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- PDB-4imi: Novel Modifications on C-terminal Domain of RNA Polymerase II can... -

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Basic information

Entry
Database: PDB / ID: 4imi
TitleNovel Modifications on C-terminal Domain of RNA Polymerase II can Fine- tune the Phosphatase Activity of Ssu72.
Components
  • CG14216
  • CTD
  • Symplekin
KeywordsHYDROLASE / Ssu72 / symplekin / CTD / phosphorylated Thr4 / CTD phosphatase
Function / homology
Function and homology information


Processing of Intronless Pre-mRNAs / histone locus body / Processing of Capped Intron-Containing Pre-mRNA / mRNA 3'-end processing / tricellular tight junction / RNA Polymerase II Transcription Termination / RNA polymerase II transcribes snRNA genes / Transport of Mature mRNA Derived from an Intronless Transcript / RNA polymerase II CTD heptapeptide repeat phosphatase activity / mRNA 3'-end processing by stem-loop binding and cleavage ...Processing of Intronless Pre-mRNAs / histone locus body / Processing of Capped Intron-Containing Pre-mRNA / mRNA 3'-end processing / tricellular tight junction / RNA Polymerase II Transcription Termination / RNA polymerase II transcribes snRNA genes / Transport of Mature mRNA Derived from an Intronless Transcript / RNA polymerase II CTD heptapeptide repeat phosphatase activity / mRNA 3'-end processing by stem-loop binding and cleavage / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / myosin phosphatase activity / termination of RNA polymerase II transcription / protein-serine/threonine phosphatase / phosphatase activity / RNA binding / nucleus
Similarity search - Function
Helix Hairpins - #550 / RNA polymerase II subunit A / Ssu72-like protein / Symplekin/Pta1 / Symplekin C-terminal / Symplekin/Pta1, N-terminal / Symplekin/PTA1 N-terminal / Symplekin tight junction protein C terminal / Leucine-rich Repeat Variant / Helix Hairpins ...Helix Hairpins - #550 / RNA polymerase II subunit A / Ssu72-like protein / Symplekin/Pta1 / Symplekin C-terminal / Symplekin/Pta1, N-terminal / Symplekin/PTA1 N-terminal / Symplekin tight junction protein C terminal / Leucine-rich Repeat Variant / Helix Hairpins / Leucine-rich Repeat Variant / Response regulator / Helix non-globular / Special / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Symplekin / RNA polymerase II subunit A C-terminal domain phosphatase SSU72
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLuo, Y. / Yogesha, S.D. / Zhang, Y.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Novel Modifications on C-terminal Domain of RNA Polymerase II Can Fine-tune the Phosphatase Activity of Ssu72.
Authors: Luo, Y. / Yogesha, S.D. / Cannon, J.R. / Yan, W. / Ellington, A.D. / Brodbelt, J.S. / Zhang, Y.
History
DepositionJan 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Symplekin
B: CG14216
C: Symplekin
D: CG14216
F: CTD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,4856
Polymers123,3905
Non-polymers951
Water3,585199
1
A: Symplekin
B: CG14216
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7213
Polymers60,6262
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-14 kcal/mol
Surface area25450 Å2
MethodPISA
2
C: Symplekin
D: CG14216
F: CTD


Theoretical massNumber of molelcules
Total (without water)62,7653
Polymers62,7653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-20 kcal/mol
Surface area24120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.335, 128.335, 106.112
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein Symplekin / LD45768p


Mass: 37495.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Sym, CG2097, Dmel_CG2097 / Plasmid: pET28b derivative plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8MSU4
#2: Protein CG14216 / LD40846p


Mass: 23130.279 Da / Num. of mol.: 2 / Mutation: C13D, D144N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Ssu72, CG14216, Dmel_CG14216 / Plasmid: pET28b derivative plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9VWE4, protein-serine/threonine phosphatase
#3: Protein/peptide CTD


Mass: 2138.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in eukayotes / Source: (synth.) Synthetic (others)
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 3.54 Å3/Da / Density % sol: 65.26 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2012
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 71363 / Num. obs: 71330 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 58.02 Å2 / Rsym value: 0.077 / Net I/σ(I): 24.3
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.889 / Mean I/σ(I) obs: 1.4 / Num. unique all: 3531 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→49.03 Å / Cor.coef. Fo:Fc: 0.9377 / Cor.coef. Fo:Fc free: 0.9287 / SU R Cruickshank DPI: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 3611 5.06 %RANDOM
Rwork0.2191 ---
obs0.2201 71311 99.46 %-
Displacement parametersBiso mean: 69.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.8964 Å20 Å20 Å2
2--0.8964 Å20 Å2
3----1.7928 Å2
Refine analyzeLuzzati coordinate error obs: 0.368 Å
Refinement stepCycle: LAST / Resolution: 2.35→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8177 0 5 199 8381
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018292HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0211177HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4050SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes254HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1167HARMONIC5
X-RAY DIFFRACTIONt_it8292HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.66
X-RAY DIFFRACTIONt_other_torsion3.12
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1095SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9751SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2819 248 5.01 %
Rwork0.2369 4704 -
all0.2391 4952 -
obs--99.46 %

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