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- PDB-2x1a: Structure of Rna15 RRM with RNA bound (G) -

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Basic information

Entry
Database: PDB / ID: 2x1a
TitleStructure of Rna15 RRM with RNA bound (G)
Components
  • 5'-R(*GP*UP*UP*GP*UP)-3'
  • MRNA 3'-END-PROCESSING PROTEIN RNA15
KeywordsTRANSCRIPTION/RNA / TRANSCRIPTION-RNA COMPLEX / TRANSLATION / NUCLEUS / RNA-BINDING / MRNA PROCESSING
Function / homology
Function and homology information


mRNA cleavage stimulating factor complex / mRNA cleavage factor complex / mRNA cleavage and polyadenylation specificity factor complex / : / mRNA processing / molecular adaptor activity / mRNA binding
Similarity search - Function
Transcription termination and cleavage factor, C-terminal domain / Transcription termination and cleavage factor, C-terminal domain superfamily / Transcription termination and cleavage factor C-terminal / 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 ...Transcription termination and cleavage factor, C-terminal domain / Transcription termination and cleavage factor, C-terminal domain superfamily / Transcription termination and cleavage factor C-terminal / 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 / mRNA 3'-end-processing protein RNA15
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.05 Å
AuthorsPancevac, C. / Goldstone, D.C. / Ramos, A. / Taylor, I.A.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Structure of the RNA15 Rrm-RNA Complex Reveals the Molecular Basis of Gu Specificity in Transcriptional 3-End Processing Factors.
Authors: Pancevac, C. / Goldstone, D.C. / Ramos, A. / Taylor, I.A.
History
DepositionJan 6, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MRNA 3'-END-PROCESSING PROTEIN RNA15
B: 5'-R(*GP*UP*UP*GP*UP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3893
Polymers12,3652
Non-polymers241
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.037, 74.967, 31.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein MRNA 3'-END-PROCESSING PROTEIN RNA15 / RNA15 RRM


Mass: 10800.948 Da / Num. of mol.: 1 / Fragment: RNA RECOGNITION MODULE, RESIDUES 16-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P25299
#2: RNA chain 5'-R(*GP*UP*UP*GP*UP)-3'


Mass: 1563.952 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.77 Å3/Da / Density % sol: 30.55 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→25 Å / Num. obs: 5957 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 6.3 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.05→37.48 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.905 / SU B: 5.546 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.25807 265 4.5 %RANDOM
Rwork0.20615 ---
obs0.20837 5604 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.647 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å20 Å20 Å2
2---1.93 Å20 Å2
3---3.68 Å2
Refinement stepCycle: LAST / Resolution: 2.05→37.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms666 24 1 44 735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022704
X-RAY DIFFRACTIONr_bond_other_d0.0030.02477
X-RAY DIFFRACTIONr_angle_refined_deg1.1072.018954
X-RAY DIFFRACTIONr_angle_other_deg0.76731159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.177586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39623.87131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6315113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.341155
X-RAY DIFFRACTIONr_chiral_restr0.0640.2103
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021779
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02144
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4421.5429
X-RAY DIFFRACTIONr_mcbond_other0.0721.5178
X-RAY DIFFRACTIONr_mcangle_it0.8742686
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5763275
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8154.5268
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 18 -
Rwork0.316 392 -
obs--94.91 %

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