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- PDB-2jzx: PCBP2 KH1-KH2 domains -

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Basic information

Entry
Database: PDB / ID: 2jzx
TitlePCBP2 KH1-KH2 domains
ComponentsPoly(rC)-binding protein 2
KeywordsRNA BINDING PROTEIN / PCBP2 / KH domains / RNA binding / DNA-binding / Nucleus / Phosphoprotein / Ribonucleoprotein / RNA-binding
Function / homology
Function and homology information


C-rich single-stranded DNA binding / mRNA metabolic process / regulation of RNA metabolic process / negative regulation of defense response to virus / IRES-dependent viral translational initiation / negative regulation of cGAS/STING signaling pathway / Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / Negative regulators of DDX58/IFIH1 signaling / SARS-CoV-1 activates/modulates innate immune responses ...C-rich single-stranded DNA binding / mRNA metabolic process / regulation of RNA metabolic process / negative regulation of defense response to virus / IRES-dependent viral translational initiation / negative regulation of cGAS/STING signaling pathway / Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / Negative regulators of DDX58/IFIH1 signaling / SARS-CoV-1 activates/modulates innate immune responses / single-stranded DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of gene expression / defense response to virus / postsynaptic density / ribonucleoprotein complex / viral RNA genome replication / focal adhesion / innate immune response / mRNA binding / ubiquitin protein ligase binding / enzyme binding / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Poly(rC)-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDu, Z. / Fenn, S. / Tjhen, R. / James, T.
CitationJournal: To be Published
Title: Structure of the first and second KH domains of human poly-C binding protein-2 reveals insights into its regulatory mechanisms
Authors: Du, Z. / Fenn, S. / Tjhen, R. / James, T.
History
DepositionJan 21, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly(rC)-binding protein 2


Theoretical massNumber of molelcules
Total (without water)17,0581
Polymers17,0581
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)12 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Poly(rC)-binding protein 2 / Alpha-CP2 / hnRNP-E2


Mass: 17057.984 Da / Num. of mol.: 1 / Fragment: KH1-KH2 domains (UNP residues 11-169)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCBP2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15366

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CO)CA
1513D H(CCO)NH
1613D C(CO)NH
1713D 1H-15N NOESY
1813D 1H-13C NOESY

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Sample preparation

DetailsContents: 1 mM [U-100% 15N] PCBP2 KH1-KH2, 0.5 mM [U-100% 13C; U-100% 15N] DTT, 0.1 mM [U-100% 13C; U-100% 15N; 60% 2H] PMSF, 50 mM sodium acetate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPCBP2 KH1-KH2[U-100% 15N]1
0.5 mMDTT[U-100% 13C; U-100% 15N]1
0.1 mMPMSF[U-100% 13C; U-100% 15N; 60% 2H]1
50 mMsodium acetate1
Sample conditionsIonic strength: 100 / pH: 5.4 / Pressure: ambient atm / Temperature: 298 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
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle 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: 12

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