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- EMDB-72905: N4 Bacteriophage Asymmetric Tail Gating Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-72905
TitleN4 Bacteriophage Asymmetric Tail Gating Complex
Map data
Sample
  • Virus: Escherichia phage N4 (virus)
    • Protein or peptide: Gp53
    • Protein or peptide: Non-contractile tail sheath
    • Protein or peptide: Gp54
Keywordsbacteriophage / 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
Similarity search - Domain/homology
Non-contractile tail sheath / Gp53 / Gp54
Similarity search - Component
Biological speciesEscherichia phage N4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.61 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)GM140733 United States
CitationJournal: To Be Published
Title: Architecture of the giant RNA polymerase ejected from the coliphage N4 Capsid
Authors: Bellis NF / Lokareddy RK / Kizziah JL / Cooper SL / Schneider DA / Forti F / Briani F / Cingolani G
History
DepositionSep 26, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72905.png

Downloads & links

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Map

FileDownload / File: emd_72905.map.gz / Format: CCP4 / Size: 105.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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 551 pix.
= 657.894 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: 0.115
Minimum - Maximum-0.4282604 - 0.7494123
Average (Standard dev.)0.0062806155 (±0.08172392)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin320251321
Dimensions225551223
Spacing223225551
CellA: 266.262 Å / B: 268.65 Å / C: 657.894 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72905_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72905_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72905_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: Gp53
    • Protein or peptide: Non-contractile tail sheath
    • 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
Host (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)

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Macromolecule #1: Gp53

MacromoleculeName: Gp53 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage N4 (virus)
Molecular weightTheoretical: 97.954336 KDa
SequenceString: MGLFSSKTKI YVASSVYNLA GDIHKRPNYL KTTVIGNIVS KSDFSMGDTI TDSYLNGPGI RLRRFPGWAA TNYDPSIGIA YGNLSILSQ VDPEVVKWQV PQKAGYEVQV QSSRIGFGDF EEWADKFLYE NYPDRITEEF EIDIMDDDRI VLTATDGSEL S FYPKNYSQ ...String:
MGLFSSKTKI YVASSVYNLA GDIHKRPNYL KTTVIGNIVS KSDFSMGDTI TDSYLNGPGI RLRRFPGWAA TNYDPSIGIA YGNLSILSQ VDPEVVKWQV PQKAGYEVQV QSSRIGFGDF EEWADKFLYE NYPDRITEEF EIDIMDDDRI VLTATDGSEL S FYPKNYSQ DAMYLYVNYY YIQPTSVADP VVHPAVSVSS ADDLPSTSEW TQVSQNHTPK SATLKTVTHI KSVFSDGRPD EE STNTEEE QVSWTNFSDV YEKEFREPSE VGLIIIRKTI MTQVQTGTVS TGSTTNTEVI DLGGGVTETR TTTVTTDTLG HTW SYQNTD VVTTLSAGGM PQLFIYKQNS GNAVLDALFI NKTTNNRFYS FIPIRSDKNW ISGSTYTLCK KAFKKATGGK ISDI MDDLK KNKDIGDIQY IYAVFGCSLN SPENTAKEYI YRFFQLVNQS MPADPNYPTM DALVEGFAQA NRDFDAYQEW WESRS GNRD IPIGKPPKRP VYPTIPSKSI NIRSNGGYRY NMTISWNFIE ESVGSGKAFS GAKKGQLKFA YEGTVVLMQK AVMYSE KGN DKVGFTIYRL DKITMYWQDG DNSWRKISVY GLNHNNNVYK NKSVSISGVD ALNDDEESGF IIPLHNNIYR SMSLVNG TQ LSTACCYLVL NSYKKVKKKW YQSGIFKVVV VVVAVVVSVF FTPAAGAGVM GTAASIGAAL GFAGLAAIIV GAVANAIA A MILMSIIQTV SVSLLGDKIG IIVATIASMV AMNVGTALST GSSMSTMLGE MMKADNIIKL TSSVGNGISD YINASAMET VKKTEKLMAE YRDQMKTIQE KYEEMFGTEG MGYIDPMNLT NVGQQFEPLD SFLSRTLMTG HDIADMSNNM ITNFTDITLQ LDLDT

UniProtKB: Gp53

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Macromolecule #2: Non-contractile tail sheath

MacromoleculeName: Non-contractile tail sheath / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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: Gp54

MacromoleculeName: Gp54 / type: protein_or_peptide / ID: 3 / 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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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 / Mesh: 300 / 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 18434
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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