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- PDB-2k2d: Solution NMR structure of C-terminal domain of human pirh2. North... -

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Basic information

Entry
Database: PDB / ID: 2k2d
TitleSolution NMR structure of C-terminal domain of human pirh2. Northeast Structural Genomics Consortium (NESG) target HT2C
ComponentsRING finger and CHY zinc finger domain-containing protein 1
KeywordsMETAL BINDING PROTEIN / zinc-binding protein / Cytoplasm / Metal-binding / Nucleus / Zinc-finger / Structural Genomics / PSI-2 / Protein Structure Initiative / 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 / p53 binding ...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 / p53 binding / Antigen processing: Ubiquitination & Proteasome degradation / 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 / cytosol / cytoplasm
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. / Rubrerythrin, domain 2 - #10 ...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. / Rubrerythrin, domain 2 - #10 / Ring finger domain / Rubrerythrin, domain 2 / Single Sheet / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Mainly Beta
Similarity search - Domain/homology
RING finger and CHY zinc finger domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsLemak, A. / Sheng, Y. / Karra, M. / Srisailam, S. / Laister, R.C. / Duan, S. / 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
DepositionMar 31, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: 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_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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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)9,1042
Polymers9,0381
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 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 / Zinc finger protein 363 / CH-rich-interacting match with PLAG1 / Androgen receptor N-terminal- ...Zinc finger protein 363 / CH-rich-interacting match with PLAG1 / Androgen receptor N-terminal-interacting protein / p53-induced RING-H2 protein / hPirh2 / RING finger protein 199


Mass: 9038.213 Da / Num. of mol.: 1 / Fragment: C-terminal domain: Residues 187-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RCHY1, ARNIP, CHIMP, PIRH2, RNF199, ZNF363 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96PM5
#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
1113D HNCO
1213D HNCA
1313D CBCA(CO)NH
1413D HBHA(CO)NH
1513D H(CCO)NH
1613D C(CO)NH
1723D (H)CCH-TOCSY
1823D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11113D 1H-13C-Aromatic NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 13C; U-99% 15N] C-terminal domain of human pirh2, 50 mM sodium phosphate, 150 mM potassium chloride, 10 uM ZnCl2, 0.8 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-99% 13C; U-99% 15N] C-terminal domain of human pirh2, 50 mM sodium phosphate, 150 mM potassium chloride, 10 uM ZnCl2, 0.8 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMC-terminal domain of human pirh2[U-99% 13C; U-99% 15N]1
50 mMsodium phosphate1
150 mMpotassium chloride1
10 uMZnCl21
0.8 mMDTT1
1 mMC-terminal domain of human pirh2[U-99% 13C; U-99% 15N]2
50 mMsodium phosphate2
150 mMpotassium chloride2
10 uMZnCl22
0.8 mMDTT2
Sample conditionsIonic strength: 150 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003
Varian INOVAVarianINOVA5004

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructureHuang, Tejero, Powers and Montelionevalidation
TALOSCornilescu, Delaglio and Baxdata analysis
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: 15

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