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- PDB-2c7h: Solution NMR structure of the DWNN domain from human RBBP6 -

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Basic information

Entry
Database: PDB / ID: 2c7h
TitleSolution NMR structure of the DWNN domain from human RBBP6
ComponentsRETINOBLASTOMA-BINDING PROTEIN 6, ISOFORM 3
KeywordsUBIQUITIN-LIKE PROTEIN / RBBP6 / P53-ASSOCIATED / MRNA PROCESSING / SPLICING-ASSOCIATED / OESOPHAGEAL CANCER
Function / homology
Function and homology information


somite development / RHOBTB1 GTPase cycle / microtubule organizing center / regulation of DNA replication / embryonic organ development / multicellular organism growth / RING-type E3 ubiquitin transferase / mRNA processing / protein polyubiquitination / ubiquitin-protein transferase activity ...somite development / RHOBTB1 GTPase cycle / microtubule organizing center / regulation of DNA replication / embryonic organ development / multicellular organism growth / RING-type E3 ubiquitin transferase / mRNA processing / protein polyubiquitination / 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 / protein ubiquitination / nuclear speck / centrosome / DNA damage response / nucleolus / protein kinase binding / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin-like (UB roll) / zinc finger / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBBP6 / E3 ubiquitin-protein ligase RBBP6
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / AUTOMATED NOE ASSIGNMENT USING CANDID
AuthorsPugh, D.J.R. / Ab, E. / Faro, A. / Lutya, P.T. / Hoffmann, E. / Rees, D.J.G.
CitationJournal: Bmc Struct.Biol. / Year: 2006
Title: Dwnn, a Novel Ubiquitin-Like Domain, Implicates Rbbp6 in Mrna Processing and Ubiquitin-Like Pathways
Authors: Pugh, D.J.R. / Ab, E. / Faro, A. / Lutya, P.T. / Hoffmann, E. / Rees, D.J.G.
History
DepositionNov 24, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RETINOBLASTOMA-BINDING PROTEIN 6, ISOFORM 3


Theoretical massNumber of molelcules
Total (without water)9,5441
Polymers9,5441
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100LOWEST ENERGY
RepresentativeModel #18

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Components

#1: Protein RETINOBLASTOMA-BINDING PROTEIN 6, ISOFORM 3 / RBBP6


Mass: 9544.000 Da / Num. of mol.: 1 / Fragment: DWNN, RESIDUES 1-81
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL 5 RESIDUES ARE ARTIFACTS OF THE PGEX-6P-2 CLONING VECTOR
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): (DE3) PLYSS / References: UniProt: Q8N0V2, UniProt: Q7Z6E9*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCO
121CBCA(CO)NH
131CBCANH
141(H)CCH-TOCSY
151(H)CCH-COSY
161HNH- HSQC-TOCSY
171HNH-HSQC-NOESY
181HCH-HSQC-NOESY
191HH-NOESY
1101HMQC-J
1111HN-EXCHANGE
1121HH- NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON A 15N,13C-LABELLED SAMPLE.

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Sample preparation

DetailsContents: 95% WATER/5% D2O
Sample conditionsIonic strength: 150 mM / pH: 6.0 / 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
CNS1.1BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
NMRViewstructure solution
CANDIDstructure solution
CYANAstructure solution
CNSstructure solution
RECOORDstructure solution
RefinementMethod: AUTOMATED NOE ASSIGNMENT USING CANDID / Software ordinal: 1
Details: THE FINAL SET OF NOE-BASED RESTRAINTS, TOGETHER WITH DIHEDRAL RESTRAINTS FOR 90 RESIDUES, WERE USED FOR REFINEMENT IN EXPLICIT SOLVENT USING CNS, ACCORDING TO THE STANDARD RECOORD PROTOCOL.
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 25

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