[English] 日本語
Yorodumi
- EMDB-52810: Salmonella typhimurium polynucleotide phosphorylase in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52810
TitleSalmonella typhimurium polynucleotide phosphorylase in complex with recognition site of RNase E
Map dataSharpened map Salmonella PNPase in complex with RNase E
Sample
  • Complex: Polynucleotide phosphorylase in complex with recognition site from ribonuclease E
    • Protein or peptide: Polyribonucleotide nucleotidyltransferase
    • Protein or peptide: Ribonuclease E
  • Ligand: water
Keywordspolynucleotide phosphorylase / ribonuclease E / RNA degradosome / RNA BINDING PROTEIN
Function / homology
Function and homology information


ribonuclease E / ribonuclease E activity / polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / RNA catabolic process / tRNA processing / mRNA catabolic process / RNA processing / cytoplasmic side of plasma membrane / rRNA processing ...ribonuclease E / ribonuclease E activity / polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / RNA catabolic process / tRNA processing / mRNA catabolic process / RNA processing / cytoplasmic side of plasma membrane / rRNA processing / 3'-5'-RNA exonuclease activity / tRNA binding / rRNA binding / magnesium ion binding / RNA binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Polyribonucleotide phosphorylase C-terminal / Polyribonucleotide phosphorylase C terminal / : / RNase E/G, Thioredoxin-like domain / Ribonuclease E/G / Ribonuclease E / RNA-binding protein AU-1/Ribonuclease E/G / Ribonuclease E/G family / Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase ...Polyribonucleotide phosphorylase C-terminal / Polyribonucleotide phosphorylase C terminal / : / RNase E/G, Thioredoxin-like domain / Ribonuclease E/G / Ribonuclease E / RNA-binding protein AU-1/Ribonuclease E/G / Ribonuclease E/G family / Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA binding domain / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / K Homology domain / K homology RNA-binding domain / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Ribonuclease E / Polyribonucleotide nucleotidyltransferase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsParis G / Luisi BF
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust222451/Z/21/Z United Kingdom
CitationJournal: To Be Published
Title: Salmonella typhimurium polynucleotide phosphorylase in complex with recognition site of RNase E
Authors: Paris G / Luisi BF
History
DepositionFeb 12, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52810.png

Downloads & links

-
Map

FileDownload / File: emd_52810.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map Salmonella PNPase in complex with RNase E
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 360 pix.
= 262.8 Å		0.73 Å/pix.
x 360 pix.
= 262.8 Å		0.73 Å/pix.
x 360 pix.
= 262.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055
Minimum - Maximum-0.19789864 - 0.41478038
Average (Standard dev.)0.00057786825 (±0.012368996)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 262.80002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map Salmonella PNPase in complex with RNase E

Fileemd_52810_half_map_1.map
AnnotationHalf map Salmonella PNPase in complex with RNase E
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map Salmonella PNPase in complex with RNase E

Fileemd_52810_half_map_2.map
AnnotationHalf map Salmonella PNPase in complex with RNase E
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Polynucleotide phosphorylase in complex with recognition site fro...

EntireName: Polynucleotide phosphorylase in complex with recognition site from ribonuclease E
Components
  • Complex: Polynucleotide phosphorylase in complex with recognition site from ribonuclease E
    • Protein or peptide: Polyribonucleotide nucleotidyltransferase
    • Protein or peptide: Ribonuclease E
  • Ligand: water

-
Supramolecule #1: Polynucleotide phosphorylase in complex with recognition site fro...

SupramoleculeName: Polynucleotide phosphorylase in complex with recognition site from ribonuclease E
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Complex prepared by co-expression and chromatographic purification
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

-
Macromolecule #1: Polyribonucleotide nucleotidyltransferase

MacromoleculeName: Polyribonucleotide nucleotidyltransferase / type: protein_or_peptide / ID: 1 / Details: Core of the enzyme without KH and S1 domains / Number of copies: 3 / Enantiomer: LEVO / EC number: polyribonucleotide nucleotidyltransferase
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 59.233332 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLNPIVRKFQ YGQHTVTLET GMMARQATAA VMVSMDDTAV FVTVVGQKKA KPGQDFFPLT VNYQERTYAA GRIPGSFFRR EGRPSEGET LIARLIDRPV RPLFPEGFVN EVQVIATVVS VNPQVNPDIV AMIGASAALS LSGIPFNGPI GAARVGYIND Q YVLNPTQD ...String:
MLNPIVRKFQ YGQHTVTLET GMMARQATAA VMVSMDDTAV FVTVVGQKKA KPGQDFFPLT VNYQERTYAA GRIPGSFFRR EGRPSEGET LIARLIDRPV RPLFPEGFVN EVQVIATVVS VNPQVNPDIV AMIGASAALS LSGIPFNGPI GAARVGYIND Q YVLNPTQD ELKESKLDLV VAGTEAAVLM VESEAELLSE DTMLGAVVFG HEQQQVVIQA INDLVKEAGK PRWDWQPEAV ND ALNARVA ALAESRLSDA YRITDKQERY AQVDVIKSET IEQLIAEDET LDANELGEIL HAIEKNVVRS RVLAGEPRID GRE KDMIRG LDVRTGVLPR THGSALFTRG ETQALVTATL GTARDAQVLD ELMGERTDSF LFHYNFPPYS VGETGMVGSP KRRE IGHGR LAKRGVLAVM PDMDKFPYTV RVVSEITESN GSSSMASVCG ASLALMDAGV PIKAAVAGIA MGLVKEGDNY VVLSD ILGD EDHLGDMDFK VAGSRDGISA LQMDIKIEGI TKEIMQVALN QAKGARLHIL GVMEQAINAP RG

UniProtKB: Polyribonucleotide nucleotidyltransferase

-
Macromolecule #2: Ribonuclease E

MacromoleculeName: Ribonuclease E / type: protein_or_peptide / ID: 2 / Details: C-terminal segment of ribonuclease E / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease E
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 6.232763 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
NHASAPMTRA PAPEYVPETP HHSDWQRPSF HFEGKGAAGG HSATRHASAP ATRPQPVE

UniProtKB: Ribonuclease E

-
Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 47 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.6 mg/mL
BufferpH: 8
Details: 20 mM Tris-HCl pH 8.0, 25 mM MgCl2, 150 mM KCl, 1 mM TCEP
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 39.0 kPa / Details: 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.2 K / Instrument: FEI VITROBOT MARK IV / Details: blotting force -4, 3 sec blot time.
DetailsPurified PNPase core and RNE-muGFP-CHis proteins were mixed in 1:2 ratio and their complex were separated on the Superdex 200 Increase 10/300 GL column (Cytiva) equilibrated with Cryo-EM buffer (20 mM Tris-HCl pH 8.0, 25 mM MgCl2, 150 mM KCl, 1 mM TCEP). Peak fractions were combined, the protein was concentrated to 15 microM using Amicon Ultra concentrator with 10 kDa cut-off (Millipore) and used to prepare Cryo-EM grids. The samples were mixed with CHAPSO (3-([3-cholamidopropyl]dimethylammonio)-2-hydroxy-1-propanesulfonate) at a final concentration of 8 mM

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 12147 / Average exposure time: 4.39 sec. / Average electron dose: 50.47 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 41901
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Detailsphenix refine and manual rebuilding using COOT
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9ibh:
Salmonella typhimurium polynucleotide phosphorylase in complex with recognition site of RNase E

+
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