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- PDB-6l99: Zinc finger of RING finger protein 144A -

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Basic information

Entry
Database: PDB / ID: 6l99
TitleZinc finger of RING finger protein 144A
ComponentsE3 ubiquitin-protein ligase RNF144A
KeywordsMETAL BINDING PROTEIN / RING finger protein 144A / Zinc Finger
Function / homology
Function and homology information


RBR-type E3 ubiquitin transferase / protein K6-linked ubiquitination / ubiquitin conjugating enzyme binding / pattern recognition receptor signaling pathway / ubiquitin ligase complex / protein polyubiquitination / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / ubiquitin-dependent protein catabolic process ...RBR-type E3 ubiquitin transferase / protein K6-linked ubiquitination / ubiquitin conjugating enzyme binding / pattern recognition receptor signaling pathway / ubiquitin ligase complex / protein polyubiquitination / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / ubiquitin-dependent protein catabolic process / endosome membrane / protein ubiquitination / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / Golgi apparatus / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
E3 ubiquitin ligase RBR family / IBR domain, a half RING-finger domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF144A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMiyamoto, K.
CitationJournal: To Be Published
Title: Zinc finger of RING finger protein 144A
Authors: Miyamoto, K.
History
DepositionNov 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF144A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3433
Polymers8,2131
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5140 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein E3 ubiquitin-protein ligase RNF144A / RING finger protein 144A / UbcM4-interacting protein 4 / Ubiquitin-conjugating enzyme 7-interacting protein 4


Mass: 8212.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P50876, RBR-type E3 ubiquitin transferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: NOESY

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Sample preparation

DetailsType: solution / Contents: 1 mM [U-13C; U-15N] RNF, 90% H2O/10% D2O / Label: RNF / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: RNF / Isotopic labeling: [U-13C; U-15N]
Sample conditionsDetails: 1 mM U 13C; 15N RNF, 90% H2O/10% D2O / Ionic strength: 20 mM / Label: conditions_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
Discovery Studio2.1Accelrys Software Inc.refinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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