[English] 日本語
Yorodumi
- PDB-3owg: Crystal structure of vaccinia virus Polyadenylate polymerase(vp55) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3owg
TitleCrystal structure of vaccinia virus Polyadenylate polymerase(vp55)
ComponentsPoly(A) polymerase catalytic subunit
KeywordsTRANSFERASE / RNA polyadenylate polymerase complex / translocation / polyadenylate polymerase
Function / homology
Function and homology information


polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / mRNA processing / ATP binding / metal ion binding
Similarity search - Function
Poxvirus poly(A) polymerase, N domain / Poxvirus poly(A) polymerase, nucleotidyltransferase domain / Poly(A) polymerase catalytic subunit, Poxviridae / Poxvirus poly(A) polymerase nucleotidyltransferase domain / Poxvirus poly(A) polymerase, catalytic subunit, C-terminal / Poxvirus poly(A) polymerase, catalytic subunit, N-terminal / Poly(A) polymerase catalytic subunit superfamily / Poxvirus poly(A) polymerase, catalytic subunit, N-terminal domain superfamily / Poxvirus poly(A) polymerase, nucleotidyltransferase domain superfamily / Poxvirus poly(A) polymerase nucleotidyltransferase domain ...Poxvirus poly(A) polymerase, N domain / Poxvirus poly(A) polymerase, nucleotidyltransferase domain / Poly(A) polymerase catalytic subunit, Poxviridae / Poxvirus poly(A) polymerase nucleotidyltransferase domain / Poxvirus poly(A) polymerase, catalytic subunit, C-terminal / Poxvirus poly(A) polymerase, catalytic subunit, N-terminal / Poly(A) polymerase catalytic subunit superfamily / Poxvirus poly(A) polymerase, catalytic subunit, N-terminal domain superfamily / Poxvirus poly(A) polymerase, nucleotidyltransferase domain superfamily / Poxvirus poly(A) polymerase nucleotidyltransferase domain / Poxvirus poly(A) polymerase C-terminal domain / Poxvirus poly(A) polymerase N-terminal domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Beta Polymerase; domain 2 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Poly(A) polymerase catalytic subunit
Similarity search - Component
Biological speciesVaccinia virus WR
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsLi, C. / Li, H. / Zhou, S. / Gershon, P.D. / Poulos, T.L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Domain-level rocking motion within a polymerase that translocates on single-stranded nucleic acid.
Authors: Li, H. / Li, C. / Zhou, S. / Poulos, T.L. / Gershon, P.D.
#1: Journal: Mol.Cell / Year: 2006
Title: Crystal structures of the vaccinia virus polyadenylate polymerase heterodimer: insights into ATP selectivity and processivity.
Authors: Moure, C.M. / Bowman, B.R. / Gershon, P.D. / Quiocho, F.A.
#2: Journal: Structure / Year: 2009
Title: Polymerase translocation with respect to single-stranded nucleic acid: looping or wrapping of primer around a poly(A) polymerase.
Authors: Li, C. / Li, H. / Zhou, S. / Sun, E. / Yoshizawa, J. / Poulos, T.L. / Gershon, P.D.
History
DepositionSep 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Poly(A) polymerase catalytic subunit
B: Poly(A) polymerase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)112,8062
Polymers112,8062
Non-polymers00
Water00
1
A: Poly(A) polymerase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)56,4031
Polymers56,4031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(A) polymerase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)56,4031
Polymers56,4031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.128, 161.290, 97.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Poly(A) polymerase catalytic subunit / Poly(A) polymerase large subunit / PAP-L / VP55


Mass: 56403.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus WR / Strain: Western Reserve / Gene: PAPL, VACWR057, E1L / Plasmid: pPG198 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
References: UniProt: P23371, polynucleotide adenylyltransferase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 12-16%PEG 3350,200mM Na-citate, 5% glycero, 1mM DTT, pH ~9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 3, 2008 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 29731 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 90 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 22.6
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2 / Rsym value: 0.577 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.2refinement
Blu-IceIcedata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GA9

2ga9


Resolution: 2.86→41.77 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1227549.9 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL USED THE NCS RESTRAINTS (WEIGHT=100)WAS IMPOSED DURING REFINEMENTS
RfactorNum. reflection% reflectionSelection details
Rfree0.316 1465 4.9 %RANDOM
Rwork0.253 ---
obs0.253 29693 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.8296 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 97.9 Å2
Baniso -1Baniso -2Baniso -3
1-14.93 Å20 Å20 Å2
2---12.17 Å20 Å2
3----2.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.86→41.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7436 0 0 0 7436
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.88
Refine LS restraints NCSNCS model details: RESTRAINT
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.416 222 5.1 %
Rwork0.365 4153 -
obs-4153 88.6 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

+
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