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- EMDB-61850: Cyanophage A4 capsid asymmetric unit -

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Basic information

Entry
Database: EMDB / ID: EMD-61850
TitleCyanophage A4 capsid asymmetric unit
Map dataCyanophage A4 capsid
Sample
  • Virus: Anabaena phage A-4L (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Plastocyanin-like domain-containing protein
    • Protein or peptide: Major cement
KeywordsCyanophage / Virus / Capsid
Function / homologyPhage capsid protein / Phage capsid protein / Uncharacterized protein / Major capsid protein / Plastocyanin-like domain-containing protein
Function and homology information
Biological speciesAnabaena phage A-4L (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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 10, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61850.png

Downloads & links

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Map

FileDownload / File: emd_61850.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCyanophage A4 capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 768 pix.
= 821.76 Å		1.07 Å/pix.
x 768 pix.
= 821.76 Å		1.07 Å/pix.
x 768 pix.
= 821.76 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: 0.015
Minimum - Maximum-0.03486578 - 0.071770765
Average (Standard dev.)0.0002918664 (±0.003375972)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 821.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cyanophage A4 capsid

Fileemd_61850_half_map_1.map
AnnotationCyanophage A4 capsid
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cyanophage A4 capsid

Fileemd_61850_half_map_2.map
AnnotationCyanophage A4 capsid
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Anabaena phage A-4L

EntireName: Anabaena phage A-4L (virus)
Components
  • Virus: Anabaena phage A-4L (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Plastocyanin-like domain-containing protein
    • Protein or peptide: Major cement

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Supramolecule #1: Anabaena phage A-4L

SupramoleculeName: Anabaena phage A-4L / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / 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)

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Anabaena phage A-4L (virus)
Molecular weightTheoretical: 38.341383 KDa
SequenceString: MALNNTTYQG SMRGYAVTKS RLDSFIPEVW TGEVLRALNQ NFVASQYVKT LDVTGKKGDR FHIPNIGRAS VFDKLPETPV QLQARQESD FYVDIDKYKE SSFLIEDLGA MQSSYDIRQE YTTEAGYALS RMMDADILGL RAAVKGLNNG SEIFNTADAT I SGASSPLN ...String:
MALNNTTYQG SMRGYAVTKS RLDSFIPEVW TGEVLRALNQ NFVASQYVKT LDVTGKKGDR FHIPNIGRAS VFDKLPETPV QLQARQESD FYVDIDKYKE SSFLIEDLGA MQSSYDIRQE YTTEAGYALS RMMDADILGL RAAVKGLNNG SEIFNTADAT I SGASSPLN YQALLTAKTI LDNRDVPMEK RVIITSPTGY NQLLAIDKFI SMDYQDGRPV KSGVVGTIFG IPVIMTTQVT VN SATGYSN GSTVTGIPTP GVSGAGALHL PTQDVFTSLP TAFTGANTGL AAQVITTLMC HSDWAVMLKS KMPSAESDRS VQY LGDIVV NSMVYGAKLF RQTNAVIINH NAVIPAVV

UniProtKB: Major capsid protein

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Macromolecule #2: Plastocyanin-like domain-containing protein

MacromoleculeName: Plastocyanin-like domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Anabaena phage A-4L (virus)
Molecular weightTheoretical: 21.217752 KDa
SequenceString: MSIAWYRELY GTEPNFNYPN GVLVPNHPGY NQTPGGIYLP NVAALSGAAI TANRIHYVYF QVAQTFVTDA LVFRVSTAVT GNARVGLYT VDPSSGFPQF LVTQGSAAAL TGGSTGDRVV LINRGIVTLP PTWYMTAIVS DVAANLAGIN GSATAQYYRQ P SIPSGGSG ...String:
MSIAWYRELY GTEPNFNYPN GVLVPNHPGY NQTPGGIYLP NVAALSGAAI TANRIHYVYF QVAQTFVTDA LVFRVSTAVT GNARVGLYT VDPSSGFPQF LVTQGSAAAL TGGSTGDRVV LINRGIVTLP PTWYMTAIVS DVAANLAGIN GSATAQYYRQ P SIPSGGSG CYTAPFTYGV LPDLAPTPDA VSTTNHPVVG LRTA

UniProtKB: Plastocyanin-like domain-containing protein

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Macromolecule #3: Major cement

MacromoleculeName: Major cement / type: protein_or_peptide / ID: 3 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Anabaena phage A-4L (virus)
Molecular weightTheoretical: 9.139288 KDa
SequenceString:
MAITCTACTF TMTDAEFAIL NEGVAAPTID PRGSFAGLQS LSGAPITASA SAGTTTVVVA ASNRNDANIR TLAQRLRRAA QANRITFTA

UniProtKB: Uncharacterized protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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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

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 124173
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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