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- PDB-8y4z: Monomeric HERC5 HECT c-lobe structure in solution -

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Basic information

Entry
Database: PDB / ID: 8y4z
TitleMonomeric HERC5 HECT c-lobe structure in solution
ComponentsE3 ISG15--protein ligase HERC5
KeywordsLIGASE / PROTEIN / HECT ligase / E3 / Ubiquitin / ISG15 / ISGylation
Function / homology
Function and homology information


ISG15 transferase activity / ISG15-protein conjugation / regulation of defense response to virus / Transferases; Acyltransferases; Aminoacyltransferases / regulation of cyclin-dependent protein serine/threonine kinase activity / Negative regulators of DDX58/IFIH1 signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / PKR-mediated signaling / ISG15 antiviral mechanism / ubiquitin-protein transferase activity ...ISG15 transferase activity / ISG15-protein conjugation / regulation of defense response to virus / Transferases; Acyltransferases; Aminoacyltransferases / regulation of cyclin-dependent protein serine/threonine kinase activity / Negative regulators of DDX58/IFIH1 signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / PKR-mediated signaling / ISG15 antiviral mechanism / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / defense response to virus / protein ubiquitination / innate immune response / perinuclear region of cytoplasm / RNA binding / cytoplasm / cytosol
Similarity search - Function
Regulator of chromosome condensation (RCC1) signature 2. / Regulator of chromosome condensation (RCC1) repeat / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with
Similarity search - Domain/homology
E3 ISG15--protein ligase HERC5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDag, C. / Lambert, M. / Kahraman, K. / Lohn, F. / Lee, W. / Gocenler, O. / Guntert, P. / Dotsch, V.
Funding support Turkey, United States, European Union, 4items
OrganizationGrant numberCountry
Other government120Z594 Turkey
National Science Foundation (NSF, United States)DBI-2051595 United States
National Science Foundation (NSF, United States)DBI-1902076 United States
European Union (EU)iNEXT DISCOVERY Horizon 2020- 871037European Union
CitationJournal: To Be Published
Title: Monomeric HERC5 HECT c-lobe structure in solution
Authors: Dag, C. / Lambert, M. / Kahraman, K. / Lohn, F. / Lee, W. / Gocenler, O. / Guntert, P. / Dotsch, V.
History
DepositionJan 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ISG15--protein ligase HERC5


Theoretical massNumber of molelcules
Total (without water)13,4451
Polymers13,4451
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein E3 ISG15--protein ligase HERC5 / Cyclin-E-binding protein 1 / HECT domain and RCC1-like domain-containing protein 5


Mass: 13445.317 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HERC5, CEB1, CEBP1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UII4, Transferases; Acyltransferases; Aminoacyltransferases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic22D 1H-15N HSQC
121anisotropic23D HNCO
131anisotropic23D HN(CA)CO
141anisotropic23D HN(CA)CB
151anisotropic23D HN(COCA)CB
1111anisotropic13D 1H-13C NOESY aliphatic
1101anisotropic13D 1H-13C NOESY aromatic
191anisotropic13D 1H-15N NOESY
181anisotropic53D H(CCO)NH
171anisotropic53D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 20 mM sodium phosphate, 100 mM sodium chloride, 3 mM DTT, 2 mM TCEP, 20 uM DSS, 95% H2O/5% D2O
Label: 1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
3 mMDTTnatural abundance1
2 mMTCEPnatural abundance1
20 uMDSSnatural abundance1
Sample conditionsIonic strength: 100 mM / Label: 1 / pH: 7.4 / Pressure: AMBIENT Pa / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III9501
Bruker AVANCE NEOBrukerAVANCE NEO9002
Bruker AVANCE NEOBrukerAVANCE NEO12003
Bruker AVANCE IIIBrukerAVANCE III8004
Bruker AVANCE IIIBrukerAVANCE III7005

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.15Guntert, Mumenthaler and Wuthrichrefinement
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leechemical shift assignment
Poky3.98.15Manthey, Tonelli, Clos II, Rahimi, Markley and Leedata analysis
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leepeak picking
Refinement
MethodSoftware ordinal
torsion angle dynamics7
torsion angle dynamics1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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