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- PDB-4pz8: PCE1 guanylyltransferase bound to SPT5 CTD -

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Basic information

Entry
Database: PDB / ID: 4pz8
TitlePCE1 guanylyltransferase bound to SPT5 CTD
Components
  • Transcription elongation factor spt5
  • mRNA-capping enzyme subunit alpha
KeywordsTRANSFERASE/TRANSCRIPTION / Nucleotidyl transferase / RNA capping enzyme / RNA polymerase II / Spt5 / guanylation / nuclear / TRANSFERASE-TRANSCRIPTION complex
Function / homology
Function and homology information


mRNA Capping / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / DSIF complex / transcription elongation factor activity / chromatin-protein adaptor activity / transcription elongation-coupled chromatin remodeling / RNA polymerase II C-terminal domain binding ...mRNA Capping / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / DSIF complex / transcription elongation factor activity / chromatin-protein adaptor activity / transcription elongation-coupled chromatin remodeling / RNA polymerase II C-terminal domain binding / 7-methylguanosine mRNA capping / regulation of DNA-templated transcription elongation / transcription elongation by RNA polymerase II / mRNA processing / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA binding / regulation of transcription by RNA polymerase II / chromatin / GTP binding / ATP binding / nucleus
Similarity search - Function
mRNA capping enzyme, alpha subunit / mRNA capping enzyme, adenylation domain / mRNA capping enzyme, C-terminal / mRNA capping enzyme, catalytic domain / mRNA capping enzyme, C-terminal domain / : / Spt5 C-terminal nonapeptide repeat binding Spt4 / DNA ligase/mRNA capping enzyme / Transcription elongation factor SPT5, second KOW domain / Transcription elongation factor SPT5, fifth KOW domain ...mRNA capping enzyme, alpha subunit / mRNA capping enzyme, adenylation domain / mRNA capping enzyme, C-terminal / mRNA capping enzyme, catalytic domain / mRNA capping enzyme, C-terminal domain / : / Spt5 C-terminal nonapeptide repeat binding Spt4 / DNA ligase/mRNA capping enzyme / Transcription elongation factor SPT5, second KOW domain / Transcription elongation factor SPT5, fifth KOW domain / Transcription elongation factor SPT5, KOWx domain / Transcription elongation factor SPT5, KOW1 domain / Transcription elongation factor SPT5, fourth KOW domain / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / D-amino Acid Aminotransferase; Chain A, domain 1 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / KOW (Kyprides, Ouzounis, Woese) motif. / Translation protein SH3-like domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2 / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Transcription elongation factor spt5 / mRNA-capping enzyme subunit alpha
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsDoamekpor, S.K. / Lima, C.D.
CitationJournal: Genes Dev. / Year: 2014
Title: How an mRNA capping enzyme reads distinct RNA polymerase II and Spt5 CTD phosphorylation codes.
Authors: Doamekpor, S.K. / Sanchez, A.M. / Schwer, B. / Shuman, S. / Lima, C.D.
History
DepositionMar 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Structure summary
Revision 1.2Sep 24, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_leaving_atom_flag / _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: mRNA-capping enzyme subunit alpha
B: Transcription elongation factor spt5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,34113
Polymers49,2842
Non-polymers1,05711
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.671, 88.512, 160.281
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein mRNA-capping enzyme subunit alpha / GTP--RNA guanylyltransferase / GTase / mRNA guanylyltransferase


Mass: 47378.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: ceg1, ceg1/pce1, pce1, SPBC2F12.08c / Plasmid: pSMT3 (SUMO) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CP-RIL / References: UniProt: P40997, mRNA guanylyltransferase
#2: Protein/peptide Transcription elongation factor spt5 / Chromatin elongation factor spt5


Mass: 1906.022 Da / Num. of mol.: 1 / Fragment: Spt5 C-terminal domain peptide / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) / References: UniProt: O13936*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.15 Å3/Da / Density % sol: 61.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.35 M lithium sulfate, 0.5 M ammonium sulfate, 0.1 M sodium citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2010
RadiationMonochromator: Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 11807 / Num. obs: 11169 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.151 / Net I/σ(I): 7.6
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2.8 / Num. unique all: 950 / % possible all: 90.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4PZ6

4pz6


Resolution: 3.1→38.458 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.53 / Phase error: 24.33 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.2534 529 4.79 %
Rwork0.2008 --
obs0.2033 11036 94.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→38.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3087 0 55 59 3201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023210
X-RAY DIFFRACTIONf_angle_d0.614339
X-RAY DIFFRACTIONf_dihedral_angle_d11.5391212
X-RAY DIFFRACTIONf_chiral_restr0.048453
X-RAY DIFFRACTIONf_plane_restr0.003543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.41190.38521140.2922509X-RAY DIFFRACTION91
3.4119-3.90520.2711140.2132589X-RAY DIFFRACTION93
3.9052-4.91850.22561370.15322626X-RAY DIFFRACTION96
4.9185-38.46120.21031640.1842783X-RAY DIFFRACTION97

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