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- EMDB-61910: portal-tail complex of mature T7 -

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Basic information

Entry
Database: EMDB / ID: EMD-61910
Titleportal-tail complex of mature T7
Map dataportal-tail complex of mature T7
Sample
  • Virus: Escherichia phage T7 (virus)
    • Protein or peptide: Protein 6.7
    • Protein or peptide: Protein 7.3
    • Protein or peptide: Tail fiber protein
    • Protein or peptide: Tail tubular protein gp12
    • Protein or peptide: Tail tubular protein gp11
    • Protein or peptide: Portal protein
KeywordsComplex / VIRAL PROTEIN
Function / homology
Function and homology information


virus tail, tube / viral portal complex / virus tail, fiber / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / viral tail assembly / virus tail / T=7 icosahedral viral capsid / adhesion receptor-mediated virion attachment to host cell / symbiont entry into host cell ...virus tail, tube / viral portal complex / virus tail, fiber / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / viral tail assembly / virus tail / T=7 icosahedral viral capsid / adhesion receptor-mediated virion attachment to host cell / symbiont entry into host cell / virion attachment to host cell / identical protein binding
Similarity search - Function
Bacteriophage T7-like virion assembly protein / Bacteriophage T7 virion assembly protein / Bacteriophage T7-like, protein 6.7 / Bacteriophage T7-like, protein 6.7 / : / Tail fibre protein gp37 trimerization region / Bacteriophage T7, Gp17, C-terminal / Tail fibre protein gp37 C terminal domain / Tail tubular protein Gp11 / Tail tubular protein ...Bacteriophage T7-like virion assembly protein / Bacteriophage T7 virion assembly protein / Bacteriophage T7-like, protein 6.7 / Bacteriophage T7-like, protein 6.7 / : / Tail fibre protein gp37 trimerization region / Bacteriophage T7, Gp17, C-terminal / Tail fibre protein gp37 C terminal domain / Tail tubular protein Gp11 / Tail tubular protein / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein, N-terminal domain / Portal protein, Caudovirales / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein
Similarity search - Domain/homology
Portal protein / Tail tubular protein gp11 / Tail tubular protein gp12 / Tail fiber protein / Protein 7.3 / Protein 6.7
Similarity search - Component
Biological speciesEscherichia phage T7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsLiu HR / Chen WY
Funding support China, 6 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)32371263 China
National Natural Science Foundation of China (NSFC)32200994 China
National Natural Science Foundation of China (NSFC)32401014 China
CitationJournal: J Virol / Year: 2025
Title: Conformational changes in and translocation of small proteins: insights into the ejection mechanism of podophages.
Authors: Jing Zheng / Hao Xiao / Hao Pang / Li Wang / Jingdong Song / Wenyuan Chen / Lingpeng Cheng / Hongrong Liu /
Abstract: Podophage tails are too short to span the cell envelope during infection. Consequently, podophages initially eject the core proteins within the head for the formation of an elongated trans-envelope ...Podophage tails are too short to span the cell envelope during infection. Consequently, podophages initially eject the core proteins within the head for the formation of an elongated trans-envelope channel for DNA ejection. Although the core proteins of bacteriophage T7 have been resolved at near-atomic resolution, the mechanisms of core proteins and DNA ejection remain to be fully elucidated. In this study, we provided improved structures of core proteins in mature T7 and the portal-tail complex in lipopolysaccharide-induced DNA-ejected T7 to resolutions of approximately 3 Å. Using these structures, we identified three small proteins, namely gp14, gp6.7, and gp7.3, and illustrated the conformational changes in and translocation of these proteins from the mature to DNA-ejected states. Our structures indicate that gp6.7, which participates in the assembly of the core and trans-envelope channel, is a core protein, and that gp7.3 serves as a structural scaffold to assist the assembly of the nozzle into the adaptor.
IMPORTANCE: Podophage T7 core proteins form an elongated trans-envelope channel for genomic DNA delivery into the host cell. The structures of the core proteins within the mature T7 and assembled in ...IMPORTANCE: Podophage T7 core proteins form an elongated trans-envelope channel for genomic DNA delivery into the host cell. The structures of the core proteins within the mature T7 and assembled in the periplasmic tunnel form in the DNA-ejected T7 have been resolved previously. Here, we resolved the structures of two new structural proteins (gp6.7 and gp7.3) within mature T7 and receptor-induced DNA-ejected T7. The gp6.7 protein participates in the assembly of the core complex within mature T7 and the trans-envelope channel during T7 infection; therefore, gp6.7 is a core protein. Before T7 infection, gp7.3 plays a role in promoting the assembly of the nozzle into the adaptor.
History
DepositionOct 13, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61910.png

Downloads & links

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Map

FileDownload / File: emd_61910.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationportal-tail complex of mature T7
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. 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: 2.0
Minimum - Maximum-33.541041999999997 - 57.230620000000002
Average (Standard dev.)-0.0018986685 (±2.1516993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map1

Fileemd_61910_half_map_1.map
Annotationhalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map2

Fileemd_61910_half_map_2.map
Annotationhalf map2
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 T7

EntireName: Escherichia phage T7 (virus)
Components
  • Virus: Escherichia phage T7 (virus)
    • Protein or peptide: Protein 6.7
    • Protein or peptide: Protein 7.3
    • Protein or peptide: Tail fiber protein
    • Protein or peptide: Tail tubular protein gp12
    • Protein or peptide: Tail tubular protein gp11
    • Protein or peptide: Portal protein

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Supramolecule #1: Escherichia phage T7

SupramoleculeName: Escherichia phage T7 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10760 / Sci species name: Escherichia phage T7 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Protein 6.7

MacromoleculeName: Protein 6.7 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T7 (virus)
Molecular weightTheoretical: 9.354512 KDa
SequenceString:
MCFSPKIKTP KMDTNQIRAV EPAPLTQEVS SVEFGGSSDE TDTEGTEVSG RKGLKVERDD SVAKSKASGN GSARMKSSIR KSAFGGKK

UniProtKB: Protein 6.7

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Macromolecule #2: Protein 7.3

MacromoleculeName: Protein 7.3 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T7 (virus)
Molecular weightTheoretical: 10.088708 KDa
SequenceString:
MGKKVKKAVK KVTKSVKKVV KEGARPVKQV AGGLAGLAGG TGEAQMVEVP QAAAQIVDVP EKEVSTEDEA QTESGRKKAR AGGKKSLSV ARSSGGGINI

UniProtKB: Protein 7.3

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Macromolecule #3: Tail fiber protein

MacromoleculeName: Tail fiber protein / type: protein_or_peptide / ID: 3 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T7 (virus)
Molecular weightTheoretical: 61.641875 KDa
SequenceString: MANVIKTVLT YQLDGSNRDF NIPFEYLARK FVVVTLIGVD RKVLTINTDY RFATRTTISL TKAWGPADGY TTIELRRVTS TTDRLVDFT DGSILRAYDL NVAQIQTMHV AEEARDLTTD TIGVNNDGHL DARGRRIVNL ANAVDDRDAV PFGQLKTMNQ N SWQARNEA ...String:
MANVIKTVLT YQLDGSNRDF NIPFEYLARK FVVVTLIGVD RKVLTINTDY RFATRTTISL TKAWGPADGY TTIELRRVTS TTDRLVDFT DGSILRAYDL NVAQIQTMHV AEEARDLTTD TIGVNNDGHL DARGRRIVNL ANAVDDRDAV PFGQLKTMNQ N SWQARNEA LQFRNEAETF RNQAEGFKNE SSTNATNTKQ WRDETKGFRD EAKRFKNTAG QYATSAGNSA SAAHQSEVNA EN SATASAN SAHLAEQQAD RAEREADKLE NYNGLAGAID KVDGTNVYWK GNIHANGRLY MTTNGFDCGQ YQQFFGGVTN RYS VMEWGD ENGWLMYVQR REWTTAIGGN IQLVVNGQII TQGGAMTGQL KLQNGHVLQL ESASDKAHYI LSKDGNRNNW YIGR GSDNN NDCTFHSYVH GTTLTLKQDY AVVNKHFHVG QAVVATDGNI QGTKWGGKWL DAYLRDSFVA KSKAWTQVWS GSAGG GVSV TVSQDLRFRN IWIKCANNSW NFFRTGPDGI YFIASDGGWL RFQIHSNGLG FKNIADSRSV PNAIMVENE

UniProtKB: Tail fiber protein

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Macromolecule #4: Tail tubular protein gp12

MacromoleculeName: Tail tubular protein gp12 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T7 (virus)
Molecular weightTheoretical: 89.480594 KDa
SequenceString: MALISQSIKN LKGGISQQPD ILRYPDQGSR QVNGWSSETE GLQKRPPLVF LNTLGDNGAL GQAPYIHLIN RDEHEQYYAV FTGSGIRVF DLSGNEKQVR YPNGSNYIKT ANPRNDLRMV TVADYTFIVN RNVVAQKNTK SVNLPNYNPN QDGLINVRGG Q YGRELIVH ...String:
MALISQSIKN LKGGISQQPD ILRYPDQGSR QVNGWSSETE GLQKRPPLVF LNTLGDNGAL GQAPYIHLIN RDEHEQYYAV FTGSGIRVF DLSGNEKQVR YPNGSNYIKT ANPRNDLRMV TVADYTFIVN RNVVAQKNTK SVNLPNYNPN QDGLINVRGG Q YGRELIVH INGKDVAKYK IPDGSQPEHV NNTDAQWLAE ELAKQMRTNL SDWTVNVGQG FIHVTAPSGQ QIDSFTTKDG YA DQLINPV THYAQSFSKL PPNAPNGYMV KIVGDASKSA DQYYVRYDAE RKVWTETLGW NTEDQVLWET MPHALVRAAD GNF DFKWLE WSPKSCGDVD TNPWPSFVGS SINDVFFFRN RLGFLSGENI ILSRTAKYFN FYPASIANLS DDDPIDVAVS TNRI AILKY AVPFSEELLI WSDEAQFVLT ASGTLTSKSV ELNLTTQFDV QDRARPFGIG RNVYFASPRS SFTSIHRYYA VQDVS SVKN AEDITSHVPN YIPNGVFSIC GSGTENFCSV LSHGDPSKIF MYKFLYLNEE LRQQSWSHWD FGENVQVLAC QSISSD MYV ILRNEFNTFL ARISFTKNAI DLQGEPYRAF MDMKIRYTIP SGTYNDDTFT TSIHIPTIYG ANFGRGKITV LEPDGKI TV FEQPTAGWNS DPWLRLSGNL EGRMVYIGFN INFVYEFSKF LIKQTADDGS TSTEDIGRLQ LRRAWVNYEN SGTFDIYV E NQSSNWKYTM AGARLGSNTL RAGRLNLGTG QYRFPVVGNA KFNTVYILSD ETTPLNIIGC GWEGNYLRRS SGI

UniProtKB: Tail tubular protein gp12

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Macromolecule #5: Tail tubular protein gp11

MacromoleculeName: Tail tubular protein gp11 / type: protein_or_peptide / ID: 5 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T7 (virus)
Molecular weightTheoretical: 22.30765 KDa
SequenceString: MRSYDMNVET AAELSAVNDI LASIGEPPVS TLEGDANADA ANARRILNKI NRQIQSRGWT FNIEEGITLL PDVYSNLIVY SDDYLSLMS TSGQSIYVNR GGYVYDRTSQ SDRFDSGITV NIIRLRDYDE MPECFRYWIV TKASRQFNNR FFGAPEVEGV L QEEEDEAR ...String:
MRSYDMNVET AAELSAVNDI LASIGEPPVS TLEGDANADA ANARRILNKI NRQIQSRGWT FNIEEGITLL PDVYSNLIVY SDDYLSLMS TSGQSIYVNR GGYVYDRTSQ SDRFDSGITV NIIRLRDYDE MPECFRYWIV TKASRQFNNR FFGAPEVEGV L QEEEDEAR RLCMEYEMDY GGYNMLDGDA FTSGLLTR

UniProtKB: Tail tubular protein gp11

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Macromolecule #6: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 6 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T7 (virus)
Molecular weightTheoretical: 59.173984 KDa
SequenceString: MAEKRTGLAE DGAKSVYERL KNDRAPYETR AQNCAQYTIP SLFPKDSDNA STDYQTPWQA VGARGLNNLA SKLMLALFPM QTWMRLTIS EYEAKQLLSD PDGLAKVDEG LSMVERIIMN YIESNSYRVT LFEALKQLVV AGNVLLYLPE PEGSNYNPMK L YRLSSYVV ...String:
MAEKRTGLAE DGAKSVYERL KNDRAPYETR AQNCAQYTIP SLFPKDSDNA STDYQTPWQA VGARGLNNLA SKLMLALFPM QTWMRLTIS EYEAKQLLSD PDGLAKVDEG LSMVERIIMN YIESNSYRVT LFEALKQLVV AGNVLLYLPE PEGSNYNPMK L YRLSSYVV QRDAFGNVLQ MVTRDQIAFG ALPEDIRKAV EGQGGEKKAD ETIDVYTHIY LDEDSGEYLR YEEVEGMEVQ GS DGTYPKE ACPYIPIRMV RLDGESYGRS YIEEYLGDLR SLENLQEAIV KMSMISSKVI GLVNPAGITQ PRRLTKAQTG DFV TGRPED ISFLQLEKQA DFTVAKAVSD AIEARLSFAF MLNSAVQRTG ERVTAEEIRY VASELEDTLG GVYSILSQEL QLPL VRVLL KQLQATQQIP ELPKEAVEPT ISTGLEAIGR GQDLDKLERC VTAWAALAPM RDDPDINLAM IKLRIANAIG IDTSG ILLT EEQKQQKMAQ QSMQMGMDNG AAALAQGMAA QATASPEAMA AAADSVGLQP GI

UniProtKB: 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 35.0 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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65620
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING

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