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- PDB-4eba: Crystal structure of the Rna14-Rna15 complex -

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Basic information

Entry
Database: PDB / ID: 4eba
TitleCrystal structure of the Rna14-Rna15 complex
Components
  • Rna15
  • mRNA 3'-end-processing protein RNA14
KeywordsSTRUCTURAL PROTEIN/RNA BINDING PROTEIN / HAT domain / HEAT repeat / monkeytail / Clp1 / Pcf11 / STRUCTURAL PROTEIN-RNA BINDING PROTEIN complex
Function / homology
Function and homology information


mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / mRNA binding / protein-containing complex / nucleus / cytoplasm
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #630 / Cleavage stimulation factor subunit 2, hinge domain / Hinge domain of cleavage stimulation factor subunit 2 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1040 / Transcription termination and cleavage factor, C-terminal domain / Transcription termination and cleavage factor, C-terminal domain superfamily / mRNA 3'-end-processing protein Rna14-like / Transcription termination and cleavage factor C-terminal / Suppressor of forked / Suppressor of forked protein (Suf) ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #630 / Cleavage stimulation factor subunit 2, hinge domain / Hinge domain of cleavage stimulation factor subunit 2 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1040 / Transcription termination and cleavage factor, C-terminal domain / Transcription termination and cleavage factor, C-terminal domain superfamily / mRNA 3'-end-processing protein Rna14-like / Transcription termination and cleavage factor C-terminal / Suppressor of forked / Suppressor of forked protein (Suf) / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Alpha
Similarity search - Domain/homology
mRNA 3'-end-processing protein RNA14 / KLLA0F09383p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsPaulson, A.R. / Tong, L.
CitationJournal: Rna / Year: 2012
Title: Crystal structure of the Rna14-Rna15 complex.
Authors: Paulson, A.R. / Tong, L.
History
DepositionMar 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references
Revision 1.2Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: mRNA 3'-end-processing protein RNA14
B: mRNA 3'-end-processing protein RNA14
C: mRNA 3'-end-processing protein RNA14
D: mRNA 3'-end-processing protein RNA14
E: mRNA 3'-end-processing protein RNA14
F: mRNA 3'-end-processing protein RNA14
G: Rna15
I: Rna15
H: Rna15


Theoretical massNumber of molelcules
Total (without water)515,6179
Polymers515,6179
Non-polymers00
Water00
1
A: mRNA 3'-end-processing protein RNA14
B: mRNA 3'-end-processing protein RNA14
G: Rna15


Theoretical massNumber of molelcules
Total (without water)171,8723
Polymers171,8723
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10230 Å2
ΔGint-66 kcal/mol
Surface area56550 Å2
MethodPISA
2
C: mRNA 3'-end-processing protein RNA14
D: mRNA 3'-end-processing protein RNA14
H: Rna15


Theoretical massNumber of molelcules
Total (without water)171,8723
Polymers171,8723
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9960 Å2
ΔGint-60 kcal/mol
Surface area57090 Å2
MethodPISA
3
E: mRNA 3'-end-processing protein RNA14
F: mRNA 3'-end-processing protein RNA14
I: Rna15


Theoretical massNumber of molelcules
Total (without water)171,8723
Polymers171,8723
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10150 Å2
ΔGint-56 kcal/mol
Surface area57050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.040, 162.040, 177.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsThe trimers are formed by two Rna14 and one Rna15.

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Components

#1: Protein
mRNA 3'-end-processing protein RNA14


Mass: 76161.523 Da / Num. of mol.: 6 / Fragment: UNP residues 18-661
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: RNA14, KLLA0F26290g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CII8
#2: Protein Rna15 / KLLA0F09383p


Mass: 19549.305 Da / Num. of mol.: 3 / Fragment: UNP residues 105-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0F09383g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CKN2

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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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM HEPES 7.0, 1% tryptone, 13% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2011 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 79000 / Num. obs: 71640 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.7 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.9049
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 1.242 / % possible all: 71.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
COMOphasing
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E85

4e85


Resolution: 3.3→47.79 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 371325.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.298 3446 5.1 %RANDOM
Rwork0.226 ---
obs0.226 67757 86.4 %-
all-79000 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.2895 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 100.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.94 Å20 Å20 Å2
2--4.94 Å20 Å2
3----9.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.86 Å0.8 Å
Refinement stepCycle: LAST / Resolution: 3.3→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30268 0 0 0 30268
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.3→3.42 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.425 246 5.2 %
Rwork0.393 4459 -
obs--59.9 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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