of human NOT-4
ComponentsTRANSCRIPTIONAL REPRESSOR NOT4
KeywordsGENE REGULATION / TRANSCRIPTIONAL CONTROL
Function / homology
Function and homology information


CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / regulation of megakaryocyte differentiation / Deadenylation of mRNA / 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 / protein autoubiquitination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process ...CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / regulation of megakaryocyte differentiation / Deadenylation of mRNA / 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 / protein autoubiquitination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / RNA 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. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 ...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. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR
AuthorsHanzawa, H. / De Ruwe, M.J. / Albert, T.K. / Van Der Vliet, P.C. / Timmers, H.T. / Boelens, R.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: The Structure of the C4C4 Ring Finger of Human not4 Reveals Features Distinct from Those of C3Hc4 Ring Fingers
Authors: Hanzawa, H. / De Ruwe, M.J. / Albert, T.K. / Van Der Vliet, P.C. / Timmers, H.T. / Boelens, R.
History
DepositionJul 12, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2001Provider: 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: TRANSCRIPTIONAL REPRESSOR NOT4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2503
Polymers9,1191
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)30 / 200TOTAL ENERGY
RepresentativeModel #29

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Components

#1: Protein TRANSCRIPTIONAL REPRESSOR NOT4


Mass: 9119.444 Da / Num. of mol.: 1 / Fragment: RING FINGER DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O95628
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

DetailsContents: 1MM PROTEIN
Sample conditionsIonic strength: 170MM KCL / pH: 7.0 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
NMR ensembleConformer selection criteria: TOTAL ENERGY / Conformers calculated total number: 200 / Conformers submitted total number: 30

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