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- PDB-2jrj: Solution structure of the human Pirh2 RING-H2 domain. Northeast S... -

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Basic information

Entry
Database: PDB / ID: 2jrj
TitleSolution structure of the human Pirh2 RING-H2 domain. Northeast Structural Genomics Consortium Target HT2B
ComponentsRing finger and CHY zinc finger domain containing protein 1
KeywordsLIGASE / Ubiquitin E3 ligase / RING domain / Structural Genomics / Protein Structure Initiative / PSI-2 / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


error-free translesion synthesis / protein autoubiquitination / ubiquitin ligase complex / rescue of stalled ribosome / positive regulation of protein ubiquitination / Translesion Synthesis by POLH / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation ...error-free translesion synthesis / protein autoubiquitination / ubiquitin ligase complex / rescue of stalled ribosome / positive regulation of protein ubiquitination / Translesion Synthesis by POLH / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitin-dependent protein catabolic process / protein ubiquitination / nuclear speck / intracellular membrane-bounded organelle / protein homodimerization activity / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Zinc finger, CHY-type / Zinc finger, CTCHY-type / Zinc finger, CHY-type superfamily / Zinc finger, CTCHY-type superfamily / RCHY1, zinc-ribbon / CHY zinc finger / Zinc-ribbon / Zinc finger CHY-type profile. / Zinc finger CTCHY-type profile. / Ring finger domain ...Zinc finger, CHY-type / Zinc finger, CTCHY-type / Zinc finger, CHY-type superfamily / Zinc finger, CTCHY-type superfamily / RCHY1, zinc-ribbon / CHY zinc finger / Zinc-ribbon / Zinc finger CHY-type profile. / Zinc finger CTCHY-type profile. / 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
RING finger and CHY zinc finger domain-containing protein 1 / RING finger and CHY zinc finger domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsSheng, Y. / Lemak, A. / Laister, R.C. / Wu, B. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Molecular basis of Pirh2-mediated p53 ubiquitylation.
Authors: Sheng, Y. / Laister, R.C. / Lemak, A. / Wu, B. / Tai, E. / Duan, S. / Lukin, J. / Sunnerhagen, M. / Srisailam, S. / Karra, M. / Benchimol, S. / Arrowsmith, C.H.
History
DepositionJun 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ring finger and CHY zinc finger domain containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1353
Polymers6,0041
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ring finger and CHY zinc finger domain containing protein 1


Mass: 6003.978 Da / Num. of mol.: 1 / Fragment: Pirh2 RING-H2 domain: Residues 138-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RCHY1 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / References: UniProt: Q86X26, UniProt: Q96PM5*PLUS
#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
1113D C(CO)NH
1213D HN(CA)CB
1313D H(CCO)NH
1413D HNCO
1513D 1H-15N NOESY
1623D 1H-13C NOESY
1723D (H)CCH-TOCSY
1823D 1H-13C aromatic NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-13C; U-15N] Pirh2 RING domain, 25 mM sodium phosphate, 150 mM potassium chloride, 10 uM ZnCl2, 2 mM [U-99% 2H] DTT, 90% H2O/10% D2O90% H2O/10% D2O
20.7 mM [U-13C; U-15N] Pirh2 RING domain, 25 mM sodium phosphate, 150 mM potassium chloride, 10 uM ZnCl2, 2 mM [U-99% 2H] DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMPirh2 RING domain[U-13C; U-15N]1
25 mMsodium phosphate1
150 mMpotassium chloride1
10 uMZnCl21
2 mMDTT[U-99% 2H]1
0.7 mMPirh2 RING domain[U-13C; U-15N]2
25 mMsodium phosphate2
150 mMpotassium chloride2
10 uMZnCl22
2 mMDTT[U-99% 2H]2
Sample conditionsIonic strength: 150 / pH: 7.0 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.peak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, 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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