[English] 日本語
Yorodumi
- EMDB-54817: Dimeric form of the Streptococcus pyogenes nuclease A (SpnA) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-54817
TitleDimeric form of the Streptococcus pyogenes nuclease A (SpnA)
Map data
Sample
  • Complex: Streptococcus pyogenes nuclease A, SpnA
    • Protein or peptide: Endonuclease/exonuclease/phosphatase domain-containing protein
KeywordsStreptococcus pyogenes / nuclease / SpnA / DNA BINDING PROTEIN
Function / homologyEndonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / catalytic activity / Endonuclease/exonuclease/phosphatase domain-containing protein
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsBennig IA / Strobaek J / Marmede R / Neumann A / Friaes A / Ramirez M / Hall M / Collin M / Malmstrom L / Ekstrom S ...Bennig IA / Strobaek J / Marmede R / Neumann A / Friaes A / Ramirez M / Hall M / Collin M / Malmstrom L / Ekstrom S / Frick I / Bjorck L / Happonen LJ
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Swedish Research Council2022-03860 Sweden
CitationJournal: To Be Published
Title: Dimeric Streptococcus pyogenes nuclease A SpnA
Authors: Bennig IA / Strobaek J / Marmede R / Neumann A / Friaes A / Ramirez M / Hall M / Collin M / Malmstrom L / Ekstrom S / Frick I / Bjorck L / Happonen HJ
History
DepositionAug 19, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_54817.png

Downloads & links

-
Map

FileDownload / File: emd_54817.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 200 pix.
= 228. Å		1.14 Å/pix.
x 200 pix.
= 228. Å		1.14 Å/pix.
x 200 pix.
= 228. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.9372473 - 1.3812742
Average (Standard dev.)-0.0003098742 (±0.034223992)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 228.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_54817_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_54817_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Streptococcus pyogenes nuclease A, SpnA

EntireName: Streptococcus pyogenes nuclease A, SpnA
Components
  • Complex: Streptococcus pyogenes nuclease A, SpnA
    • Protein or peptide: Endonuclease/exonuclease/phosphatase domain-containing protein

-
Supramolecule #1: Streptococcus pyogenes nuclease A, SpnA

SupramoleculeName: Streptococcus pyogenes nuclease A, SpnA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptococcus pyogenes (bacteria)

-
Macromolecule #1: Endonuclease/exonuclease/phosphatase domain-containing protein

MacromoleculeName: Endonuclease/exonuclease/phosphatase domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pyogenes (bacteria)
Molecular weightTheoretical: 62.087613 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VKIGEIQGAS HTSPLLKKAV TVEQVVVTYL DDSTHFYVQD LNGDGDLATS DGIRVFAKNA KVQVGDVLTI SGEVEEFFGR GYEERKQTD LTITQIVAKA VTKTGTAQVP SPLVLGKDRI APANIIDNDG LRVFDPEEDA IDYWESMEGM LVAVDDAKIL G PMKNKEIY ...String:
VKIGEIQGAS HTSPLLKKAV TVEQVVVTYL DDSTHFYVQD LNGDGDLATS DGIRVFAKNA KVQVGDVLTI SGEVEEFFGR GYEERKQTD LTITQIVAKA VTKTGTAQVP SPLVLGKDRI APANIIDNDG LRVFDPEEDA IDYWESMEGM LVAVDDAKIL G PMKNKEIY VLPGSSTRPL NNSGGVLLPA NSYNTDVIPV LFKKGKQIIK AGDSYKGRLA GPVSYSYGNY KVFVDDSKNM PS LMDGHLK PEKTNLQKDL SKLSIASYNI ENFSANPSST KDEKVKRIAE SFIHDLNAPD IIGLIEVQDN NGPTDDGTTD ATQ SAQRLI DAIKKLGGPT YRYVDIAPEN NVDGGQPGGN IRTGFLYQPE RVSLSDKPKG GARDALTWVN GELNLSVGRI DPTN AAWKD VRKSLAAEFI FQGRKVVVVA NHLNSKRGDN ALYGCVQPVT FKSEQRRHVL ANMLAQFAKE GAKHQANIVM LGDFN DFEF TKTIQLIEEG DMVNLVSRHD ISDRYSYFHQ GNNQTLDNIL VSRHLLDHYE FDMVHVNSPF MEAHGRASDH DPLLLQ LSF

UniProtKB: Endonuclease/exonuclease/phosphatase domain-containing protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 126766
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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