[English] 日本語
Yorodumi
- EMDB-51566: Cryo-EM structure of a contractile injection system in Streptomyc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51566
TitleCryo-EM structure of a contractile injection system in Streptomyces coelicolor, the cap portion in extended state.
Map data
Sample
  • Complex: The cap module of a contractile injection system in Streptomyces coelicolor
    • Protein or peptide: Phage tail protein
    • Protein or peptide: Phage tail sheath family protein
    • Protein or peptide: Pvc16 N-terminal domain-containing protein
KeywordsContractile injection system / STRUCTURAL PROTEIN
Function / homology
Function and homology information


structural molecule activity
Similarity search - Function
Pvc16, N-terminal / Pvc16 N-terminal domain / Conserved hypothetical protein CHP02241 / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / : / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain ...Pvc16, N-terminal / Pvc16 N-terminal domain / Conserved hypothetical protein CHP02241 / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / : / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
Pvc16 N-terminal domain-containing protein / Phage tail sheath family protein / Phage tail protein
Similarity search - Component
Biological speciesStreptomyces coelicolor A3(2) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsCasu B / Sallmen JW / Hass PE / Afanasyev P / Xu J / Schlimpert S / Pilhofer M
Funding support Switzerland, European Union, United Kingdom, 4 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_179255 Switzerland
European Research Council (ERC)679209European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T015349/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X01097X/1 United Kingdom
CitationJournal: To Be Published
Title: Firing and cellular function of the Streptomyces coelicolor contractile injection system require the membrane protein CisA
Authors: Casu B / Sallmen JW / Hass PE / Afanasyev P / Xu J / Schlimpert S / Pilhofer M
History
DepositionSep 18, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51566.png

Downloads & links

-
Map

FileDownload / File: emd_51566.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 420 pix.
= 447.3 Å		1.07 Å/pix.
x 420 pix.
= 447.3 Å		1.07 Å/pix.
x 420 pix.
= 447.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.421
Minimum - Maximum-1.8494335 - 3.2251318
Average (Standard dev.)0.0024821006 (±0.119147025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 447.30002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_51566_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_51566_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_51566_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : The cap module of a contractile injection system in Streptomyces ...

EntireName: The cap module of a contractile injection system in Streptomyces coelicolor
Components
  • Complex: The cap module of a contractile injection system in Streptomyces coelicolor
    • Protein or peptide: Phage tail protein
    • Protein or peptide: Phage tail sheath family protein
    • Protein or peptide: Pvc16 N-terminal domain-containing protein

-
Supramolecule #1: The cap module of a contractile injection system in Streptomyces ...

SupramoleculeName: The cap module of a contractile injection system in Streptomyces coelicolor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)

-
Macromolecule #1: Phage tail protein

MacromoleculeName: Phage tail protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 16.493668 KDa
SequenceString:
MSLPKPEDVL VAPNFGIQID GVMVEYLNSV SNLQIEQDVI RYQQNQGTTG RNNVTLMPGV AKDGSVQVER GMSQSSVFTQ WINDSMAGR MATARKNATI IVMDYEDNPV KRWNLRNAWC SKVVAGTLKA GDTNALTETI TIVFEELVVE

UniProtKB: Phage tail protein

-
Macromolecule #2: Phage tail sheath family protein

MacromoleculeName: Phage tail sheath family protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 57.465113 KDa
SequenceString: MPSYLSPGVY VEEVASGSRP IEGVGIEGVG TSVAAFVGLA PTGPLNEPTL VTNWTQYVAA FGDFTGGYYL AHSVYGFFNN GGSAAYVVR VGGSAEDAAA DGSVNGAAAP AAVTGSTAKA LPAAEPKQLG TFAVTATAAG QSGPLTVEVA DPEGEGPAER F KLIVKDGD ...String:
MPSYLSPGVY VEEVASGSRP IEGVGIEGVG TSVAAFVGLA PTGPLNEPTL VTNWTQYVAA FGDFTGGYYL AHSVYGFFNN GGSAAYVVR VGGSAEDAAA DGSVNGAAAP AAVTGSTAKA LPAAEPKQLG TFAVTATAAG QSGPLTVEVA DPEGEGPAER F KLIVKDGD KPVETFDVSA KKGNRSYVVT QVKERSKLIT VTEAAPSAQL VRPENQSLTL PAPPSAAPAV PAGQAESAHP GP AQYLGDS SDRTGFGGLE AIDEISMVAV PDLMAAYQRG AIDLEAVKAV QLGLIAHCEL MGDRVAIIDP PPNQNARQIR VWR QETAGY DSKYAALYYP WIKSFDPATG QSRLVPPSGH VAGIWARNDS ERGVHKAPAN EVVRGAVDLE LQITRGEQDL LNPI GVNCI RSFPGRGIRV WGARTLSSDP AWRYLNIRRY FNYLEESILI GTQWVVFEPN DHNLWARIRR NVSAFLVNEW RNGAL FGQS PDQAYYVKCD EETNPPESVD LGRVVCEIGI APVKPAEFVI FRLAQFSSGG GELDE

UniProtKB: Phage tail sheath family protein

-
Macromolecule #3: Pvc16 N-terminal domain-containing protein

MacromoleculeName: Pvc16 N-terminal domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces coelicolor A3(2) (bacteria)
Molecular weightTheoretical: 24.713115 KDa
SequenceString: MIHEVDEVLK ALLKGGALTD SGIDVAFEAP TRDWAARRNA PVVNAYLYDI REDVGRRHRG QVAVRDQDDI VVKRRQPPRW FRLSYLVTA WTKTPQDEHR LLSAVLATLL PREQLPPYEL PGALGAMNLP VPMTVAGVQT ESRSLAEIWS ALGGELKPSL D LVVTAPFP ...String:
MIHEVDEVLK ALLKGGALTD SGIDVAFEAP TRDWAARRNA PVVNAYLYDI REDVGRRHRG QVAVRDQDDI VVKRRQPPRW FRLSYLVTA WTKTPQDEHR LLSAVLATLL PREQLPPYEL PGALGAMNLP VPMTVAGVQT ESRSLAEIWS ALGGELKPSL D LVVTAPFP AYPEYDAGPP VTEGATVRIG GVEGDPPMSE GRSHRPHQVA AARAARKAVT DGRTKRQ

UniProtKB: Pvc16 N-terminal domain-containing protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19218
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