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- PDB-2l33: Solution NMR Structure of DRBM 2 domain of Interleukin enhancer-b... -

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Basic information

Entry
Database: PDB / ID: 2l33
TitleSolution NMR Structure of DRBM 2 domain of Interleukin enhancer-binding factor 3 from Homo sapiens, Northeast Structural Genomics Consortium Target HR4527E
ComponentsInterleukin enhancer-binding factor 3
KeywordsTranscription regulator / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative / DRBM / dsRNA-binding / ILF3 / NF90
Function / homology
Function and homology information


spliceosome-depend formation of circular RNA / Regulation of CDH11 gene transcription / mRNA 3'-UTR AU-rich region binding / negative regulation of viral genome replication / PKR-mediated signaling / double-stranded RNA binding / virus receptor activity / defense response to virus / negative regulation of translation / single-stranded RNA binding ...spliceosome-depend formation of circular RNA / Regulation of CDH11 gene transcription / mRNA 3'-UTR AU-rich region binding / negative regulation of viral genome replication / PKR-mediated signaling / double-stranded RNA binding / virus receptor activity / defense response to virus / negative regulation of translation / single-stranded RNA binding / ribonucleoprotein complex / protein phosphorylation / negative regulation of DNA-templated transcription / nucleolus / positive regulation of DNA-templated transcription / mitochondrion / DNA binding / RNA binding / extracellular region / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Interleukin enhancer-binding factor 3 / DZF domain / : / : / DZF N-terminal domain / DZF C-terminal domain / DZF domain profile. / domain in DSRM or ZnF_C2H2 domain containing proteins / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif ...Interleukin enhancer-binding factor 3 / DZF domain / : / : / DZF N-terminal domain / DZF C-terminal domain / DZF domain profile. / domain in DSRM or ZnF_C2H2 domain containing proteins / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Interleukin enhancer-binding factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, molecular dynamics, torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsLiu, G. / Janjua, H. / Xiao, R. / Acton, T.B. / Ciccosanti, A. / Shastry, R.B. / Everett, J. / Montelione, G.T. / Northeast Structural Genomics Consortium / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target HR4527E
Authors: Liu, G. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J. / Montelione, G.T.
History
DepositionSep 3, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status / struct_ref
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4May 15, 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:
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Assembly

Deposited unit
A: Interleukin enhancer-binding factor 3


Theoretical massNumber of molelcules
Total (without water)10,1901
Polymers10,1901
Non-polymers00
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Interleukin enhancer-binding factor 3 / Nuclear factor of activated T-cells 90 kDa / NF-AT-90 / Double-stranded RNA-binding protein 76 / ...Nuclear factor of activated T-cells 90 kDa / NF-AT-90 / Double-stranded RNA-binding protein 76 / DRBP76 / Translational control protein 80 / TCP80 / Nuclear factor associated with dsRNA / NFAR / M-phase phosphoprotein 4 / MPP4


Mass: 10189.675 Da / Num. of mol.: 1 / Fragment: DRBM 2 domain residues 521-600
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ILF3, DRBF, MPHOSPH4, NF90 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q12906

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: double-stranded RNA-binding domains DRBM2
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D 1H-13C arom NOESY
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-100% 13C; U-100% 15N] HR4527E, 95% H2O/5% D2O95% H2O/5% D2O
20.7 mM [U-5% 13C; U-100% 15N] HR4527E, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMHR4527E-1[U-100% 13C; U-100% 15N]1
0.7 mMHR4527E-2[U-5% 13C; U-100% 15N]2
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis,peak picking,chemical shift assignment
TopSpinBruker Biospincollection
VnmrJVariancollection
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: distance geometry, molecular dynamics, torsion angle dynamics, simulated annealing
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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