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- PDB-3zzz: Crystal structure of a Raver1 PRI4 peptide in complex with polypy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zzz | ||||||
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Title | Crystal structure of a Raver1 PRI4 peptide in complex with polypyrimidine tract binding protein RRM2 | ||||||
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![]() | PROTEIN BINDING / PEPTIDE BINDING / RNA RECOGNITION MOTIF | ||||||
Function / homology | ![]() negative regulation of muscle cell differentiation / poly-pyrimidine tract binding / IRES-dependent viral translational initiation / positive regulation of calcineurin-NFAT signaling cascade / pre-mRNA binding / negative regulation of RNA splicing / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / regulation of cell differentiation / regulation of RNA splicing ...negative regulation of muscle cell differentiation / poly-pyrimidine tract binding / IRES-dependent viral translational initiation / positive regulation of calcineurin-NFAT signaling cascade / pre-mRNA binding / negative regulation of RNA splicing / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / regulation of cell differentiation / regulation of RNA splicing / negative regulation of mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / : / mRNA Splicing - Major Pathway / RNA splicing / mRNA processing / mRNA binding / nucleolus / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joshi, A. / Kotik-Kogan, O. / Curry, S. | ||||||
![]() | ![]() Title: Crystallographic Analysis of Polypyrimidine Tract-Binding Protein-Raver1 Interactions Involved in Regulation of Alternative Splicing. Authors: Joshi, A. / Coelho, M.B. / Kotik-Kogan, O. / Simpson, P.J. / Matthews, S.J. / Smith, C.W. / Curry, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.9 KB | Display | ![]() |
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PDB format | ![]() | 43.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3zzySC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.1983, 0.03711, 0.9794), Vector: |
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Components
#1: Protein | Mass: 14169.072 Da / Num. of mol.: 2 / Fragment: RNA RECOGNITION MOTIF 2, RESIDUES 156-285 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1399.572 Da / Num. of mol.: 2 / Fragment: MOTIF PRI4, RESIDUES 680-692 Source method: isolated from a genetically manipulated source Details: THIS FRAGMENT IS ACTUALLY FUSED TO THE N-TERMINUS OF MOLECULE 1, SEE REMARK 999 Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-IOD / #4: Water | ChemComp-HOH / | Sequence details | FIRST 3 RESIDUES (GAM) ARE VECTOR DERIVED. RESIDUES 4 - 16 CORRESPOND TO RESIDUES 680-692 OF RAVER1 ...FIRST 3 RESIDUES (GAM) ARE VECTOR DERIVED. RESIDUES 4 - 16 CORRESPOND | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.94 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: SEE PAPER., pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2009 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→35.49 Å / Num. obs: 36184 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ZZY Resolution: 1.55→20.07 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1123728.72 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF Details: BULK SOLVENT MODEL USED. THE CRYSTALLISED PROTEIN HAS A RAVER1 PEPTIDE GENETICALLY FUSED AS AN N-TERMINAL EXTENSION OF PTB RRM3. OWING TO LINKER DISORDER WE CANNOT DETERMINE WHICH RRM DOMAIN ...Details: BULK SOLVENT MODEL USED. THE CRYSTALLISED PROTEIN HAS A RAVER1 PEPTIDE GENETICALLY FUSED AS AN N-TERMINAL EXTENSION OF PTB RRM3. OWING TO LINKER DISORDER WE CANNOT DETERMINE WHICH RRM DOMAIN (CHAINS A, B) IS COVALENTLY LINKED TO WHICH RAVER1 PEPTIDE (CHAINS C,D).
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.8846 Å2 / ksol: 0.5 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→20.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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