[English] 日本語
Yorodumi
- PDB-4pz6: PCE1 guanylyltransferase bound to SER2/SER5 phosphorylated RNA po... -

+
Open data


ID or keywords:

Loading...

-
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


RNA polymerase II, holoenzyme / 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 / mRNA Capping / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex ...RNA polymerase II, holoenzyme / 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 / mRNA Capping / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Estrogen-dependent gene expression / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / co-transcriptional lncRNA 3' end processing, cleavage and polyadenylation pathway / mRNA Splicing - Major Pathway / 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 RNA polymerase / DNA-directed RNA polymerase activity / mRNA guanylyltransferase activity / mRNA guanylyltransferase / transcription by RNA polymerase II / chromatin / GTP binding / mitochondrion / DNA binding / ATP binding / metal ion 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 / : / DNA ligase/mRNA capping enzyme / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. ...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 Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / 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 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more