[English] 日本語
Yorodumi
- EMDB-70280: C1 reconstruction of the thermophilic bacteriophage P74-26 Portal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-70280
TitleC1 reconstruction of the thermophilic bacteriophage P74-26 Portal and Portal Vertex
Map data
Sample
  • Virus: Oshimavirus P7426
    • Complex: Neck
      • Protein or peptide: Major head protein
      • Protein or peptide: P74-26 Head Decoration Protein
    • Protein or peptide: Portal Vertex Protein
    • Protein or peptide: Portal protein
    • Protein or peptide: Adaptor (P74p90)
    • DNA: DNA (31-MER)
    • DNA: DNA (31-MER)
Keywordsbacteriophage / thermophilic / Neck / Portal / VIRUS
Function / homology
Function and homology information


host cell cytoplasm
Similarity search - Function
: / Phage P23-45 portal protein / Major capsid protein GpE / Phage major capsid protein E
Similarity search - Domain/homology
Uncharacterized protein / Portal protein / Uncharacterized protein / Major head protein / Uncharacterized protein
Similarity search - Component
Biological speciesOshimavirus P7426
Methodsingle particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsSedivy EL / Agnello E / Song K / Xu C / Kelch BA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1817338 United States
CitationJournal: J Mol Biol / Year: 2026
Title: The structure of a thermostable phage's portal vertex and neck complex illuminates the headful maturation mechanism.
Authors: Emma L Sedivy / Emily Agnello / Julia E Hobaugh / Rakeyah Ahsan / Kangkang Song / Chen Xu / Brian A Kelch /
Abstract: Viruses assemble from component parts inside their host cells, but the mechanisms coordinating this complex process are not completely understood. In tailed bacteriophages, the genome is packaged ...Viruses assemble from component parts inside their host cells, but the mechanisms coordinating this complex process are not completely understood. In tailed bacteriophages, the genome is packaged into its capsid shell through the portal complex. The portal complex then closes to retain DNA and connects to the tail, which is required for host recognition and infection. The trigger to stop pumping DNA and assemble the mature virus has been a longstanding conundrum in the field. We determined the structure of the portal, the proteins that connect it to the tail, and portal vertex in the hyperthermophilic phage Oshimavirus using cryo-Electron Microscopy (cryo-EM). We find highly intertwined loop structures, like in a wicker basket, potentially stabilizing the portal vertex against high temperatures. Moreover, we observe that the portal protrudes from the capsid in mature virions. We propose that portal is repositioned by packaged DNA, forming a pressure-sensitive switch that terminates genome packaging and triggers tail attachment in headful phages.
History
DepositionApr 21, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_70280.png

Downloads & links

-
Map

FileDownload / File: emd_70280.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.30210647 - 0.5253878
Average (Standard dev.)-0.0032305731 (±0.04782997)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 381.59998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_70280_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_70280_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_70280_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Oshimavirus P7426

EntireName: Oshimavirus P7426
Components
  • Virus: Oshimavirus P7426
    • Complex: Neck
      • Protein or peptide: Major head protein
      • Protein or peptide: P74-26 Head Decoration Protein
    • Protein or peptide: Portal Vertex Protein
    • Protein or peptide: Portal protein
    • Protein or peptide: Adaptor (P74p90)
    • DNA: DNA (31-MER)
    • DNA: DNA (31-MER)

-
Supramolecule #1: Oshimavirus P7426

SupramoleculeName: Oshimavirus P7426 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Virions were purified from infected Thermus thermophilus using cesium chloride and sucrose gradient ultracentrifugation.
NCBI-ID: 466052 / Sci species name: Oshimavirus P7426 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Thermus thermophilus HB8 (bacteria) / Strain: HB8

-
Supramolecule #2: Neck

SupramoleculeName: Neck / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Oshimavirus P7426

-
Macromolecule #1: Major head protein

MacromoleculeName: Major head protein / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: Oshimavirus P7426
Molecular weightTheoretical: 46.680754 KDa
SequenceString: MRVPININNA LARVRDPLSI GGLKFPTTKE IQEAVAAIAD KFNQENDLVD RFFPEDSTFA SELELYLLRT QDAEQTGMTF VHQVGSTSL PVEARVAKVD LAKATWSPLA FKESRVWDEK EILYLGRLAD EVQAGVINEQ IAESLTWLMA RMRNRRRWLT W QVMRTGRI ...String:
MRVPININNA LARVRDPLSI GGLKFPTTKE IQEAVAAIAD KFNQENDLVD RFFPEDSTFA SELELYLLRT QDAEQTGMTF VHQVGSTSL PVEARVAKVD LAKATWSPLA FKESRVWDEK EILYLGRLAD EVQAGVINEQ IAESLTWLMA RMRNRRRWLT W QVMRTGRI TIQPNDPYNP NGLKYVIDYG VTDIELPLPQ KFDAKDGNGN SAVDPIQYFR DLIKAATYFP DRRPVAIIVG PG FDEVLAD NTFVQKYVEY EKGWVVGQNT VQPPREVYRQ AALDIFKRYT GLEVMVYDKT YRDQDGSVKY WIPVGELIVL NQS TGPVGR FVYTAHVAGQ RNGKVVYATG PYLTVKDHLQ DDPPYYAIIA GFHGLPQLSG YNTEDFSFHR FKWLKYANNV QSYL PPFPP KVEL

UniProtKB: Major head protein

-
Macromolecule #2: P74-26 Head Decoration Protein

MacromoleculeName: P74-26 Head Decoration Protein / type: protein_or_peptide / ID: 2 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: Oshimavirus P7426
Molecular weightTheoretical: 16.37663 KDa
SequenceString:
MDKIQLFRTI GRVQYWERVP RLHAYGVFAL PFPMDPDVEW GNWFAGPHPK AFLVSVHPSG PKAGHVYPTD LSDPDSVANV IGMVLDGHD YEADHNVTVT LRAAVPIEYV QQGIEAPPLQ PDPAVLNAAP QLKLKVIKGH YFFDYTR

UniProtKB: Uncharacterized protein

-
Macromolecule #3: Portal Vertex Protein

MacromoleculeName: Portal Vertex Protein / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Oshimavirus P7426
Molecular weightTheoretical: 8.431445 KDa
SequenceString:
MRPRRYENPE LEQDDLPQPR RKTAYRVYAS RRDGKISAWF VVEADSAEEA LQLVEQGVYG KGWVPVTAEV LTP

UniProtKB: Uncharacterized protein

-
Macromolecule #4: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 4 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Oshimavirus P7426
Molecular weightTheoretical: 49.731172 KDa
SequenceString: MAKRGRKPKE LVPGPGSIDP SDVPKLEGAS VPVMSTSYDV VVDREFDELL QGKDGLLVYH KMLSDGTVKN ALNYIFGRIR SAKWYVEPA STDPEDIAIA AFIHAQLGID DASVGKYPFG RLFAIYENAY IYGMAAGEIV LTLGADGKLI LDKIVPIHPF N IDEVLYDE ...String:
MAKRGRKPKE LVPGPGSIDP SDVPKLEGAS VPVMSTSYDV VVDREFDELL QGKDGLLVYH KMLSDGTVKN ALNYIFGRIR SAKWYVEPA STDPEDIAIA AFIHAQLGID DASVGKYPFG RLFAIYENAY IYGMAAGEIV LTLGADGKLI LDKIVPIHPF N IDEVLYDE EGGPKALKLS GEVKGGSQFV SGLEIPIWKT VVFLHNDDGS FTGQSALRAA VPHWLAKRAL ILLINHGLER FM IGVPTLT IPKSVRQGTK QWEAAKEIVK NFVQKPRHGI ILPDDWKFDT VDLKSAMPDA IPYLTYHDAG IARALGIDFN TVQ LNMGVQ AINIGEFVSL TQQTIISLQR EFASAVNLYL IPKLVLPNWP SATRFPRLTF EMEERNDFSA AANLMGMLIN AVKD SEDIP TELKALIDAL PSKMRRALGV VDEVREAVRQ PADSRYLYTR RRR

UniProtKB: Portal protein

-
Macromolecule #5: Adaptor (P74p90)

MacromoleculeName: Adaptor (P74p90) / type: protein_or_peptide / ID: 5 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Oshimavirus P7426
Molecular weightTheoretical: 14.556551 KDa
SequenceString:
MLPEVSVDEV WYYMPAEVRR PEEVVREGQG GVSLAAFRHI KNGVLAEAAS HLKANGVPEG LWNHELIRDY ILMQIAARIL RRVRAYQEL ADSLFADSNI KLRAFLEGVA QVAPDVGTGD WVEDEAILPP F

UniProtKB: Uncharacterized protein

-
Macromolecule #6: DNA (31-MER)

MacromoleculeName: DNA (31-MER) / type: dna / ID: 6 / Number of copies: 5 / Classification: DNA
Source (natural)Organism: Oshimavirus P7426
Molecular weightTheoretical: 9.38502 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)

-
Macromolecule #7: DNA (31-MER)

MacromoleculeName: DNA (31-MER) / type: dna / ID: 7 / Number of copies: 5 / Classification: DNA
Source (natural)Organism: Oshimavirus P7426
Molecular weightTheoretical: 9.664453 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: EMS Lacey Carbon / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV
DetailsVirions were purified from infected Thermus thermophilus using cesium chloride gradient ultracentrifugation.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 16184 / Average electron dose: 49.0571 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF
Details: FSC was calculated using the provided mask, which excludes solvent
Number images used: 39382
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: Initial model was created by ModelAngelo
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9oad:
C1 reconstruction of the thermophilic bacteriophage P74-26 Portal and Portal Vertex

+
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