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- PDB-3ztg: Solution structure of the RING finger-like domain of Retinoblasto... -

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Basic information

Entry
Database: PDB / ID: 3ztg
TitleSolution structure of the RING finger-like domain of Retinoblastoma Binding Protein-6 (RBBP6)
ComponentsE3 UBIQUITIN-PROTEIN LIGASE RBBP6
KeywordsLIGASE / RBBP6 / PACT / U-BOX / MRNA PROCESSING / MRNA SPLICING
Function / homology
Function and homology information


somite development / RHOBTB1 GTPase cycle / regulation of DNA replication / embryonic organ development / RING-type E3 ubiquitin transferase / multicellular organism growth / mRNA processing / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation ...somite development / RHOBTB1 GTPase cycle / regulation of DNA replication / embryonic organ development / RING-type E3 ubiquitin transferase / multicellular organism growth / mRNA processing / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / chromosome / ubiquitin-dependent protein catabolic process / in utero embryonic development / DNA replication / nuclear speck / protein ubiquitination / DNA damage response / centrosome / protein kinase binding / nucleolus / protein-containing complex / RNA binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
Zinc knuckle CX2CX3GHX4C / E3 ubiquitin-protein ligase RBBP6 family / Zinc knuckle / DWNN domain / DWNN domain / DWNN domain profile. / DWNN / U-box domain / U-box domain / Zinc/RING finger domain, C3HC4 (zinc finger) ...Zinc knuckle CX2CX3GHX4C / E3 ubiquitin-protein ligase RBBP6 family / Zinc knuckle / DWNN domain / DWNN domain / DWNN domain profile. / DWNN / U-box domain / U-box domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / zinc finger / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBBP6
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / CYANA, HADDOCK
AuthorsKappo, M.A. / Ab, E. / Atkinson, R.A. / Faro, A. / Muleya, V. / Mulaudzi, T. / Poole, J.O. / McKenzie, J.M. / Pugh, D.J.R.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Solution Structure of the Ring Finger-Like Domain of Retinoblastoma Binding Protein-6 (Rbbp6) Suggests It Functions as a U-Box
Authors: Kappo, M.A. / Ab, E. / Hassem, F. / Atkinson, R.A. / Faro, A. / Muleya, V. / Mulaudzi, T. / Poole, J.O. / Mckenzie, J.M. / Chibi, M. / Moolman-Smook, J.C. / Rees, D.J.G. / Pugh, D.J.R.
History
DepositionJul 7, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Other
Revision 2.0Jun 14, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _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_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 2.1Jun 19, 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

Downloads & links

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Assembly

Deposited unit
A: E3 UBIQUITIN-PROTEIN LIGASE RBBP6
B: E3 UBIQUITIN-PROTEIN LIGASE RBBP6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7436
Polymers20,4812
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)32 / 400HADDOCK ENERGY, RAMACHANDRAN QUALITY
RepresentativeModel #1

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Components

#1: Protein E3 UBIQUITIN-PROTEIN LIGASE RBBP6 / RETINOBLASTOMA BINDING PROTEIN-6 / PROLIFERATION POTENTIAL-RELATED PROTEIN / PROTEIN P2P-R / ...RETINOBLASTOMA BINDING PROTEIN-6 / PROLIFERATION POTENTIAL-RELATED PROTEIN / PROTEIN P2P-R / RETINOBLASTOMA-BINDING Q PROTEIN 1 / RBQ-1 / RETINOBLASTOMA-BINDING PROTEIN 6 / P53-ASSOCIATED CELLULAR PROTEIN OF TESTIS


Mass: 10240.604 Da / Num. of mol.: 2 / Fragment: RING FINGER-LIKE DOMAIN, RESIDUES 249-335
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q7Z6E9, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 15N-HSQC-NOESY 13C-HSQC- NOESY
NMR detailsText: THE STRUCTURE WAS DTERMINED USING THE FOLLOWING NMR EXPERIMENTS 2D-NOESY 13C-NOESY 15N-NOESY

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Sample preparation

DetailsContents: 95% H2O, 5% D2O
Sample conditionsIonic strength: 150 mM / pH: 6 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS2.1BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
CYANAstructure solution
NMRViewstructure solution
RefinementMethod: CYANA, HADDOCK / Software ordinal: 1
NMR ensembleConformer selection criteria: HADDOCK ENERGY, RAMACHANDRAN QUALITY
Conformers calculated total number: 400 / Conformers submitted total number: 32

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