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- PDB-2mul: Solution Structure of the UBM1 domain of human HUWE1/ARF-BP1 -

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Basic information

Entry
Database: PDB / ID: 2mul
TitleSolution Structure of the UBM1 domain of human HUWE1/ARF-BP1
ComponentsE3 ubiquitin-protein ligase HUWE1
KeywordsPROTEIN BINDING / Ubiquitin Binding Motif
Function / homology
Function and homology information


histone ubiquitin ligase activity / negative regulation of mitochondrial fusion / : / HECT-type E3 ubiquitin transferase / positive regulation of protein targeting to mitochondrion / Golgi organization / protein monoubiquitination / positive regulation of protein ubiquitination / circadian regulation of gene expression / base-excision repair ...histone ubiquitin ligase activity / negative regulation of mitochondrial fusion / : / HECT-type E3 ubiquitin transferase / positive regulation of protein targeting to mitochondrion / Golgi organization / protein monoubiquitination / positive regulation of protein ubiquitination / circadian regulation of gene expression / base-excision repair / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / secretory granule lumen / ficolin-1-rich granule lumen / membrane fusion / cell differentiation / Golgi membrane / Neutrophil degranulation / mitochondrion / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
HUWE1, UBA domain / E3 ubiquitin ligase, domain of unknown function DUF908 / E3 ubiquitin ligase, domain of unknown function DUF913 / Domain of Unknown Function (DUF908) / Domain of Unknown Function (DUF913) / WWE domain / UBA-like domain / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / WWE domain superfamily ...HUWE1, UBA domain / E3 ubiquitin ligase, domain of unknown function DUF908 / E3 ubiquitin ligase, domain of unknown function DUF913 / Domain of Unknown Function (DUF908) / Domain of Unknown Function (DUF913) / WWE domain / UBA-like domain / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / WWE domain superfamily / WWE domain / WWE domain profile. / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Armadillo-type fold
Similarity search - Domain/homology
E3 ubiquitin-protein ligase HUWE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsFarhadi, S. / Khatun, R. / Lemak, A. / Kaustov, L. / Ramabadran, R. / Hunter, H. / Sheng, Y.
CitationJournal: To be Published
Title: Solution structure of Ubiquitin Binding Motif of human Arf-bp1
Authors: Khatun, R. / Sheng, Y.
History
DepositionSep 12, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase HUWE1


Theoretical massNumber of molelcules
Total (without water)5,6631
Polymers5,6631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein E3 ubiquitin-protein ligase HUWE1


Mass: 5663.181 Da / Num. of mol.: 1 / Fragment: UNP residues 2951-3003
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX2TK / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z6Z7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D (H)CCH-TOCSY
1713D HBHA(CO)NH
1813D CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.4 mM [U-13C; U-15N] protein, 300 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 2 mM potassium phosphate, 0.05 mM CHAPS, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMprotein-1[U-13C; U-15N]1
300 mMsodium chloride-21
2.7 mMpotassium chloride-31
10 mMsodium phosphate-41
2 mMpotassium phosphate-51
0.05 mMCHAPS-61
Sample conditionsIonic strength: 300 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
FMCGUILemak A., Gutmanas A., Chitayat S., Karra M., Far s C., Sunnerhagen M., and Arrowsmith CHchemical shift assignment
FMCGUILemak A., Gutmanas A., Chitayat S., Karra M., Far s C., Sunnerhagen M., and Arrowsmith CHstructure solution
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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