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

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Basic information

Entry
Database: PDB / ID: 4imj
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 / 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 transcribes snRNA genes / RNA Polymerase II Transcription Termination / 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 transcribes snRNA genes / RNA Polymerase II Transcription Termination / 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 / 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: 2.58 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 23, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)123,4056
Polymers123,3105
Non-polymers951
Water3,729207
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 area2580 Å2
ΔGint-14 kcal/mol
Surface area25410 Å2
MethodPISA
2
C: Symplekin
D: CG14216
F: CTD


Theoretical massNumber of molelcules
Total (without water)62,6853
Polymers62,6853
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-18 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.992, 127.992, 105.775
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: 2058.997 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in eukaryotes. / Source: (synth.) Synthetic (others)
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 207 / 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: 3.51 Å3/Da / Density % sol: 64.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Optimized Ssu72-symplekin crystals were obtained with reservoir solution consisting of 12% PEG3350 (w/v) and 100 mM HEPE pH 8.5. To obtain the tertiary complex structure of Drosophila Ssu72- ...Details: Optimized Ssu72-symplekin crystals were obtained with reservoir solution consisting of 12% PEG3350 (w/v) and 100 mM HEPE pH 8.5. To obtain the tertiary complex structure of Drosophila Ssu72-symplekin-CTD(phos.Ser5), crystals of Ssu72-symplekin were soaked in a mother solution containing 2 mM 19mer CTD(phos.Ser5) peptides overnight at room temperature , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2012
RadiationMonochromator: Asymmetric cut single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / Num. all: 53994 / Num. obs: 53955 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 65.87 Å2 / Rsym value: 0.096 / Net I/σ(I): 24.2
Reflection shellResolution: 2.58→2.62 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 2 / Num. unique all: 2693 / % 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: 2.58→37.77 Å / Cor.coef. Fo:Fc: 0.9354 / Cor.coef. Fo:Fc free: 0.9213 / SU R Cruickshank DPI: 0.349 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2437 2731 5.08 %RANDOM
Rwork0.2107 ---
obs0.2123 53782 99.96 %-
Displacement parametersBiso mean: 70.94 Å2
Baniso -1Baniso -2Baniso -3
1--1.9107 Å20 Å20 Å2
2---1.9107 Å20 Å2
3---3.8213 Å2
Refine analyzeLuzzati coordinate error obs: 0.368 Å
Refinement stepCycle: LAST / Resolution: 2.58→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8166 0 5 207 8378
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018290HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0511175HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4052SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes256HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1167HARMONIC5
X-RAY DIFFRACTIONt_it8290HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion3.14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1096SEMIHARMONIC5
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_contact9863SEMIHARMONIC4
LS refinement shellResolution: 2.58→2.65 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2569 212 5.37 %
Rwork0.2444 3739 -
all0.245 3951 -
obs-2731 99.96 %

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