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- PDB-2n8m: Zipcode-binding-protein-1 KH3(DD)KH4 domains in complex with the ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2n8m | ||||||
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Title | Zipcode-binding-protein-1 KH3(DD)KH4 domains in complex with the KH4 RNA target | ||||||
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![]() | RNA Binding Protein/RNA / KH Domain / RNA Binding Protein-RNA complex | ||||||
Function / homology | ![]() CRD-mediated mRNA stability complex / CRD-mediated mRNA stabilization / N6-methyladenosine-containing RNA reader activity / mRNA transport / filopodium / mRNA 3'-UTR binding / P-body / positive regulation of neuron projection development / cytoplasmic stress granule / lamellipodium ...CRD-mediated mRNA stability complex / CRD-mediated mRNA stabilization / N6-methyladenosine-containing RNA reader activity / mRNA transport / filopodium / mRNA 3'-UTR binding / P-body / positive regulation of neuron projection development / cytoplasmic stress granule / lamellipodium / nervous system development / growth cone / regulation of gene expression / negative regulation of translation / mRNA binding / perinuclear region of cytoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
![]() | Nicastro, G. / Ramos, A. / Candel, A. / Hollingworth, D. | ||||||
![]() | ![]() Title: Zipcode-binding-protein-1 KH3(DD)KH4 domains in complex with the RNA target UCGGACU Authors: Nicastro, G. / Ramos, A. / Candel, A. / Hollingworth, D. #1: Journal: Nucleic Acids Res. / Year: 2012 Title: KH domains with impaired nucleic acid binding as a tool for functional analysis. Authors: Hollingworth, D. / Candel, A.M. / Nicastro, G. / Martin, S.R. / Briata, P. / Gherzi, R. / Ramos, A. #2: ![]() Title: ZBP1 recognition of beta-actin zipcode induces RNA looping. Authors: Chao, J.A. / Patskovsky, Y. / Patel, V. / Levy, M. / Almo, S.C. / Singer, R.H. #3: Journal: Genes Dev. / Year: 2012 Title: Spatial arrangement of an RNA zipcode identifies mRNAs under post-transcriptional control. Authors: Patel, V.L. / Mitra, S. / Harris, R. / Buxbaum, A.R. / Lionnet, T. / Brenowitz, M. / Girvin, M. / Levy, M. / Almo, S.C. / Singer, R.H. / Chao, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 740.2 KB | Display | ![]() |
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PDB format | ![]() | 617.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 503.4 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 127.6 KB | Display | |
Data in CIF | ![]() | 115 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 20613.498 Da / Num. of mol.: 1 / Fragment: KH domain (UNP residues 387-573) / Mutation: Y14F, K40D, K41D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: RNA chain | Mass: 2197.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 0.3 mM [U-100% 13C; U-100% 15N] protein, 95% H2O/5% D2O Solvent system: 95% H2O/5% D2O |
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Sample | Conc.: 0.3 mM / Component: protein-1 / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Ionic strength: 0.02 / pH: 6.5 / Pressure: ambient / Temperature: 310 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 12 |