[English] 日本語
Yorodumi
- PDB-8tg4: tRNA 2'-phosphotransferase (Tpt1) from Aeropyrum pernix in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tg4
TitletRNA 2'-phosphotransferase (Tpt1) from Aeropyrum pernix in complex with ADP-ribose-2"-phosphate and 2'-OH RNA
Components
  • Probable RNA 2'-phosphotransferase
  • RNA (5'-R(*UP*GP*UP*A)-3')
KeywordsTRANSFERASE / tRNA 2'-PHOSPHOTRANSFERASE / TPT1 / tRNA SPLICING / ADP-ribose-2"-phosphate / Aeropyrum pernix
Function / homology
Function and homology information


tRNA 2'-phosphotransferase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / tRNA splicing, via endonucleolytic cleavage and ligation / NAD+-protein poly-ADP-ribosyltransferase activity
Similarity search - Function
RNA 2'-phosphotransferase KptA, putative / Phosphotransferase KptA/Tpt1 / RNA 2'-phosphotransferase, N-terminal domain / RNA 2'-phosphotransferase, C-terminal domain / RNA 2'-phosphotransferase, Tpt1 / KptA family
Similarity search - Domain/homology
Chem-9SO / : / NITRATE ION / RNA / Probable RNA 2'-phosphotransferase
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsJacewicz, A. / Dantuluri, S. / Shuman, S.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126945 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
Department of Energy (DOE, United States)DE-SC0012704 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30-GM124165 United States
Other governmentHEI-S10OD021527 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Structural basis for Tpt1-catalyzed 2'-PO 4 transfer from RNA and NADP(H) to NAD.
Authors: Jacewicz, A. / Dantuluri, S. / Shuman, S.
History
DepositionJul 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable RNA 2'-phosphotransferase
C: RNA (5'-R(*UP*GP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,92111
Polymers24,9302
Non-polymers9919
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.844, 55.701, 42.249
Angle α, β, γ (deg.)90.000, 97.790, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein / RNA chain , 2 types, 2 molecules AC

#1: Protein Probable RNA 2'-phosphotransferase


Mass: 23382.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Gene: kptA, APE_0204.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Codon Plus
References: UniProt: Q9YFP5, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: RNA chain RNA (5'-R(*UP*GP*UP*A)-3')


Mass: 1547.952 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 6 types, 154 molecules

#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-9SO / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(2R,3R,4R,5R)-3,5-dihydroxy-4-(phosphonooxy)oxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)


Mass: 639.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N5O17P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M KNO3, 24% PEG-3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.37→41.86 Å / Num. obs: 38249 / % possible obs: 99.3 % / Redundancy: 6.3 % / Biso Wilson estimate: 18.38 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.016 / Net I/σ(I): 22.4
Reflection shellResolution: 1.37→1.39 Å / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1848 / CC1/2: 0.741 / Rpim(I) all: 0.337

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wfx

1wfx


Resolution: 1.37→41.86 Å / SU ML: 0.136 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.4102
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.175 1935 5.06 %
Rwork0.1486 36296 -
obs0.1499 38231 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.04 Å2
Refinement stepCycle: LAST / Resolution: 1.37→41.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1463 48 54 145 1710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091607
X-RAY DIFFRACTIONf_angle_d1.21662193
X-RAY DIFFRACTIONf_chiral_restr0.0823241
X-RAY DIFFRACTIONf_plane_restr0.0184266
X-RAY DIFFRACTIONf_dihedral_angle_d14.1825242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.40.25271390.19872535X-RAY DIFFRACTION97.91
1.4-1.440.26371390.17662525X-RAY DIFFRACTION98.16
1.44-1.480.20551380.16142583X-RAY DIFFRACTION98.8
1.48-1.530.18911340.14272566X-RAY DIFFRACTION98.43
1.53-1.590.18961240.13962629X-RAY DIFFRACTION99.64
1.59-1.650.15671360.1342559X-RAY DIFFRACTION99.67
1.65-1.730.18661670.13362569X-RAY DIFFRACTION99.67
1.73-1.820.17321420.13252601X-RAY DIFFRACTION99.67
1.82-1.930.17621420.13132607X-RAY DIFFRACTION99.71
1.93-2.080.16631320.14382597X-RAY DIFFRACTION99.27
2.08-2.290.19091380.13922597X-RAY DIFFRACTION99.89
2.29-2.620.20421510.15882609X-RAY DIFFRACTION99.89
2.62-3.30.16511250.16212640X-RAY DIFFRACTION99.71
3.3-41.860.15151280.14572679X-RAY DIFFRACTION99.36

+
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