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- EMDB-72877: N4 Empty Particle C6 Tail -

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Basic information

Entry
Database: EMDB / ID: EMD-72877
TitleN4 Empty Particle C6 Tail
Map dataN4 Empty Particle C6 Tail
Sample
  • Virus: Escherichia phage N4 (virus)
    • Protein or peptide: 30 kDa protein
  • Protein or peptide: Non-contractile tail sheath
  • Protein or peptide: Gp64
  • Protein or peptide: Gp54
  • Protein or peptide: 60 kDa protein
  • Protein or peptide: Probable portal protein
Keywordsdodecamer / bacteriophage portal / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, short tail mechanism / virus tail / adhesion receptor-mediated virion attachment to host cell / virion component / 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 / : / Phage SU10 portal protein / Leucine-rich repeat profile. / Leucine-rich repeat
Similarity search - Domain/homology
Probable portal protein / Gp64 / Non-contractile tail sheath / 60 kDa protein / 30 kDa protein / Gp54
Similarity search - Component
Biological speciesEscherichia phage N4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsBellis NF / Cingolani G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Res Sq / Year: 2025
Title: Structure of the giant RNA polymerase ejected from coliphage N4.
Authors: Nathan F Bellis / Ravi K Lokareddy / Mikhail Pavlenok / Stephanie L Cooper Horton / James L Kizziah / Francesca Forti / David A Schneider / Michael Niederweis / Federica Briani / Gino Cingolani /
Abstract: are widespread prokaryotic viruses that encapsidate a giant (~3,500-residue) virion-associated RNA polymerase (vRNAP). During infection, vRNAP is expelled into Gram-negative bacteria, along with two ... are widespread prokaryotic viruses that encapsidate a giant (~3,500-residue) virion-associated RNA polymerase (vRNAP). During infection, vRNAP is expelled into Gram-negative bacteria, along with two additional ejection proteins, to assemble a transient DNA-ejectosome that becomes transcriptionally active, initiating viral replication. Here, we present an integrative structural analysis of the coliphage N4 vRNAP (gp50). We find that this 383 kDa enzyme is a multi-domain, single-chain RNA polymerase, structurally distinct from both compact single-chain RNAPs and large multi-subunit holoenzymes. vRNAP is composed of loosely connected domains and exhibits an intramolecular mode of allosteric regulation through its C-terminal domain. Comparative analysis of intact and genome-released virions identified gp51, which forms an outer-membrane complex, and gp52, which assembles a periplasmic tunnel. These proteins generate heterogeneous pores that facilitate the release of vRNAP. We further uncover a signaling hub in the phage tail, composed of the receptor-binding protein, tail tube, and tail plug, that detects receptor engagement and orchestrates the release of ejection proteins. We propose that the beads-on-a-string architecture of vRNAP enables the translocation of megadalton-scale protein complexes through the ~35 Å channel formed by the tail and ejection proteins. These findings establish N4 as a distinctive model for protein translocation through biological channels.
History
DepositionSep 25, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72877.png

Downloads & links

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Map

FileDownload / File: emd_72877.map.gz / Format: CCP4 / Size: 73.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationN4 Empty Particle C6 Tail
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.19 Å/pix.
x 223 pix.
= 266.262 Å		1.19 Å/pix.
x 225 pix.
= 268.65 Å		1.19 Å/pix.
x 382 pix.
= 456.108 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.194 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.14120908 - 0.44285363
Average (Standard dev.)0.00938314 (±0.055729236)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin320288321
Dimensions225382223
Spacing223225382
CellA: 266.262 Å / B: 268.65 Å / C: 456.108 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72877_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_72877_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_72877_half_map_2.map
AnnotationHalf Map A
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: 30 kDa protein
  • Protein or peptide: Non-contractile tail sheath
  • Protein or peptide: Gp64
  • Protein or peptide: Gp54
  • Protein or peptide: 60 kDa protein
  • Protein or peptide: Probable portal protein

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Supramolecule #1: Escherichia phage N4

SupramoleculeName: Escherichia phage N4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 2886925 / Sci species name: Escherichia phage N4 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)

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Macromolecule #1: 30 kDa protein

MacromoleculeName: 30 kDa protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia 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 #2: Non-contractile tail sheath

MacromoleculeName: Non-contractile tail sheath / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia 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 #3: Gp64

MacromoleculeName: Gp64 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia 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 #4: Gp54

MacromoleculeName: Gp54 / type: protein_or_peptide / ID: 4 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia 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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Macromolecule #5: 60 kDa protein

MacromoleculeName: 60 kDa protein / type: protein_or_peptide / ID: 5 / Number of copies: 36 / Enantiomer: LEVO
Source (natural)Organism: Escherichia 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 #6: Probable portal protein

MacromoleculeName: Probable portal protein / type: protein_or_peptide / ID: 6 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage N4 (virus)
Molecular weightTheoretical: 85.642523 KDa
SequenceString: MEQNTDSMVP LPDPSQATKL TSWKNELSLQ ALKADLDAAK PSHTAMMIKV KEWNDLMRIE GKAKPPKVKG RSQVQPKLVR RQAEWRYSA LTEPFLGSNK LFKVTPVTWE DVQGARQNEL VLNYQFRTKL NRVSFIDNYV RSVVDDGTGI VRVGWNREIR K EKQEVPVF ...String:
MEQNTDSMVP LPDPSQATKL TSWKNELSLQ ALKADLDAAK PSHTAMMIKV KEWNDLMRIE GKAKPPKVKG RSQVQPKLVR RQAEWRYSA LTEPFLGSNK LFKVTPVTWE DVQGARQNEL VLNYQFRTKL NRVSFIDNYV RSVVDDGTGI VRVGWNREIR K EKQEVPVF SLFPIQTQEQ ADALQQALQL RTDNPRGYEE NVDEAIKESV RFFDETGQAT YAVQTGTTTT EVEVPLANHP TV EMLNPEN IIIDPSCQGD INKAMFAIVS FETCKADLLK EKDRYHNLNK IDWQSSAPVN EPDHATTTPQ EFQISDPMRK RVV AYEYWG FWDIEGNGVL EPIVATWIGS TLIRLEKNPY PDGKLPFVLI PYMPVKRDMY GEPDAELLGD NQAVLGAVMR GMID LLGRS ANGQRGMPKG MLDALNSRRY REGEDYEYNP TQNPAQMIIE HKFPELPQSA LTMATLQNQE AESLTGVKAF AGGVT GESY GDVAAGIRGV LDAASKREMA ILRRLAKGMS EIGNKIIAMN AVFLAEHEVV RITNEEFVTI KREDLKGNFD LEVDIS TAE VDNQKSQDLG FMLQTIGPNV DQQITLNILA EIADLKRMPK LAHDLRTWQP QPDPVQEQLK QLAVEKAQLE NEELRSK IR LNDAQAQKAM AERDNKNLDY LEQESGTKHA RDLEKMKAQS QGNQQLEITK ALTKPRKEGE LPPNLSAAIG YNALTNGE D TGIQSVSERD IAAEANPAYS LGSSQFDPTR DPALNPGIRL GN

UniProtKB: Probable portal 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
GridModel: C-flat-2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 10265
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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