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- EMDB-61942: Cyanophage A4 portal-tail complex -

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Basic information

Entry
Database: EMDB / ID: EMD-61942
TitleCyanophage A4 portal-tail complex
Map data
Sample
  • Virus: Anabaena phage A-4L (virus)
    • Protein or peptide: Tail fiber protein
    • Protein or peptide: Portal protein
    • Protein or peptide: Tail tubular protein B
    • Protein or peptide: Tail tubular protein A
KeywordsCyanophage / Virus / Tail / Portal / Zozzle / Adaptor / Tail Fiber / VIRAL PROTEIN
Function / homology: / SU10 adaptor protein / : / Phage SU10 portal protein / Tail tubular protein A / Tail fiber protein / Portal protein / Tail tubular protein B
Function and homology information
Biological speciesAnabaena phage A-4L (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 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 15, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61942.png

Downloads & links

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Map

FileDownload / File: emd_61942.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 416 pix.
= 445.12 Å		1.07 Å/pix.
x 416 pix.
= 445.12 Å		1.07 Å/pix.
x 416 pix.
= 445.12 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: 0.01
Minimum - Maximum-0.03929484 - 0.07641664
Average (Standard dev.)0.00028134816 (±0.0029988147)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 445.12003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61942_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_61942_half_map_2.map
Projections & Slices
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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 fiber protein
    • Protein or peptide: Portal protein
    • Protein or peptide: Tail tubular protein B
    • Protein or peptide: Tail tubular protein A

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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 fiber protein

MacromoleculeName: Tail fiber protein / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Anabaena phage A-4L (virus)
Molecular weightTheoretical: 39.873277 KDa
SequenceString: MATSNVVVSR TGTGWTVDVT ACNLLSDTGI KDFIVLHNAI VVSNVTYAKT TATTLTYTGA ALPSNTPVEI RRKTPNSIIQ LVTYGQKLS SNLWNSEIDR NIRWREEVDL NGAGLVASTP TPQNDAYGLV WAGDTFYPPT RKSVYDKIET LATKSGAVLT G ATANVSPS ...String:
MATSNVVVSR TGTGWTVDVT ACNLLSDTGI KDFIVLHNAI VVSNVTYAKT TATTLTYTGA ALPSNTPVEI RRKTPNSIIQ LVTYGQKLS SNLWNSEIDR NIRWREEVDL NGAGLVASTP TPQNDAYGLV WAGDTFYPPT RKSVYDKIET LATKSGAVLT G ATANVSPS TADNTLALAT TAYVKANLAD YATLVSPILT GDPRAVTTSV TDNDTSIATT AHVRAFANSR LAFNAFRGGQ QG VPSLNYI TTVCQFTSSA VRSGWGDNFS SNRWLVGQGG TYYVSVTCRF ATTGGTPPTY MDVLLFVGLS PTGVENFVIR QQT NYPSFG YTLTWSGVLF FNTNDNVYLT YQAQAIGGGG YAVVIEDARF NAIQLS

UniProtKB: Tail fiber protein

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Macromolecule #2: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / 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

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Macromolecule #3: Tail tubular protein B

MacromoleculeName: Tail tubular protein B / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Anabaena phage A-4L (virus)
Molecular weightTheoretical: 113.330102 KDa
SequenceString: MTDQFERNNI RNNEVAAEQS IQSNNFGGLN TLASPLNVPY QDSPLLLNTT VDTSGQVYKR KGTRITYTTT GTSTGCYITG FTSGLAYQF QVAKRGRDIL LFQTTNDVTS LLLTKSNVWD TRAEAVRPSV VTTSEVTPRV IFATGVNKPV QLLFVEQQTT Q TANGTSVV ...String:
MTDQFERNNI RNNEVAAEQS IQSNNFGGLN TLASPLNVPY QDSPLLLNTT VDTSGQVYKR KGTRITYTTT GTSTGCYITG FTSGLAYQF QVAKRGRDIL LFQTTNDVTS LLLTKSNVWD TRAEAVRPSV VTTSEVTPRV IFATGVNKPV QLLFVEQQTT Q TANGTSVV FSSADRFVNA STANCLVYVN RVLVSAPSFS YNAGTKQLTV SNLGSTVIGD VIDLVSVTWQ WWAESQFWYG DR FFGSTTR FNSVSFDRVV KIPTSITTQN NGSDPYYRMR LYKQSNRTGS PNLNEVVQPQ LADDWAFSDG SIYNYSVNDY PNP SPFWVV FGALVGGGQP STVYFSRRRG LGFANGTSVQ ASKIDVVVNG VQRTPIYTPG SAPDSVYRNY YTYFADTTGA ATGT SSTSL VNGIFFDAIP LGLATNDTVE ASNNTNIHIG SASIATRYNY NDGSYIPAFG LGDFADYLNG YYPSVVTFFQ GRLVF GGFP HRPLQVVFSN VNDNITPGRY YNSFSITDDN TALSSAFDII LNSRPDDRVV ALIEWQSSLF ILTRQAVFRA NGGSSI LSS TNRVISYVSS NGCTNSRCIV RTDFNVMYLS DTGVYNINPL VENGEYTVKE LSIKIRDKFG VTREPVYEEL PWMAYDS VN KQVLLGYPDV GQTNTSRYVY VYNTYRESWT EYNTPCGFNI WSTTEYTDRL LGTSVCSILY TTTSSGTPSN FIIIRWNA S LYIDFIQRKT HNGSSYELTT QPAVTHTTNV NQRRYGVNFT LTRQNTAFTI NPVTTVNDLY VTLDGTLLTP NVDYIKEET GYIYLLSTFS TGQTLKIASS PEGNTTPNSW YTVYVNNIRQ VSPTPSAGTF TLGATNGDII NWGVNYLTIY TTPQFLWNSL GNFKRTQHA YLFLDNRDGV GVYVASDVNN GQDINQLTEL YRVPINFNLS VMYNNQLDGS TSYDVMGYDS MYWDEGVFDV S SPYDQYQP YQTLKIPITG IGYAFQMLIW NHSDEYFKLG GYQIIAKQKG KRHIGRY

UniProtKB: Tail tubular protein B

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Macromolecule #4: Tail tubular protein A

MacromoleculeName: Tail tubular protein A / type: protein_or_peptide / ID: 4 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Anabaena phage A-4L (virus)
Molecular weightTheoretical: 24.783678 KDa
SequenceString: MPKTTTFIQL VNKCLENIGE RPVISFNNSV ARKAADTVRD AITDVSYSYD WSWLTTSIIA NSWINERADL GDVQSVKHVS YGSSSDGYR ELTFTDERTF DAAKIYPGVG QVFTFNEYGG VRINPYPETV EEQVKYKFYV VKEATLPSVE IDVINIPDRF I QLITYNAC ...String:
MPKTTTFIQL VNKCLENIGE RPVISFNNSV ARKAADTVRD AITDVSYSYD WSWLTTSIIA NSWINERADL GDVQSVKHVS YGSSSDGYR ELTFTDERTF DAAKIYPGVG QVFTFNEYGG VRINPYPETV EEQVKYKFYV VKEATLPSVE IDVINIPDRF I QLITYNAC TQLSISHLDD AQASQMWNSK YIDQLSRLRA RERNTTQSGA NMFKFRGTR

UniProtKB: Tail tubular protein A

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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

MicroscopeFEI TECNAI F30
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: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 106052
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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