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- PDB-1sza: The RNA polymerase II CTD in mRNA processing: beta-turn recogniti... -

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Basic information

Entry
Database: PDB / ID: 1sza
TitleThe RNA polymerase II CTD in mRNA processing: beta-turn recognition and beta-spiral model
Components
  • CTD-peptide
  • PCF11 protein
KeywordsTRANSCRIPTION / Pcf11 / RNA polymerase II CTD interacting domain / arm repeats / phosphoserine
Function / homology
Function and homology information


termination of RNA polymerase II transcription, poly(A)-coupled / termination of RNA polymerase II transcription, exosome-dependent / mRNA cleavage factor complex / mRNA 3'-end processing / termination of RNA polymerase II transcription / RNA polymerase II complex binding / mRNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Pfc11 Rna14/15 interacting domain / Subunit of cleavage factor IA Pcf11, C-terminal / Protein PCF11-like / : / : / Pcf11, Clp1-interaction domain / Pcf11, C-terminal domain / CID domain / RPR ...: / Pfc11 Rna14/15 interacting domain / Subunit of cleavage factor IA Pcf11, C-terminal / Protein PCF11-like / : / : / Pcf11, Clp1-interaction domain / Pcf11, C-terminal domain / CID domain / RPR / CID domain / CID domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMeinhart, A. / Cramer, P.
CitationJournal: Nature / Year: 2004
Title: Recognition of RNA polymerase II carboxy-terminal domain by 3'-RNA-processing factors.
Authors: Meinhart, A. / Cramer, P.
History
DepositionApr 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: PCF11 protein
B: PCF11 protein
C: PCF11 protein
Z: CTD-peptide


Theoretical massNumber of molelcules
Total (without water)51,4104
Polymers51,4104
Non-polymers00
Water2,612145
1
A: PCF11 protein


Theoretical massNumber of molelcules
Total (without water)16,6241
Polymers16,6241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PCF11 protein
Z: CTD-peptide


Theoretical massNumber of molelcules
Total (without water)18,1622
Polymers18,1622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-2 kcal/mol
Surface area8110 Å2
MethodPISA
3
C: PCF11 protein


Theoretical massNumber of molelcules
Total (without water)16,6241
Polymers16,6241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.620, 67.000, 135.000
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 PCF11 protein


Mass: 16624.145 Da / Num. of mol.: 3 / Fragment: CTD interacting domain of Pcf11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PCF11, YDR228C, YD9934.13C / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)-RIL / References: UniProt: P39081
#2: Protein/peptide CTD-peptide


Mass: 1537.475 Da / Num. of mol.: 1 / Fragment: CTD repeat derived peptide / Source method: obtained synthetically
Details: Peptide derived from the conserved repeat sequence in RNA polymerase II CTD.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 25 % (v/v) ethylene glycol, 5 % (v/v) PEG 550, pH 7.5, VAPOR DIFFUSION, HANGING DROP; native crystals were soaked with synthetic peptide, temperature 298K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9782
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 25002 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.5
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 7.3 / % possible all: 98.6

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Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
AMoREphasing
CNSrefinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→20 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1265 4.6 %RANDOM
Rwork0.211 ---
obs0.211 25002 99.4 %-
all-27237 --
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3508 0 0 145 3653
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.104
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.408
X-RAY DIFFRACTIONc_mcangle_it2.196
X-RAY DIFFRACTIONc_scbond_it2.301
X-RAY DIFFRACTIONc_scangle_it3.294
LS refinement shellResolution: 2.2→2.23 Å / Total num. of bins used: 25 /
RfactorNum. reflection
Rfree0.289 42
Rwork0.216 1037

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