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- EMDB-62961: tail complex of mature phage N4 -

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Basic information

Entry
Database: EMDB / ID: EMD-62961
Titletail complex of mature phage N4
Map data
Sample
  • Virus: Escherichia phage N4 (virus)
    • Protein or peptide: 60 kDa protein
    • Protein or peptide: Gp64
    • Protein or peptide: Non-contractile tail sheath
    • Protein or peptide: 30 kDa protein
    • Protein or peptide: Gp54
KeywordsComplex / VIRAL PROTEIN
Function / homology
Function and homology information


virus tail / adhesion receptor-mediated virion attachment to host cell / symbiont entry into host cell
Similarity search - Function
: / Non-contractile tail sheath N-terminal domain / Non-contractile tail sheath protein TIM barrel / : / SU10 adaptor protein / Leucine-rich repeat profile. / Leucine-rich repeat
Similarity search - Domain/homology
Gp64 / Non-contractile tail sheath / 60 kDa protein / 30 kDa protein / Gp54
Similarity search - Component
Biological speciesEnterobacteria phage N4 (virus) / Escherichia phage N4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLiu H / Chen W
Funding support China, 7 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32071209 China
National Natural Science Foundation of China (NSFC)32200994 China
National Natural Science Foundation of China (NSFC)32401014 China
National Natural Science Foundation of China (NSFC)32271329 China
National Natural Science Foundation of China (NSFC)32071262 China
CitationJournal: Structure / Year: 2025
Title: Asymmetric structure of podophage N4 from the Schitoviridae family reveals a type of tube-sheath short-tail architecture.
Authors: Jing Zheng / Hao Pang / Hao Xiao / Junquan Zhou / Zhonghua Liu / Wenyuan Chen / Hongrong Liu /
Abstract: The tails of the majority of reported podophages are typically composed of an adaptor, a nozzle, and a needle, and flanked by six or twelve fibers. However, the Schitoviridae family, as represented ...The tails of the majority of reported podophages are typically composed of an adaptor, a nozzle, and a needle, and flanked by six or twelve fibers. However, the Schitoviridae family, as represented by podophage N4, exhibits a different tail architecture that remains poorly understood. In this study, we employed cryoelectron microscopy (cryo-EM) to determine the atomic structures of mature and empty podophage N4 particles. The N4 tail, which is connected to the head by a portal and flanked by 12 fibers, comprises an adaptor, a 12-fold extended tail tube encircled by a 6-fold tail sheath, and a plug. The extended tail sheath is composed of two proteins, gp65 and gp64. Furthermore, we identified two distinct tail conformations in the mature podophage N4. Our structures provide insights into the mechanisms of ejection and early transcription of podophage N4, as well as for N4-like phages and CrAssphages.
History
DepositionJan 3, 2025-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62961.png

Downloads & links

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Map

FileDownload / File: emd_62961.map.gz / Format: CCP4 / Size: 421.9 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 480 pix.
= 508.8 Å		1.06 Å/pix.
x 480 pix.
= 508.8 Å		1.06 Å/pix.
x 480 pix.
= 508.8 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: 5.2
Minimum - Maximum-45.212580000000003 - 57.334359999999997
Average (Standard dev.)-0.00042485562 (±1.8151966)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-240-240-240
Dimensions480480480
Spacing480480480
CellA=B=C: 508.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62961_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_62961_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia phage N4

EntireName: Escherichia phage N4 (virus)
Components
  • Virus: Escherichia phage N4 (virus)
    • Protein or peptide: 60 kDa protein
    • Protein or peptide: Gp64
    • Protein or peptide: Non-contractile tail sheath
    • Protein or peptide: 30 kDa protein
    • Protein or peptide: Gp54

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Supramolecule #1: Escherichia phage N4

SupramoleculeName: Escherichia phage N4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2886925 / Sci species name: Escherichia phage N4 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: 60 kDa protein

MacromoleculeName: 60 kDa protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage N4 (virus)
Molecular weightTheoretical: 58.943914 KDa
SequenceString: MSGHTPFNTI PNEGYCCETL NDPIVDKMIG NAYYVVKFVA LRMPFIKNVS DNMTQLLAIH NKLTELSAIY TKLDELQLIH NNLDKLQEL YNQLSKLTGL YDNLQALLRV YDNLTPINTV ASNIDAVNTV ATDIAKVIIV SAQIDKVITV ANSITNVNTV A GSIDAVNT ...String:
MSGHTPFNTI PNEGYCCETL NDPIVDKMIG NAYYVVKFVA LRMPFIKNVS DNMTQLLAIH NKLTELSAIY TKLDELQLIH NNLDKLQEL YNQLSKLTGL YDNLQALLRV YDNLTPINTV ASNIDAVNTV ATDIAKVIIV SAQIDKVITV ANSITNVNTV A GSIDAVNT VSTNINAIKN VNTNMAALLD LDNHMTELLA VHARLGDLVT IAEQLDTIIA DHEKYATAEG AGLIGFNQAQ TY AANTVGA MLRQVITMGN DKGGYAVAGK LTSARGVWSL ATGSINMNAP TAGAVANLVL NYKAGKVSGL LVAPSQQMAL DGL IMGAST ADNTATVSVT APLRFKADLT AKTISGVNTR IMPSSAVTLN VDAYGGITLG YPPSLQTVEP VMTFITPTGK APLT PRFSS VTAGAAVLVM VGEAEAQLKY SGGGWAAVSD WDSGTYCAFD TVSGELTVYH STLIKDSTVT FSLLLPTDDT QLTAQ LKSH TDSSFVVKIA KPDGSLLDAP LEGMGIMYSR GMHGIYKVPY GSLIVDVGRV QVKFSEFNTT EGISVVGINS NA

UniProtKB: 60 kDa protein

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Macromolecule #2: Gp64

MacromoleculeName: Gp64 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage N4 (virus)
Molecular weightTheoretical: 48.100742 KDa
SequenceString: MSNAAVVPMP YSPTTVPREQ IREIQLQLIN EMTDVHMGAL TAQYMPDDFT FEPGIGQIHF NVETSRKVCL DLAKSVLRLV PVYPLVSPV KKQHDDYWFV GRLGLDPVSE PEPINMPTME FYKRFLSLLH ERDMKFVNSV AYEILNFFMP DEWKQLNWKG D PALSGWYP ...String:
MSNAAVVPMP YSPTTVPREQ IREIQLQLIN EMTDVHMGAL TAQYMPDDFT FEPGIGQIHF NVETSRKVCL DLAKSVLRLV PVYPLVSPV KKQHDDYWFV GRLGLDPVSE PEPINMPTME FYKRFLSLLH ERDMKFVNSV AYEILNFFMP DEWKQLNWKG D PALSGWYP PSSFIQPTNK DALDFVSKAQ CQILKECQNL GMELYFQIGE PWWWDGSYNT GEGKNAPCIY DPKTMALYKE ET GNDVPTP WIKDIFAPVE EHQWPYVDWL CTKLGQSTNY IRDYVKGKFP DAQATLLFFT PQIMSPASEL TGRLNFPESE WIF PNYDFV QIEDYDWIID GRLDLVPLTF DAAVNRLGYP LNVVHYFIGF VLLPEDAKKI WADVDKAWGL ALEAGIPHIY PWSY TQVMR DGVIYAVPKV CG

UniProtKB: Gp64

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Macromolecule #3: Non-contractile tail sheath

MacromoleculeName: Non-contractile tail sheath / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage N4 (virus)
Molecular weightTheoretical: 154.255078 KDa
SequenceString: MSIEDYLKGK NCLASPNYDP DDQHSSWRED LPQFKKDREH LTLVNTRRNR TYNTKLNRFD PEYWVVDYNA LMVATIIPYG SKSFKVPCQ WRTNKDFLGV RWMTEDTFDH HLYRYETDPN YLGLILAFRH NPDEPDKFTV TIQTPEKAYT YRLAPYGFNN K TRRWECLD ...String:
MSIEDYLKGK NCLASPNYDP DDQHSSWRED LPQFKKDREH LTLVNTRRNR TYNTKLNRFD PEYWVVDYNA LMVATIIPYG SKSFKVPCQ WRTNKDFLGV RWMTEDTFDH HLYRYETDPN YLGLILAFRH NPDEPDKFTV TIQTPEKAYT YRLAPYGFNN K TRRWECLD TKYGTKRTYQ ADIFVATDED IPESEMTEVY GTKDYIFILD FADLRTGVAF NGVTINPRNI TMISFDCTEA HH GLGKDAY IAAMYNNDDG ATFQMEIGGI HTNAALAAGD KLQCIWRYLD VNGNAQAAEN EFEVVSYEGF GTSNFSVKCK GML PGKFIG CDAFYGKYLQ TDGPIKQVDS VKWFTNLTVS GSGRKQLGQR KYPQVVMGMG MTSGFDDGYN LTPERQVKMA YGLG YRDWW TTYIGMSHYW KGLTAFQDKE TGELITEQTV LDYPILFAGE SQVAIHFMSG AYPDRGYDVF QKYMTETWGI NYAGV HPIN GTTGSTAVDR ACAVNPNSEV FDPTQSSGAG GLWWWDLEAD KPGPALLHCV GQVGKLKPKA IIWGQGDQDA TALAYP GDR NPAPSLTRTK QATKKVFEYL RSLYGQIPIF IQELSYAWGI TNTDAPNVPI RTGLPSFLAA RRNTWGDIEF RWKSYGL DP ALAQYRIEIY NPSNLNQILH SFVVSGTQEA NGYVYADFTV EDWIPVMMEA VGSPNPWEFM KWRVVCLYQE REIPSAPW S DNIPLDNAGL VKKTILVGIN QFGGGHFTDM SDPTATTANG AIGRKDKVSA STLRLTFAEK AGLRPIQVMP VNVAADSAG MTVGTHKWWN TSSNSPGDAL LAINDMVKGL GVKPDYFIEA NPWETMYMKD VNSSTWPALM TAFESSNKAM LAWMRTNWGN PNLEIWFQG ATTVWFGVAP PNDLNSEATV TVRDKQIQMA TANIGFKLGS FVPGSNLYTA YRNVESSWIY YTVEAFHATA I ELGEALAL NINRATNPPD WSYLRPPANL QGRKLATRDI KMTWDNRAGI THWKYANRHV TTGAEISSGI LTSPEYVFTL ND QQNAYNG DTLNMSFSVS EYAADSGAVG ASSSFVGVVQ NGSYMQTPTQ LKAAKQLNGD IIFTWVGRPS WQHFWVVNTS VND SKTVIF SKEWSSESLT WTVAEQNEFY GLEEGGATHV IFMVSEYDPS NGLVSIGAQV TGQAEQPSNP MNPVAGLYAV FTGD PGNSN IKIMWDKPSV GGRDVRIRNM HVTSSATISD QFVSDNNLVF TREEQVAAYG FTASSVSVRA QEHDIESGAL GLTTE YVAV PETAGTVGQG FAKKDSVGNC TMSWEVGDAV QWQVEILNAE NSTVVKTEIV VAPTITWMAE EITAEYGYLT DHMVWR VRP YRADGASNVA KQFDMTATL

UniProtKB: Non-contractile tail sheath

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Macromolecule #4: 30 kDa protein

MacromoleculeName: 30 kDa protein / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage N4 (virus)
Molecular weightTheoretical: 27.192412 KDa
SequenceString: MYYIEELFCR LANGVLNNTG IVTDDRGDIE DDSKPFIIVA ANEALTRLHG RFNMRNNNVV VEMQEGRTNY PLLAKYAVQS YDPNEVKCP FIMDLAGEKF AEDVIRILEV YDDKGRRRPL NDRNNPCSLF TPRPNVLQNN APKAWEVLNV MYQAKHPKLS T AEDGYNEI ...String:
MYYIEELFCR LANGVLNNTG IVTDDRGDIE DDSKPFIIVA ANEALTRLHG RFNMRNNNVV VEMQEGRTNY PLLAKYAVQS YDPNEVKCP FIMDLAGEKF AEDVIRILEV YDDKGRRRPL NDRNNPCSLF TPRPNVLQNN APKAWEVLNV MYQAKHPKLS T AEDGYNEI DIPDTLDPAL DAYIAYRYYT SLNTPESSAK AAEYLSFYDS ICREVVEYDL TSDTEVDTNT LFRKRGWR

UniProtKB: 30 kDa protein

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Macromolecule #5: Gp54

MacromoleculeName: Gp54 / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage N4 (virus)
Molecular weightTheoretical: 32.438443 KDa
SequenceString: MSCGAELEAN ALLTALVAGE DFTLPDIDMS GSEYDIPGGI NSPIYAEIEK ITTEQLTTRE VGGSGVFDAL MQSASNHLLA EFKNNRITG GDYVKAYIAT MEACMANAVQ FLTTKDQAYW NAVTAQVAAI TARANLGIIK ANFVTAKIQA LATKAEYALT K LKLSNESV ...String:
MSCGAELEAN ALLTALVAGE DFTLPDIDMS GSEYDIPGGI NSPIYAEIEK ITTEQLTTRE VGGSGVFDAL MQSASNHLLA EFKNNRITG GDYVKAYIAT MEACMANAVQ FLTTKDQAYW NAVTAQVAAI TARANLGIIK ANFVTAKIQA LATKAEYALT K LKLSNESV TYCTAQYNLS SMLPQQLLML KNQTTQVAEQ TKLTTEQINM TKEQKEAQRA QTSDTRTDGT RVAGSVGKQK EL YDQQITS YKRDAEVKAA KLFTDAWVTQ KTIDEGLSPP NGFTNSSLDS ILTALKNNNA LG

UniProtKB: Gp54

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47179
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING

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