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- PDB-2n9o: Solution structure of RNF126 N-terminal zinc finger domain -

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Basic information

Entry
Database: PDB / ID: 2n9o
TitleSolution structure of RNF126 N-terminal zinc finger domain
ComponentsE3 ubiquitin-protein ligase RNF126
KeywordsLIGASE / Zinc finger / E3 ligase
Function / homology
Function and homology information


cytoplasm protein quality control by the ubiquitin-proteasome system / protein K29-linked ubiquitination / protein K27-linked ubiquitination / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / retrograde transport, endosome to Golgi / epidermal growth factor receptor binding / negative regulation of epidermal growth factor receptor signaling pathway / protein monoubiquitination / protein K63-linked ubiquitination / positive regulation of double-strand break repair via homologous recombination ...cytoplasm protein quality control by the ubiquitin-proteasome system / protein K29-linked ubiquitination / protein K27-linked ubiquitination / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / retrograde transport, endosome to Golgi / epidermal growth factor receptor binding / negative regulation of epidermal growth factor receptor signaling pathway / protein monoubiquitination / protein K63-linked ubiquitination / positive regulation of double-strand break repair via homologous recombination / protein K48-linked ubiquitination / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / regulation of cell population proliferation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase RNF126-like, zinc-ribbon / zinc-ribbon / 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 RNF126
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model3
AuthorsMartinez-Lumbreras, S. / Krysztofinska, E.M. / Thapaliya, A. / Isaacson, R.L.
CitationJournal: Sci Rep / Year: 2016
Title: Structural and functional insights into the E3 ligase, RNF126.
Authors: Krysztofinska, E.M. / Martinez-Lumbreras, S. / Thapaliya, A. / Evans, N.J. / High, S. / Isaacson, R.L.
History
DepositionDec 1, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF126
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,7712
Polymers4,7051
Non-polymers651
Water0
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/peptide E3 ubiquitin-protein ligase RNF126 / RING finger protein 126


Mass: 4705.398 Da / Num. of mol.: 1 / Fragment: N-terminal zinc finger domain residues 1-40
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF126 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q9BV68, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H NOESY
1522D 1H-1H NOESY
1613D CBCA(CO)NH
1713D HN(CA)CB
1813D HNCO
1913D HN(CA)CO
11023D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
1350-750 uM [U-99% 13C; U-99% 15N] RNF126, 350-750 uM ZINC ION, 10 mM potassium phosphate, 100 mM sodium chloride, 250 uM TCEP, 10 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
2350-750 uM [U-99% 13C; U-99% 15N] RNF126, 350-750 uM ZINC ION, 10 mM potassium phosphate, 100 mM sodium chloride, 250 uM TCEP, 10 uM DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
uMentity_1-1[U-99% 13C; U-99% 15N]350-7501
uMZINC ION-2350-7501
10 mMpotassium phosphate-31
100 mMsodium chloride-41
250 uMTCEP-51
10 uMDSS-61
uMentity_1-7[U-99% 13C; U-99% 15N]350-7502
uMZINC ION-8350-7502
10 mMpotassium phosphate-92
100 mMsodium chloride-102
250 uMTCEP-112
10 uMDSS-122
Sample conditionsIonic strength: 0.12 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
TopSpin3.2Bruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr Analysis2.3CCPNpeak picking
CcpNmr Analysis2.3CCPNchemical shift assignment
CcpNmr Analysis2.3CCPNstructure solution
ARIA2.1Linge, O'Donoghue and Nilgesstructure solution
ARIA2.1Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Refinement in water with default parametres
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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