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- EMDB-62011: Cyanophage A4 pre-ejectosome with C1 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-62011
TitleCyanophage A4 pre-ejectosome with C1 symmetry
Map data
Sample
  • Virus: Anabaena phage A-4L (virus)
    • Protein or peptide: Tail protein
    • Protein or peptide: Tail protein
KeywordsCyanophage / Virus / Capsid / VIRAL PROTEIN
Function / homologyTail protein / Tail protein
Function and homology information
Biological speciesAnabaena phage A-4L (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62011.png

Downloads & links

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Map

FileDownload / File: emd_62011.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-0.027811063 - 0.042537708
Average (Standard dev.)0.00000007469928 (±0.0016009067)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #2

Fileemd_62011_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62011_half_map_2.map
Projections & Slices
AxesZYX

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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: Tail protein
    • Protein or peptide: Tail protein

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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: Tail protein

MacromoleculeName: Tail protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Anabaena phage A-4L (virus)
Molecular weightTheoretical: 125.851086 KDa
SequenceString: MSKHCGLEAN QKATDNEPKK RIRWNKSQRT LIEKLTADKH RKLRQSRRTA DIYGDEVSAA QSQKLAEIEE VLIRSAGDVI SLDRGQYDK WASLVSAKLG WRRGNPLNPS LNYSQAGEVR EALKDARRVA QNLINDASHI RMLDGIKRFD DIYRQIMKPL G MTTDDARA ...String:
MSKHCGLEAN QKATDNEPKK RIRWNKSQRT LIEKLTADKH RKLRQSRRTA DIYGDEVSAA QSQKLAEIEE VLIRSAGDVI SLDRGQYDK WASLVSAKLG WRRGNPLNPS LNYSQAGEVR EALKDARRVA QNLINDASHI RMLDGIKRFD DIYRQIMKPL G MTTDDARA LFNETIEIGS IPKNNKIYGN SEGVRLINSL RHSDYIERAK GYGLNDEAIE TLLRAATDVH SVFDEMRVIA EA TGHNIEE LQNLGYFPRI ATRDFNIRLR KALETDTALA DVIMSEGVEQ VKALNPLSSV WQKSRKFNYF VPDDLEVASK LLN TSSDEI AEMLLNPREW MEFLTSSVSS SQIETMTELG VMSKLPMTSR EVFEQLVDQY ELPYKHINEM FKLDPHVAAE EYAR VLRQA VGNSAMLKTV VKDGLAAGWA VPEKMLKDLS PKERANFVPL SFQKLDQFMS PEQLEAAGKV YVHRVVSDQW RSMLE ISMS ANKLGAFASA WSHLSTFLNK SVLASRNVLY VGTNFLSGFV LTNAVGANVF TVPHAMMDIS NYLAKGLDAF DGTKPF AKI GGEWISKREF FKQFLLKRGS DITPGTVSTT SSGGDANPFT SFKSIGALAD VRSAKRALEY LWSYSSSFGD PVRGTKG AA EYVGSLLNEA TDNFFSPFAK MASFLDTMYK WNAYTSLVER QGAAELANTI AQGMTLEPIS RIGRKFDNWR DLSRHIDD Y FFTFDDPGTT TKVISKYVRP FANWSMQSTP AMLRAALRSP QKFSAYAKLL QLYNRGNNDD EPLNQSQLTD WQDDEYPVI LQRDALQTGD GNGGLLVLFP HTFDPITDTL NVIDNAGRTV NILFGNKYGG NERDNRNSVT GKKDGLTSML TELFNDTYWA KPAGLLLGI DSFTGQKIDA SKYNNYLGFE MHPLAEALLG MYTPLDAINR TNLFDTFGRR EYKDYRDRTV VEEKPGLFGG Q RTNSDAQS LAWETAVKNG NWSALALMTM GARVRLIDTA RNTQMTLDEI KTGIDELQKA NVNAARQLTL NPEKLSESER NK RTERLTE SLTAEYQMKY DYARLINYMK AKRIPPKRLL FEMQQRSVNV SDLEPVGGKQ RLQLESDFRR RIEEINK

UniProtKB: Tail protein

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Macromolecule #2: Tail protein

MacromoleculeName: Tail protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Anabaena phage A-4L (virus)
Molecular weightTheoretical: 189.859203 KDa
SequenceString: MSIIKDVQDS NDPQLDKFNN EDAPKLAPVI PTPQPTDAGL SLGSTPVGVN PQAVIETEST PQPLTPEQQA LTDSYNEASR LTTNVQPMS ELVQPQQALP TPTNIDSQQP TVFESANQFN LSATDNLLQQ GKITQELINE TQLTQSHIPT VYSTPYDGDE W DLDFEASL ...String:
MSIIKDVQDS NDPQLDKFNN EDAPKLAPVI PTPQPTDAGL SLGSTPVGVN PQAVIETEST PQPLTPEQQA LTDSYNEASR LTTNVQPMS ELVQPQQALP TPTNIDSQQP TVFESANQFN LSATDNLLQQ GKITQELINE TQLTQSHIPT VYSTPYDGDE W DLDFEASL ERAGVLPGQK PSPETFNSQF NAQPTNEDAS RSFNPNALKR SQFDVEGALA AIRNINTQEG LTGYQTIKPW GE GALSSLM YGLGVVSNTI RGGVIDAVNV RNRVVNQLPK PIQGVLNFNP ASALTGQQLI RPDANYRGSY TLDAIRGRQY SFT ANSTNK DEPIGITGFK AFDDLAERMR QNRNARYNAI NKTFGREIAK PVAVEERWST DLSFWAGFGL DTILDPIDSI GVAW KASGL LLGNAPSYVK RGIPTNTGRV IVTPAASERK LLPPGRTRYT PPGKPDGYEL GLTEPLTNNK YQVVQTPKGE VSIPV GQPT VQAKLPSIAS NNKVTSLTLR REIRRPDGVI DVEFTPNPGA FDRVTGISNE PLAQLPSSEA RRPLEPTQFE TIQTPN GEV QVPINQPSAP RQLPGTRTYS QPNWRWSRVV DGYINPEGMQ PIIEVVRRKP EVFTTNSTSG YSPNWEYWSA PKVDDLY IP APIDVEFKVI PNKPSNLPLK PSSLSEDIVQ GVDGEVRVPS STQPNSQLAL PYGEPYPLTQ WDLSLETNPP QIGQRIDN N ITVAKNQGEA IDDVINNAPR TVEYNVSGLE IPRRNVTPQG FPKLEPRYDI KPPETPRVIE LAPESVTVIR EALDSNDWV KAYDELLRKR VPVSDIKRKL ETGRIDEAVN DLRKLIGDIK PKTAPEPKPV APKRQRRRVI KADGTAVYET VRVNPETQLL DAAITNINV VANVVDVPSM SVSQSTPASP LAIDAASDAL RPVSPGTPLV APTSEVNKQL VDQLTRLTET ERMMKRRGAS P ETLERIRT QKLELRKAIA DGDELAEPKV KPEPVTPAIN KTVLTGTMTM SELSQQLLDN VPGSRIDPDK VRRVERKLSE VE ALMKVIP NPITGEPLLG SANTRKFRTW AKDSSTSPTA YLNKLGLQEY PLLYRLFERD GAAIDIDALA HPEFRVILDK PLP DKTSRQ VVVSNTPSLT KPTVQSESKA ITEMTINELR SERKLLKSQI NELDDPSDLI ERLMELDDAI NNLDITKPEN LKVV QDEVI PETQHGTSPE VVKLTQQKLD IENEVINTGV RVQELELELA RQKVQLEDAL SRIEETADIN PHDVISEPLP SGRAR RVPT EIPPNDGTIL TQKEAARFYD ISEGNFKNGD TKPRPALVHT KHMVSDVVVP NDVIQREFDN IMNMGGITQP IVITPV GLD DVYIKYAVVD NHAIYEAAKL AREADPRKFE NVNVIVIHPS KADPSYFADE VLPTNTTEGS LYHGTRVKGW TPGNGGV GE WGSGTYFSKS SQAASDNAIK PLRPALGEVI DNVTQPTIHE VLPDFKRTVD VNSPVDGDFS AALLMSANEL MDGSEFTS F KRSIMKPGTV QLRDTIKTPA DIYAAIEKYA AKNDIEWTPE RTHKFKSRIN ERLRLVGVDA LTDGDTTLVI NPDAVSVIN SHLLDETDAI GTSIARYNSA SEAAGRNSGI PTANANQAEA SVMLQRQMYE ETIEKLEDAK RQQRTAITKS HEIDEQLTQT AQAEQTTKR QQRVAKSQKR AEREAERLGK KRDNPCQF

UniProtKB: Tail 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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 535710
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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