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- PDB-4ygx: Crystal Structure of D. melanogaster Ssu72+Symplekin bound to cis... -

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Basic information

Entry
Database: PDB / ID: 4ygx
TitleCrystal Structure of D. melanogaster Ssu72+Symplekin bound to cis peptidomimetic CTD phospho-Ser5 peptide
Components
  • LD40846p
  • Symplekin
  • cis peptidomimetic CTD phospho-Ser5 peptide
KeywordsHYDROLASE / Phosphatase / Peptidomimetic / Complex
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
Symplekin / RNA polymerase II subunit A C-terminal domain phosphatase SSU72
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
AuthorsMayfield, J.E. / Zhang, Y.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Chemical Tools To Decipher Regulation of Phosphatases by Proline Isomerization on Eukaryotic RNA Polymerase II.
Authors: Mayfield, J.E. / Fan, S. / Wei, S. / Zhang, M. / Li, B. / Ellington, A.D. / Etzkorn, F.A. / Zhang, Y.J.
History
DepositionFeb 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Symplekin
B: LD40846p
C: Symplekin
D: LD40846p
E: cis peptidomimetic CTD phospho-Ser5 peptide


Theoretical massNumber of molelcules
Total (without water)122,5105
Polymers122,5105
Non-polymers00
Water18010
1
A: Symplekin
B: LD40846p


Theoretical massNumber of molelcules
Total (without water)60,6262
Polymers60,6262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Symplekin
D: LD40846p
E: cis peptidomimetic CTD phospho-Ser5 peptide


Theoretical massNumber of molelcules
Total (without water)61,8853
Polymers61,8853
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.880, 127.880, 105.861
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4

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Components

#1: Protein Symplekin


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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8MSU4
#2: Protein LD40846p / Ssu72 ortholog / isoform A / isoform C


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 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9VWE4, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases, protein-serine/threonine phosphatase, EC: 3.1.3.41
#3: Protein/peptide cis peptidomimetic CTD phospho-Ser5 peptide


Mass: 1259.238 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.62 Å3/Da / Density % sol: 66.04 %
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. 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. To obtain the tertiary complex structure of Drosophila Ssu72-symplekin-Cis-locked peptide, crystals of Ssu72-symplekin were soaked in a mother solution containing 2 mM 11mer peptide overnight at room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 35810 / % possible obs: 99.2 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.104 / Χ2: 1.35 / Net I/av σ(I): 20.452 / Net I/σ(I): 8.2 / Num. measured all: 245848
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.95-34.50.89916981.00796.2
3-3.065.40.92417631.04697.7
3.06-3.116.10.82918111.05598.7
3.11-3.186.70.70917831.07899.7
3.18-3.256.90.61917451.16499.4
3.25-3.3270.51217991.20799.3
3.32-3.417.10.38417891.21599.7
3.41-3.570.33917621.35499.5
3.5-3.67.10.26618151.32499.3
3.6-3.7270.20717741.43999.4
3.72-3.857.10.1818001.36299.3
3.85-47.10.15417851.47999.3
4-4.197.10.11417941.499.2
4.19-4.417.10.08917851.40798.7
4.41-4.687.20.07617741.48999.2
4.68-5.047.10.07918091.66699.6
5.04-5.557.20.07918201.54799.9
5.55-6.357.40.07318211.40199.8
6.35-87.60.0518201.421100
8-507.40.03418631.56899.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 16.393 / SU ML: 0.296 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.548 / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 1844 5.1 %RANDOM
Rwork0.2057 33965 --
obs0.2081 33965 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 218.67 Å2 / Biso mean: 87.964 Å2 / Biso min: 37.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2--0.79 Å20 Å2
3----1.59 Å2
Refinement stepCycle: final / Resolution: 2.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8147 0 0 10 8157
Biso mean---62.6 -
Num. residues----1029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198264
X-RAY DIFFRACTIONr_bond_other_d0.0020.028114
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.97111137
X-RAY DIFFRACTIONr_angle_other_deg0.9318668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.07751023
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.42325.051390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.963151583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1581555
X-RAY DIFFRACTIONr_chiral_restr0.0970.21295
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029281
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021807
X-RAY DIFFRACTIONr_mcbond_it6.5088.5674114
X-RAY DIFFRACTIONr_mcbond_other6.5088.5664113
X-RAY DIFFRACTIONr_mcangle_it9.78912.8445132
LS refinement shellResolution: 2.949→3.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 139 -
Rwork0.327 2411 -
all-2550 -
obs--96.19 %

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