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- PDB-2l0b: Solution NMR structure of zinc finger domain of E3 ubiquitin-prot... -

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Basic information

Entry
Database: PDB / ID: 2l0b
TitleSolution NMR structure of zinc finger domain of E3 ubiquitin-protein ligase praja-1 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) target HR4710B
ComponentsE3 ubiquitin-protein ligase Praja-1
KeywordsLIGASE / Zinc finger / NESG / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


protein catabolic process / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / protein ubiquitination / zinc ion binding / cytoplasm
Similarity search - Function
Ring finger domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Praja-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsLiu, G. / Tong, S. / Hamilton, K. / Ciccosanti, C. / Shastry, R. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution structure of zinc finger domain of E3 ubiquitin-protein ligase protein praja-1 from Homo sapiens, northeast structural genomics consortium (NESG) target HR4710B
Authors: Liu, G. / Tong, S. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T.
History
DepositionJun 30, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase Praja-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2433
Polymers10,1121
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein E3 ubiquitin-protein ligase Praja-1 / Praja1 / RING finger protein 70


Mass: 10111.733 Da / Num. of mol.: 1 / Fragment: RING-type zinc finger residues 564-643
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PJA1, RNF70 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NG27, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D 1H-13C-15N SIMUTANEOUS NOESY
1413D 1H-13C aromatic NOESY
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D C(CO)NH
1813D HNCO
1913D (H)CCH-TOCSY
11013D HBHA(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
10.94 mM [U-100% 13C; U-100% 15N] pja1 zinc finger domain, 90% H2O/10% D2O90% H2O/10% D2O
20.82 mM [U-10% 13C; U-100% 15N] pja1 zinc finger domain, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.94 mMpja1 zinc finger domain-1[U-100% 13C; U-100% 15N]1
0.82 mMpja1 zinc finger domain-2[U-10% 13C; U-100% 15N]2
Sample conditionsIonic strength: n.a. / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AutoStructureHuang, Tejero, Powers and Montelionerefinement
AutoStructureHuang, Tejero, Powers and Montelionegeometry optimization
AutoStructureHuang, Tejero, Powers and Montelionedata analysis
TALOS+Shen, Delaglio and Baxdata analysis
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
XEASYBartels et al.refinement
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VnmrJVariancollection
TopSpinBruker Biospincollection
RefinementMethod: distance geometry, simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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