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- PDB-3nnc: Crystal Structure of CUGBP1 RRM1/2-RNA Complex -

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Basic information

Entry
Database: PDB / ID: 3nnc
TitleCrystal Structure of CUGBP1 RRM1/2-RNA Complex
Components
  • CUGBP Elav-like family member 1
  • RNA (5'-R(*UP*GP*UP*GP*UP*GP*UP*UP*GP*UP*GP*UP*G)-3')
KeywordsRNA BINDING PROTEIN/RNA / RRM / pre-mRNA splicing / RNA / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


BRE binding / perinucleolar compartment / post-transcriptional gene silencing / regulatory ncRNA-mediated post-transcriptional gene silencing / mRNA splice site recognition / pre-mRNA binding / embryo development ending in birth or egg hatching / regulation of alternative mRNA splicing, via spliceosome / mRNA destabilization / regulation of RNA splicing ...BRE binding / perinucleolar compartment / post-transcriptional gene silencing / regulatory ncRNA-mediated post-transcriptional gene silencing / mRNA splice site recognition / pre-mRNA binding / embryo development ending in birth or egg hatching / regulation of alternative mRNA splicing, via spliceosome / mRNA destabilization / regulation of RNA splicing / germ cell development / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / mRNA processing / cytoplasmic stress granule / regulation of inflammatory response / ribonucleoprotein complex / negative regulation of cell population proliferation / negative regulation of gene expression / mRNA binding / positive regulation of gene expression / RNA binding / nucleoplasm / membrane / nucleus / cytoplasm
Similarity search - Function
CELF1/2, RNA recognition motif 2 / CELF1/2, RNA recognition motif 3 / CELF1/2, RNA recognition motif 1 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily ...CELF1/2, RNA recognition motif 2 / CELF1/2, RNA recognition motif 3 / CELF1/2, RNA recognition motif 1 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / CUGBP Elav-like family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2005 Å
AuthorsTeplova, M. / Song, J. / Gaw, H. / Teplov, A. / Patel, D.J.
CitationJournal: Structure / Year: 2010
Title: Structural Insights into RNA Recognition by the Alternate-Splicing Regulator CUG-Binding Protein 1.
Authors: Teplova, M. / Song, J. / Gaw, H.Y. / Teplov, A. / Patel, D.J.
History
DepositionJun 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 8, 2014Group: Structure summary
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CUGBP Elav-like family member 1
B: RNA (5'-R(*UP*GP*UP*GP*UP*GP*UP*UP*GP*UP*GP*UP*G)-3')


Theoretical massNumber of molelcules
Total (without water)23,9272
Polymers23,9272
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-10 kcal/mol
Surface area11440 Å2
MethodPISA
2
A: CUGBP Elav-like family member 1
B: RNA (5'-R(*UP*GP*UP*GP*UP*GP*UP*UP*GP*UP*GP*UP*G)-3')

A: CUGBP Elav-like family member 1
B: RNA (5'-R(*UP*GP*UP*GP*UP*GP*UP*UP*GP*UP*GP*UP*G)-3')

A: CUGBP Elav-like family member 1
B: RNA (5'-R(*UP*GP*UP*GP*UP*GP*UP*UP*GP*UP*GP*UP*G)-3')

A: CUGBP Elav-like family member 1
B: RNA (5'-R(*UP*GP*UP*GP*UP*GP*UP*UP*GP*UP*GP*UP*G)-3')


Theoretical massNumber of molelcules
Total (without water)95,7098
Polymers95,7098
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area14910 Å2
ΔGint-56 kcal/mol
Surface area35420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.713, 70.039, 132.548
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-8-

HOH

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Components

#1: Protein CUGBP Elav-like family member 1 / CELF-1 / CUG-BP- and ETR-3-like factor 1 / Bruno-like protein 2 / RNA-binding protein BRUNOL-2 / ...CELF-1 / CUG-BP- and ETR-3-like factor 1 / Bruno-like protein 2 / RNA-binding protein BRUNOL-2 / CUG triplet repeat RNA-binding protein 1 / CUG-BP1 / Deadenylation factor CUG-BP / 50 kDa nuclear polyadenylated RNA-binding protein / Embryo deadenylation element-binding protein homolog / EDEN-BP homolog


Mass: 19757.828 Da / Num. of mol.: 1 / Fragment: RRM1-RRM2 domain (UNP Residues 14-187)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRUNOL2, CELF1, CUGBP, CUGBP1, CUGPB1, NAB50 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q92879
#2: RNA chain RNA (5'-R(*UP*GP*UP*GP*UP*GP*UP*UP*GP*UP*GP*UP*G)-3')


Mass: 4169.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M ammonium acetate, 45% MPD, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 11418 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 11.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 3 / Num. unique all: 1083 / % possible all: 95.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NMR

3nmr


Resolution: 2.2005→39.432 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 24.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2555 539 4.73 %RANDOM
Rwork0.195 ---
obs0.1979 11390 97.7 %-
all-11418 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.731 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4571 Å2-0 Å20 Å2
2---3.188 Å20 Å2
3---4.645 Å2
Refinement stepCycle: LAST / Resolution: 2.2005→39.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 130 0 63 1568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091546
X-RAY DIFFRACTIONf_angle_d1.0712107
X-RAY DIFFRACTIONf_dihedral_angle_d17.25608
X-RAY DIFFRACTIONf_chiral_restr0.072234
X-RAY DIFFRACTIONf_plane_restr0.005253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2005-2.42190.28931210.20812594X-RAY DIFFRACTION95
2.4219-2.77230.31211550.21862699X-RAY DIFFRACTION99
2.7723-3.49240.27381410.19462731X-RAY DIFFRACTION99
3.4924-39.43880.21631220.18462827X-RAY DIFFRACTION97

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