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- PDB-3p9y: Crystal structure of the Drosophila melanogaster Ssu72-pCTD complex -

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Basic information

Entry
Database: PDB / ID: 3p9y
TitleCrystal structure of the Drosophila melanogaster Ssu72-pCTD complex
Components
  • CG14216
  • pSer5 CTD peptide
KeywordsHYDROLASE / Phosphatase / cis proline / LMW PTP-like fold / RNA polymerase II CTD
Function / homology
Function and homology information


RNA polymerase II transcribes snRNA genes / RNA polymerase II CTD heptapeptide repeat phosphatase activity / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / termination of RNA polymerase II transcription / protein-serine/threonine phosphatase / phosphatase activity / nucleus
Similarity search - Function
Helix Hairpins - #550 / RNA polymerase II subunit A / Ssu72-like protein / Helix Hairpins / Response regulator / Helix non-globular / Special / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / 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 / Resolution: 2.1 Å
AuthorsWerner-Allen, J.W. / Zhou, P.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: cis-Proline-mediated Ser(P)5 Dephosphorylation by the RNA Polymerase II C-terminal Domain Phosphatase Ssu72.
Authors: Werner-Allen, J.W. / Lee, C.J. / Liu, P. / Nicely, N.I. / Wang, S. / Greenleaf, A.L. / Zhou, P.
History
DepositionOct 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 17, 2016Group: Non-polymer description
Revision 1.3Mar 26, 2025Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CG14216
B: CG14216
C: CG14216
D: CG14216
E: pSer5 CTD peptide
F: pSer5 CTD peptide
G: pSer5 CTD peptide
H: pSer5 CTD peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,13513
Polymers95,6648
Non-polymers4715
Water11,854658
1
A: CG14216
E: pSer5 CTD peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2485
Polymers23,9162
Non-polymers3323
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-7 kcal/mol
Surface area11260 Å2
MethodPISA
2
B: CG14216
F: pSer5 CTD peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9853
Polymers23,9162
Non-polymers691
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-9 kcal/mol
Surface area10950 Å2
MethodPISA
3
C: CG14216
G: pSer5 CTD peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9853
Polymers23,9162
Non-polymers691
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-8 kcal/mol
Surface area10380 Å2
MethodPISA
4
D: CG14216
H: pSer5 CTD peptide


Theoretical massNumber of molelcules
Total (without water)23,9162
Polymers23,9162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-8 kcal/mol
Surface area10310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.459, 157.459, 118.802
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
CG14216 / LD40846p


Mass: 23057.209 Da / Num. of mol.: 4 / Mutation: C13D,D144N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG14216, Dmel_CG14216 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: Q9VWE4
#2: Protein/peptide
pSer5 CTD peptide


Mass: 858.787 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetic phosphopeptide / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / 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: 2.96 Å3/Da / Density % sol: 58.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22% PEG monomethyl ether 550, 100 mM imidazole pH 6.5, 150 mM DL-malic acid, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 27, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 63987 / Num. obs: 63898 / % possible obs: 99.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.061
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 4.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→36 Å / SU ML: 0.29 / σ(F): 0.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 3052 5.1 %RANDOM
Rwork0.209 ---
obs0.2107 59898 93.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.352 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8591 Å2-0 Å20 Å2
2---0.8591 Å20 Å2
3---1.7181 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6596 0 31 658 7285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036739
X-RAY DIFFRACTIONf_angle_d0.7489070
X-RAY DIFFRACTIONf_dihedral_angle_d16.2892603
X-RAY DIFFRACTIONf_chiral_restr0.107984
X-RAY DIFFRACTIONf_plane_restr0.0031191
LS refinement shellResolution: 2.1015→2.1766 Å
RfactorNum. reflection% reflection
Rfree0.2974 277 -
Rwork0.2556 5369 -
obs--88 %

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