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- PDB-2jwo: A PHD finger motif in the C-terminus of RAG2 modulates recombinat... -

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Basic information

Entry
Database: PDB / ID: 2jwo
TitleA PHD finger motif in the C-terminus of RAG2 modulates recombination activity
ComponentsV(D)J recombination-activating protein 2
KeywordsRECOMBINATION / V(D)J recombination / phosphoinositide signaling / RAG2 / PHD domain / DNA recombination / DNA-binding / Endonuclease / Hydrolase / Nuclease / Nucleus
Function / homology
Function and homology information


mature B cell differentiation involved in immune response / DNA recombinase complex / B cell homeostatic proliferation / negative regulation of T cell differentiation in thymus / DN2 thymocyte differentiation / pre-B cell allelic exclusion / positive regulation of organ growth / V(D)J recombination / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,5-bisphosphate binding ...mature B cell differentiation involved in immune response / DNA recombinase complex / B cell homeostatic proliferation / negative regulation of T cell differentiation in thymus / DN2 thymocyte differentiation / pre-B cell allelic exclusion / positive regulation of organ growth / V(D)J recombination / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,5-bisphosphate binding / organ growth / T cell lineage commitment / B cell lineage commitment / phosphatidylinositol-3,4,5-trisphosphate binding / T cell differentiation / phosphatidylinositol-4,5-bisphosphate binding / methylated histone binding / B cell differentiation / phosphatidylinositol binding / ubiquitin protein ligase activity / chromatin organization / T cell differentiation in thymus / DNA recombination / sequence-specific DNA binding / defense response to bacterium / chromatin binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Rag2 PHD finger / Recombination activating protein 2 / RAG2 PHD domain / V-D-J recombination activating protein 2 / Recombination activating protein 2, PHD domain / Galactose oxidase/kelch, beta-propeller / Kelch-type beta propeller / Double Stranded RNA Binding Domain / Zinc finger, FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
V(D)J recombination-activating protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsIvanov, D. / Hyberts, S.G. / Sun, Z. / Wagner, G.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: A PHD finger motif in the C terminus of RAG2 modulates recombination activity.
Authors: Elkin, S.K. / Ivanov, D. / Ewalt, M. / Ferguson, C.G. / Hyberts, S.G. / Sun, Z.Y. / Prestwich, G.D. / Yuan, J. / Wagner, G. / Oettinger, M.A. / Gozani, O.P.
History
DepositionOct 17, 2007Deposition site: BMRB / Processing site: RCSB
SupersessionNov 6, 2007ID: 2A23
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: V(D)J recombination-activating protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4913
Polymers9,3601
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 V(D)J recombination-activating protein 2 / RAG-2


Mass: 9360.498 Da / Num. of mol.: 1 / Fragment: PHD finger motif: Residues 414-487
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rag2, Rag-2 / Plasmid: pGEX-6P-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P21784
#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
1213D HNCA
1313D HN(CO)CA
1413D HN(CA)CB
1513D HNCO
1613D 1H-13C NOESY
1713D 1H-13C NOESY
1813D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 0.5 mM [U-99% 13C; U-99% 15N] RAG2 PHD domain, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: RAG2 PHD domain / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
DYANAGuntert, Braun and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
XEASYBartels et al.data analysis
RefinementMethod: simulated annealing / 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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