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- PDB-4pz6: PCE1 guanylyltransferase bound to SER2/SER5 phosphorylated RNA po... -

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Basic information

Entry
Database: PDB / ID: 4pz6
TitlePCE1 guanylyltransferase bound to SER2/SER5 phosphorylated RNA pol II CTD
Components
  • DNA-directed RNA polymerase II subunit rpb1
  • 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


co-transcriptional lncRNA 3' end processing, cleavage and polyadenylation pathway / RNA polymerase II transcribes snRNA genes / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA polymerase II, holoenzyme / mRNA Capping / RNA Pol II CTD phosphorylation and interaction with CE ...co-transcriptional lncRNA 3' end processing, cleavage and polyadenylation pathway / RNA polymerase II transcribes snRNA genes / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA polymerase II, holoenzyme / mRNA Capping / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of the Early Elongation Complex / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / Transcriptional regulation by small RNAs / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / intracellular phosphate ion homeostasis / chromatin-protein adaptor activity / termination of RNA polymerase II transcription / RNA polymerase II C-terminal domain binding / 7-methylguanosine mRNA capping / RNA polymerase II, core complex / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / mRNA guanylyltransferase activity / mRNA guanylyltransferase / transcription by RNA polymerase II / chromatin / GTP binding / DNA binding / ATP binding / nucleus / metal ion binding
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 / : / DNA ligase/mRNA capping enzyme / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 ...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 / : / DNA ligase/mRNA capping enzyme / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / D-amino Acid Aminotransferase; Chain A, domain 1 / Nucleic acid-binding proteins / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE / DNA-directed RNA polymerase II subunit rpb1 / mRNA-capping enzyme subunit alpha
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.406 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: mRNA-capping enzyme subunit alpha
P: DNA-directed RNA polymerase II subunit rpb1
Q: DNA-directed RNA polymerase II subunit rpb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6665
Polymers99,3824
Non-polymers2831
Water3,819212
1
A: mRNA-capping enzyme subunit alpha
Q: DNA-directed RNA polymerase II subunit rpb1


Theoretical massNumber of molelcules
Total (without water)49,6912
Polymers49,6912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-12 kcal/mol
Surface area20610 Å2
MethodPISA
2
B: mRNA-capping enzyme subunit alpha
P: DNA-directed RNA polymerase II subunit rpb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9743
Polymers49,6912
Non-polymers2831
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-5 kcal/mol
Surface area20480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.406, 78.614, 115.716
Angle α, β, γ (deg.)90.00, 91.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 47034.062 Da / Num. of mol.: 2
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 DNA-directed RNA polymerase II subunit rpb1 / RNA polymerase II subunit 1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit


Mass: 2657.111 Da / Num. of mol.: 2
Fragment: phosphorylated C-terminal domain peptide (UNP residues 1578-1598)
Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P36594
#3: Chemical ChemComp-GMP / GUANOSINE


Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 23% PEG400, 0.1 M sodium acetate, pH 7.0, 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: Aug 5, 2009
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: 2.406→50 Å / Num. all: 39406 / Num. obs: 38342 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 45.5 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 9.6
Reflection shellResolution: 2.406→2.49 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3511 / % possible all: 89.4

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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 1P16

1p16


Resolution: 2.406→36.274 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 24.78 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.2327 1925 5.02 %
Rwork0.1798 --
obs0.1826 38338 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.406→36.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6271 0 13 212 6496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036439
X-RAY DIFFRACTIONf_angle_d0.6928689
X-RAY DIFFRACTIONf_dihedral_angle_d11.6532479
X-RAY DIFFRACTIONf_chiral_restr0.052917
X-RAY DIFFRACTIONf_plane_restr0.0031106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.406-2.46660.32411130.23962321X-RAY DIFFRACTION87
2.4666-2.53320.29911260.24022554X-RAY DIFFRACTION96
2.5332-2.60780.32411530.2422562X-RAY DIFFRACTION97
2.6078-2.69190.30261500.23192597X-RAY DIFFRACTION97
2.6919-2.78810.3241210.2262586X-RAY DIFFRACTION98
2.7881-2.89970.27291340.21262595X-RAY DIFFRACTION98
2.8997-3.03160.28391120.21972659X-RAY DIFFRACTION98
3.0316-3.19130.26661620.20152599X-RAY DIFFRACTION98
3.1913-3.39110.28881340.20462624X-RAY DIFFRACTION98
3.3911-3.65270.25821450.19062617X-RAY DIFFRACTION98
3.6527-4.01990.25661250.16232681X-RAY DIFFRACTION99
4.0199-4.60060.18581500.14252646X-RAY DIFFRACTION99
4.6006-5.79240.17491440.14452670X-RAY DIFFRACTION99
5.7924-36.27770.17511560.15732702X-RAY DIFFRACTION98

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