[English] 日本語
Yorodumi
- EMDB-61998: Cyanophage A4 pre-ejectosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61998
TitleCyanophage A4 pre-ejectosome
Map data
Sample
  • Virus: Anabaena phage A-4L (virus)
    • Protein or peptide: Portal protein
    • Protein or peptide: Internal virion protein
    • Protein or peptide: Internal protein
  • Ligand: ZINC ION
KeywordsCyanophage / Virus / Ejectosome / VIRAL PROTEIN
Function / homology
Function and homology information


metalloendopeptidase activity / killing of cells of another organism / defense response to bacterium
Similarity search - Function
: / Phage SU10 portal protein / : / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif
Similarity search - Domain/homology
Internal virion protein / Internal protein / Portal protein
Similarity search - Component
Biological speciesAnabaena phage A-4L (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsHou P / Li Q / Zhou CZ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U19A2020 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Cryo-EM structure of cyanopodophage A4 reveals a pentameric pre-ejectosome in the double-stabilized capsid.
Authors: Pu Hou / Rui-Qian Zhou / Yong-Liang Jiang / Rong-Cheng Yu / Kang Du / Nanqin Gan / Fei Ke / Qi-Ya Zhang / Qiong Li / Cong-Zhao Zhou /
Abstract: Upon infection, the podophages usually eject a couple of proteins from the capsid to form a transmembrane ejectosome on the host cell membrane that facilitates the ejection of viral genome. However, ...Upon infection, the podophages usually eject a couple of proteins from the capsid to form a transmembrane ejectosome on the host cell membrane that facilitates the ejection of viral genome. However, it remains unclear how these proteins of pre-ejectosome are finely assembled at the center of highly packaged genome. Here, we report the intact structure of cyanopodophage A4, which consists of a capsid stabilized by two types of cement proteins and a short tail attached with six tail fibers. Notably, we find a pentameric pre-ejectosome at the core of capsid, which is composed of four ejection proteins wrapped into a coaxial cylinder of triple layers. Moreover, a segment of genomic DNA runs along the positively charged circular cleft formed by two ejection proteins. Based on the mortise-and-tenon architecture of pre-ejectosome in combination with previous studies, we propose a putative DNA packaging process and ejection mechanism for podophages. These findings largely enrich our knowledge on the assembly mechanism of podophages, which might facilitate the application of A4 as a chassis cyanophage in synthetic biology.
History
DepositionOct 18, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_61998.png

Downloads & links

-
Map

FileDownload / File: emd_61998.map.gz / Format: CCP4 / Size: 103 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 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.029777935 - 0.04705266
Average (Standard dev.)0.00006778108 (±0.002331221)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_61998_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61998_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Anabaena phage A-4L

EntireName: Anabaena phage A-4L (virus)
Components
  • Virus: Anabaena phage A-4L (virus)
    • Protein or peptide: Portal protein
    • Protein or peptide: Internal virion protein
    • Protein or peptide: Internal protein
  • Ligand: ZINC ION

-
Supramolecule #1: Anabaena phage A-4L

SupramoleculeName: Anabaena phage A-4L / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 1357732 / Sci species name: Anabaena phage A-4L / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)

-
Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Anabaena phage A-4L (virus)
Molecular weightTheoretical: 74.284602 KDa
SequenceString: MIRIKDFNHV ITGREQPLDI NEAIASYITS RYVYFKDARR VAEETWLEAW SLYSGTPEAV DHQRTQTINT VGEVNNDWRH RLNTGKAYE CIETVHGYLM GALFPNREWF DLTPNNPGYA NEARIIRKYL TKKFNEGKFR VSFEKYLRQL LVCGYSVMAL P WRYESRPY ...String:
MIRIKDFNHV ITGREQPLDI NEAIASYITS RYVYFKDARR VAEETWLEAW SLYSGTPEAV DHQRTQTINT VGEVNNDWRH RLNTGKAYE CIETVHGYLM GALFPNREWF DLTPNNPGYA NEARIIRKYL TKKFNEGKFR VSFEKYLRQL LVCGYSVMAL P WRYESRPY KYNVTIKREE NEYYDNSTQK ANYRTVTENR VTRNAPEFEC LDVFDVYLSP TSNDPNESDF IRRIKKTRAD II TAIKRGY YTDIDPYDIV NMSAYEVNDR VDKLTSFQGI ETNHPYCMDD IIEVVEYWGD LHLDGVSLYD VKATVIGQTL VCC EPNPFW AGKPFVVGSI TELPETPYSV GLLQPNMGLL HQLNIITNQR CDNLELAIDE MWTLVQNSSL NPDEVQVAPG KVFL VDSHD DLRPIQRGGN NFVVSYQEAG LLESTIDRNT GTGNLISANA SRSGERVTAA EIQAVRDAGG NRLSNIHRHI EDTSL MEIL RRVYRSAQQF VTEPEMIRVS GAKPGEYLFL EVDPESLNKE YSLEPIGADF VTDATKYVRQ RMDFIAFASQ IPQMAE RLN YEALLNDVVN HSGFDDPYSY IVKPQQPAPQ PDMGATPEPQ TGQAPPDEQT NPFYDIGGVS LQNAIGANIQ ADGANEL IN FTTGVNTNAD Q

UniProtKB: Portal protein

-
Macromolecule #2: Internal virion protein

MacromoleculeName: Internal virion protein / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Anabaena phage A-4L (virus)
Molecular weightTheoretical: 40.871699 KDa
SequenceString: MGGAAIGGIL GGVQLVAGIS QANSQANAQR QSLQAQAQTT VDASRIRQME ILQARDQSRF NSSMNELARQ QNYQNQTFLI QRQLLQEQM DAETTKQQAE QQRLQTMSGI EQKDRQTEQQ MVGAEVNFQQ TLQQLAQQLG VVNAQSSQQL TGAEDATKEL G QRLDTRDV ...String:
MGGAAIGGIL GGVQLVAGIS QANSQANAQR QSLQAQAQTT VDASRIRQME ILQARDQSRF NSSMNELARQ QNYQNQTFLI QRQLLQEQM DAETTKQQAE QQRLQTMSGI EQKDRQTEQQ MVGAEVNFQQ TLQQLAQQLG VVNAQSSQQL TGAEDATKEL G QRLDTRDV LAMASGVGLG SSTSSQQQNA DLLGTIDKVA KVLQGTQVGM EVQQRMTELA SASSESERNI KLSELGSYLS DS DFMRNIA NIQASATNQN VDSTMGVNAA ARETAVNAIN AADMMNRQTD TVNNDLAEMG YQVQTSAVNS SQNNAMSGIN AQY GSIGGN TFAGLLSSGV NAFNTYQGVL GQQNALNQQK QMTYLNSGIL SNGATNNNTF KGYN

UniProtKB: Internal virion protein

-
Macromolecule #3: Internal protein

MacromoleculeName: Internal protein / type: protein_or_peptide / ID: 3 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Anabaena phage A-4L (virus)
Molecular weightTheoretical: 116.336844 KDa
SequenceString: MTIKLIGVDN LDNSQQYNEA TNSALVQSLE RNQQSVSKTQ QILEAGNAAI AQQAVSIGQA SQQKAQANAN RGSGIGGLLE GVSKAVGTY WEINQNQQLK QAQIDAKTQV IQREQAEAVA RAAEKAAAEA AEANKQQALT VSEQEANAVR VELGDLYNEW R SGDKFRSE ...String:
MTIKLIGVDN LDNSQQYNEA TNSALVQSLE RNQQSVSKTQ QILEAGNAAI AQQAVSIGQA SQQKAQANAN RGSGIGGLLE GVSKAVGTY WEINQNQQLK QAQIDAKTQV IQREQAEAVA RAAEKAAAEA AEANKQQALT VSEQEANAVR VELGDLYNEW R SGDKFRSE PGGMTKFRDA GLARIMSRTN ITEAQKKELI NLHYGNWDAE MKAYSDRTAK YAEEVSQVRR ESVIKERTFR VN SVVSGLT WDADPTDAIK KVDAMVSSTV NDQNLPLLDR LQAANSMYNT AYEKVVNNAT ARAEVERKMK ALQAYQYEAI TNW NDQTKP RAEREAFDQQ LQAKHGLNVD SSYMAWENSR KQYIEFQQQS RQLQDLEQNG LIDSARKVNL SDDFVGSVVQ LILY GEGNT AALKERFTDN RNFEANTAGA GEVRRLLEAV PRMRRETDSL RSDNAALQVA RTRLQREGVT FLMNADARTR GLLES FAQQ FMVNLPKSNV GLTPEQQAEY ARQTNQVQQA IEQQIIINDQ RVQNNAAELA KYGLSEPEDV LRKNAATRRK LVNDTM YQL GTQAEQVRRT QTSGYGQLGI TSPTTALGEG ANRERLTFVA PDGYRRLRPP VVANLATVKF TGSSRNGIVP GSKVMLP FM AADAGRVRVN SDNHREARAK HTHAGEDIAA PGGTKVVSYV SGQVIKVTRQ KGIGYGRYIT IKGDDGMYHR FAHLSAHN V KQGQRVEAGH VIGLVGDDGS PGSYHLHWEV RDNDGYGANG TVNPLKYMGG VNFKESSAPP PQGNTNGWGY NVNNPPTAR VPANAIKLPN GKFLVNNRTG ALGNPTARAA SEQYTVGRPV NTGKVSGSSW SGTNDYGETY GYAYLANNPE FTKKLAITAT RLGISAQWL VDIMAFETGN FKKATNWSHS RTGVVGLIGF TPATARALGT TTYALAKMPP EKQLDYVYKY LSDPQLKPHL S KGVEYVAA SIFGGSPLVR KMVNNRSGAM QRGDGDINLQ NYLKKLGRDV GRRYDIRSMS RADRLIGSAV HTGFHEGCAT CA ALRSSGS DIVPHNAEFD A

UniProtKB: Internal protein

-
Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107142
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

+
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