[English] 日本語
Yorodumi
- EMDB-14509: gp6/gp15/gp16 connector complex of bacteriophage SPP1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14509
Titlegp6/gp15/gp16 connector complex of bacteriophage SPP1
Map data
Sample
  • Complex: gp6(12) gp15(12) gp16(6) portal complex (connector) of SPP1 bacteriophage
    • Protein or peptide: Portal protein
    • Protein or peptide: Head completion protein gp15
    • Protein or peptide: Head completion protein gp16
  • Ligand: water
Function / homology
Function and homology information


viral DNA genome packaging, headful / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral portal complex / viral procapsid / virion component
Similarity search - Function
Portal protein, SPP1-type / Portal protein / : / Phage portal protein, SPP1 Gp6-like / Phage gp6-like head-tail connector protein / Phage gp6-like head-tail connector protein / Bacteriophage SPP1, head-tail adaptor / Phage head-tail joining protein / Bacteriophage SPP1, head-tail adaptor superfamily
Similarity search - Domain/homology
Head completion protein gp16 / Portal protein / Head completion protein gp15
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsOrlov I / Roche S / Tavares P / Orlova EV
Funding support France, 1 items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS)CNRS funding France
CitationJournal: Nat Commun / Year: 2022
Title: CryoEM structure and assembly mechanism of a bacterial virus genome gatekeeper.
Authors: Igor Orlov / Stéphane Roche / Sandrine Brasilès / Natalya Lukoyanova / Marie-Christine Vaney / Paulo Tavares / Elena V Orlova /
Abstract: Numerous viruses package their dsDNA genome into preformed capsids through a portal gatekeeper that is subsequently closed. We report the structure of the DNA gatekeeper complex of bacteriophage SPP1 ...Numerous viruses package their dsDNA genome into preformed capsids through a portal gatekeeper that is subsequently closed. We report the structure of the DNA gatekeeper complex of bacteriophage SPP1 (gp6gp15gp16) in the post-DNA packaging state at 2.7 Å resolution obtained by single particle cryo-electron microscopy. Comparison of the native SPP1 complex with assembly-naïve structures of individual components uncovered the complex program of conformational changes leading to its assembly. After DNA packaging, gp15 binds via its C-terminus to the gp6 oligomer positioning gp15 subunits for oligomerization. Gp15 refolds its inner loops creating an intersubunit β-barrel that establishes different types of contacts with six gp16 subunits. Gp16 binding and oligomerization is accompanied by folding of helices that close the portal channel to keep the viral genome inside the capsid. This mechanism of assembly has broad functional and evolutionary implications for viruses of the prokaryotic tailed viruses-herpesviruses lineage.
History
DepositionMar 5, 2022-
Header (metadata) releaseNov 30, 2022-
Map releaseNov 30, 2022-
UpdateDec 7, 2022-
Current statusDec 7, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_14509.png

Downloads & links

-
Map

FileDownload / File: emd_14509.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 460 pix.
= 317.4 Å		0.69 Å/pix.
x 460 pix.
= 317.4 Å		0.69 Å/pix.
x 460 pix.
= 317.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.0963162 - 1.8154542
Average (Standard dev.)0.0022672438 (±0.057758823)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 317.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : gp6(12) gp15(12) gp16(6) portal complex (connector) of SPP1 bacte...

EntireName: gp6(12) gp15(12) gp16(6) portal complex (connector) of SPP1 bacteriophage
Components
  • Complex: gp6(12) gp15(12) gp16(6) portal complex (connector) of SPP1 bacteriophage
    • Protein or peptide: Portal protein
    • Protein or peptide: Head completion protein gp15
    • Protein or peptide: Head completion protein gp16
  • Ligand: water

-
Supramolecule #1: gp6(12) gp15(12) gp16(6) portal complex (connector) of SPP1 bacte...

SupramoleculeName: gp6(12) gp15(12) gp16(6) portal complex (connector) of SPP1 bacteriophage
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Bacillus subtilis (bacteria) / Strain: YB886
Molecular weightTheoretical: 0.902 kDa/nm

-
Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 57.390277 KDa
SequenceString: MADIYPLGKT HTEELNEIIV ESAKEIAEPD TTMIQKLIDE HNPEPLLKGV RYYMCENDIE KKRRTYYDAA GQQLVDDTKT NNRTSHAWH KLFVDQKTQY LVGEPVTFTS DNKTLLEYVN ELADDDFDDI LNETVKNMSN KGIEYWHPFV DEEGEFDYVI F PAEEMIVV ...String:
MADIYPLGKT HTEELNEIIV ESAKEIAEPD TTMIQKLIDE HNPEPLLKGV RYYMCENDIE KKRRTYYDAA GQQLVDDTKT NNRTSHAWH KLFVDQKTQY LVGEPVTFTS DNKTLLEYVN ELADDDFDDI LNETVKNMSN KGIEYWHPFV DEEGEFDYVI F PAEEMIVV YKDNTRRDIL FALRYYSYKG IMGEETQKAE LYTDTHVYYY EKIDGVYQMD YSYGENNPRP HMTKGGQAIG WG RVPIIPF KNNEEMVSDL KFYKDLIDNY DSITSSTMDS FSDFQQIVYV LKNYDGENPK EFTANLRYHS VIKVSGDGGV DTL RAEIPV DSAAKELERI QDELYKSAQA VDNSPETIGG GATGPALENL YALLDLKANM AERKIRAGLR LFFWFFAEYL RNTG KGDFN PDKELTMTFT RTRIQNDSEI VQSLVQGVTG GIMSKETAVA RNPFVQDPEE ELARIEEEMN QYAEMQGNLL DDEGG DDDL EEDDPNAGAA ESGGAGQVS

-
Macromolecule #2: Head completion protein gp15

MacromoleculeName: Head completion protein gp15 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 11.629402 KDa
SequenceString:
MDIQRVKRLL SITNDKHDEY LTEMVPLLVE FAKDECHNPF IDKDGNESIP SGVLIFVAKA AQFYMTNAGL TGRSMDTVSY NFATEIPST ILKKLNPYRK MAR

-
Macromolecule #3: Head completion protein gp16

MacromoleculeName: Head completion protein gp16 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 12.55499 KDa
SequenceString:
MYEEFPDVIT FQSYVEQSNG EGGKTYKWVD EFTAAAHVQP ISQEEYYKAQ QLQTPIGYNI YTPYDDRIDK KMRVIYRGKI VTFIGDPVD LSGLQEITRI KGKEDGAYVG

-
Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 406 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.64 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
50.0 mMTris-HCl pH 7.5
50.0 mMSodium ChlorideNaClSodium chloride
5.0 mMMagnesium ChlorideMgCl2
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 96 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 3876 / Average exposure time: 1.0 sec. / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 520000
Startup modelType of model: EMDB MAP
EMDB ID:

1021


Details: The map has been low pass filtered to 20 Angstrom.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.0)
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC (ver. 2)
Details: After three rounds of 2D classification in CryoSPARC 401,807 particle images were selected for the next two rounds of refinement.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.0)
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 2)
Details: Local resolution variations in the reconstruction was estimated using ResMap
Number images used: 401807

-
Atomic model buiding 1

Initial modelPDB ID:

2jes


Chain - Residue range: 254-344
DetailsManual inspection of the residues in the complete gp6, gp15 and gp16 polypeptide chains tracing was done using COOT and refined in Phenix
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 90
Output model

PDB-7z4w:
gp6/gp15/gp16 connector complex of bacteriophage SPP1

+
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