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- PDB-2kiz: Solution structure of Arkadia RING-H2 finger domain -

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Basic information

Entry
Database: PDB / ID: 2kiz
TitleSolution structure of Arkadia RING-H2 finger domain
ComponentsE3 ubiquitin-protein ligase Arkadia
KeywordsMETAL BINDING PROTEIN / ARKADIA / RING-H2 FINGER / E3 LIGASE / ZN BINDING DOMAIN / Metal-binding / Zinc-finger
Function / homology
Function and homology information


SUMO polymer binding / global genome nucleotide-excision repair / pattern specification process / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / positive regulation of protein ubiquitination / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / RING-type E3 ubiquitin transferase / PML body ...SUMO polymer binding / global genome nucleotide-excision repair / pattern specification process / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / positive regulation of protein ubiquitination / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / RING-type E3 ubiquitin transferase / PML body / Formation of Incision Complex in GG-NER / protein polyubiquitination / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / protein ubiquitination / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase Arkadia, N-terminal / E3 ubiquitin-protein ligase Arkadia N-terminus / Ring finger domain / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Arkadia
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsKandias, N.G. / Chasapis, C.T. / Bentrop, D. / Episkopou, V. / Spyroulias, G.A.
Citation
Journal: Proteins / Year: 2012
Title: NMR-based insights into the conformational and interaction properties of Arkadia RING-H2 E3 Ub ligase.
Authors: Chasapis, C.T. / Kandias, N.G. / Episkopou, V. / Bentrop, D. / Spyroulias, G.A.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: High yield expression and NMR characterization of Arkadia E3 ubiquitin ligase RING-H2 finger domain.
Authors: Kandias, N.G. / Chasapis, C.T. / Bentrop, D. / Episkopou, V. / Spyroulias, G.A.
History
DepositionMay 13, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase Arkadia
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0913
Polymers7,9601
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)31 / 31target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein E3 ubiquitin-protein ligase Arkadia / RING finger protein 111


Mass: 7960.034 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF111 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZNA4
#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 / Details: Recombinant RING finger polypeptide (RING-H2 type)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CO)CA
1413D HNCA
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D HNCO
1813D (H)CCH-TOCSY
1913D HBHA(CO)NH
11012D (HB)CB(CGCD)HDarom
11112D 2J-edited 1H-15N HSQC
11213D 1H-15N NOESY
11313D 1H-13C NOESY

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Sample preparation

DetailsContents: 1.0 mM [U-98% 13C; U-98% 15N] RING Finger monomer, 50 mM Pi, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMRING Finger monomer[U-98% 13C; U-98% 15N]1
50 mMPi1
Sample conditionsIonic strength: 50 / pH: 6.9 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.8.4Keller, R. et al.chemical shift assignment
AMBER 4.1EARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON, SEIBEL,SINGH,WEINER,KOLLMANrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 31 / Conformers submitted total number: 31

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