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- PDB-3nnh: Crystal Structure of the CUGBP1 RRM1 with GUUGUUUUGUUU RNA -

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Basic information

Entry
Database: PDB / ID: 3nnh
TitleCrystal Structure of the CUGBP1 RRM1 with GUUGUUUUGUUU RNA
Components
  • CUGBP Elav-like family member 1
  • RNA (5'-R(*GP*UP*UP*GP*UP*UP*UP*UP*GP*UP*UP*U)-3')
KeywordsRNA BINDING PROTEIN/RNA / RNA recognition motif / 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: 2.7501 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
C: CUGBP Elav-like family member 1
E: RNA (5'-R(*GP*UP*UP*GP*UP*UP*UP*UP*GP*UP*UP*U)-3')
B: CUGBP Elav-like family member 1
D: CUGBP Elav-like family member 1
F: RNA (5'-R(*GP*UP*UP*GP*UP*UP*UP*UP*GP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)47,9316
Polymers47,9316
Non-polymers00
Water52229
1
A: CUGBP Elav-like family member 1
C: CUGBP Elav-like family member 1
E: RNA (5'-R(*GP*UP*UP*GP*UP*UP*UP*UP*GP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)23,9653
Polymers23,9653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-20 kcal/mol
Surface area11030 Å2
MethodPISA
2
B: CUGBP Elav-like family member 1
D: CUGBP Elav-like family member 1
F: RNA (5'-R(*GP*UP*UP*GP*UP*UP*UP*UP*GP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)23,9653
Polymers23,9653
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-20 kcal/mol
Surface area11740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.180, 62.074, 122.052
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 10109.561 Da / Num. of mol.: 4 / Fragment: RRM1 domain (UNP residues 14-100)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRUNOL2, CELF1, CUGBP, CUGBP1, NAB50 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q92879
#2: RNA chain RNA (5'-R(*GP*UP*UP*GP*UP*UP*UP*UP*GP*UP*UP*U)-3')


Mass: 3746.152 Da / Num. of mol.: 2 / 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.: 29 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M potassium sodium tartrate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: Dec 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.75→40 Å / Num. all: 12400 / Num. obs: 12357 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 13.1
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1213 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NMR

3nmr


Resolution: 2.7501→19.596 Å / SU ML: 0.32 / σ(F): 0.27 / Phase error: 22.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2628 1155 9.81 %RANDOM
Rwork0.1832 ---
all0.1909 12357 --
obs0.1909 11775 96.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 17.165 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.5135 Å20 Å20 Å2
2--0.5822 Å2-0 Å2
3---0.9286 Å2
Refinement stepCycle: LAST / Resolution: 2.7501→19.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2771 419 0 29 3219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073298
X-RAY DIFFRACTIONf_angle_d1.0314544
X-RAY DIFFRACTIONf_dihedral_angle_d20.7511270
X-RAY DIFFRACTIONf_chiral_restr0.062501
X-RAY DIFFRACTIONf_plane_restr0.004525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7501-2.87490.29651440.20321233X-RAY DIFFRACTION92
2.8749-3.0260.34081460.20251239X-RAY DIFFRACTION93
3.026-3.21480.26511370.19411279X-RAY DIFFRACTION95
3.2148-3.46170.2561360.17931357X-RAY DIFFRACTION97
3.4617-3.80780.27441400.16771327X-RAY DIFFRACTION98
3.8078-4.35350.24281350.15761364X-RAY DIFFRACTION99
4.3535-5.46520.20681630.15531376X-RAY DIFFRACTION99
5.4652-19.59610.2771540.20041445X-RAY DIFFRACTION98

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