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- EMDB-69212: The composite Cryo-EM structure of the tail region of bacteriopha... -

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Basic information

Entry
Database: EMDB / ID: EMD-69212
TitleThe composite Cryo-EM structure of the tail region of bacteriophage RAN69
Map data
Sample
  • Virus: Klebsiella phage RAN69 (virus)
    • Protein or peptide: tail spike gp1
    • Protein or peptide: nozzle gp13
    • Protein or peptide: tail fiber gp9
    • Protein or peptide: adaptor gp14
    • Protein or peptide: portal gp19
Keywordsbacteriophage / RAN69 / tail / VIRUS
Biological speciesKlebsiella phage RAN69 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsRuan Z / Hu H / Wang A / Shao Q / Li X / Xie L / Sun Z / Yu J / Fang Q
Funding support China, 3 items
OrganizationGrant numberCountry
Other governmentJCYJ20250604174416022
Other governmentA2402025
National Natural Science Foundation of China (NSFC)32371285 China
CitationJournal: To Be Published
Title: Near-complete cryo-EM structure of the Klebsiella pneumoniae podophage RAN69 reveals tail fiber-spike interface and a divergent pre-ejectosome
Authors: Ruan Z / Hu H / Wang A / Shao Q / Li X / Xie L / Sun Z / Yu J / Fang Q
History
DepositionFeb 15, 2026-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_69212.png

Downloads & links

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Map

FileDownload / File: emd_69212.map.gz / Format: CCP4 / Size: 282.6 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 420 pix.
= 499.8 Å		1.19 Å/pix.
x 420 pix.
= 499.8 Å		1.19 Å/pix.
x 420 pix.
= 499.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.19 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.7
Minimum - Maximum-18.411239999999999 - 36.764429999999997
Average (Standard dev.)0.024155313 (±1.2934271)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 499.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Klebsiella phage RAN69

EntireName: Klebsiella phage RAN69 (virus)
Components
  • Virus: Klebsiella phage RAN69 (virus)
    • Protein or peptide: tail spike gp1
    • Protein or peptide: nozzle gp13
    • Protein or peptide: tail fiber gp9
    • Protein or peptide: adaptor gp14
    • Protein or peptide: portal gp19

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Supramolecule #1: Klebsiella phage RAN69

SupramoleculeName: Klebsiella phage RAN69 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 3683496 / Sci species name: Klebsiella phage RAN69 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: tail spike gp1

MacromoleculeName: tail spike gp1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage RAN69 (virus)
Molecular weightTheoretical: 60.926059 KDa
SequenceString: MALVDVVRAG GYSIEYPQFS SMAKLKAFPH SEDGQLVRLL SWHEGVGLGG GLFKVSTSST ATGNDGTVVV ASNGVRLLRV VNGPIWADM FGALPNSDID SKPAVAAAYA YAASVNTDLY IGVAAYKFKG STPINVDPSR AGIIGYQGKV RIDCSEFTGS V VFSINSSY ...String:
MALVDVVRAG GYSIEYPQFS SMAKLKAFPH SEDGQLVRLL SWHEGVGLGG GLFKVSTSST ATGNDGTVVV ASNGVRLLRV VNGPIWADM FGALPNSDID SKPAVAAAYA YAASVNTDLY IGVAAYKFKG STPINVDPSR AGIIGYQGKV RIDCSEFTGS V VFSINSSY SYTPAAYYNN LSPALQGLYV FGAKTSGVDG LLVGRETVGS DESYNGQTEV RECTFDKFDR NIRMGHNSWR FV FYKVNSL NALNPNGILY VPAGLDDSGE ILSFYHCQFF DGAGSNIRLS CSSYTMVFNT CSFLNITFFV DSASSATVTC NGC NFENPG SASTRRYVDI SAGHTNVFNI IGGSIVTNSN PGQTQALLYV STDNLLNLVG VTVPYGGHYQ QEQELGYHAF IGGA GTVTT SGVMLQLRNG AGTCPLHPSL STFSNWDFGY GNLNAWTVDK GTGTSSVVEY LANAGPKGTE GAMRVAPVSV GTNVS QVQA VTNPGMFSMS CMVNIATTPG NAGQVSIGFL DAAGNRLPGG VSANLGTTTG WKVIGKNTLR GKVPIGAKQV RVNIQT VAG ADVKYAYLLC NVVK

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Macromolecule #2: nozzle gp13

MacromoleculeName: nozzle gp13 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage RAN69 (virus)
Molecular weightTheoretical: 86.632773 KDa
SequenceString: MAQSLEGTIQ SLLQGVSQQV PRERQPGQLG AQLNMLSDPV SGIRRRPPGE IVWESTIDNP GLDSLFTEYV ERGTDGRHML INTSNGNWW LLAKNGKTVV NSGNDPYFIA TAGQTSLQTA SIAGLTYILN TEMAPVTAVD NTGRIDPSTT GFFYVKAAAF Q KRWEVTVT ...String:
MAQSLEGTIQ SLLQGVSQQV PRERQPGQLG AQLNMLSDPV SGIRRRPPGE IVWESTIDNP GLDSLFTEYV ERGTDGRHML INTSNGNWW LLAKNGKTVV NSGNDPYFIA TAGQTSLQTA SIAGLTYILN TEMAPVTAVD NTGRIDPSTT GFFYVKAAAF Q KRWEVTVT WSGGSVTGYY NVPDASSGTE SAEWASASFV INALINGDPN GYGIGAAITA AGGTVVGFGA YMYIAGLPNL VV STSSGDT YAVASGQSRV PQEQDLPAQL PAEADGAMCR VGTASSETAW YQFNYSERTW YEVGAYGSIT KITNMPRELA ADD NIIARD WEGRLAGNDD NNSNPGFIEN GYITGIAAFQ GRLVLLSGSS VDMSASGLYQ RFYRSTVTSL LDTDRISISS ASAQ DSVYR TAVQFNRDLV LFANSMQAVV PGSAVLTPTN ASISITSTYD CDSRVTPVMA GQTVIYPNKR NDSYAGILEL IPSPY TAAQ YTTQDATVHL PRYIPGRVLQ MQNSSVTNMA FSRMSGERNS LLVYEFMWGG SDGAKMQAAW HKWSFPYPIL SVQALE DEV FLYMQGPSPS NKLLIVSMDP REGYQLGSEY REAYSDLQKQ VQVQDGVFTV PAVLRPVGWA DNYKEELILT YLPSNPM GP TEVGIKEIAG ENTLRVVRGV PDGTYVIGRR YRSTFTLTTP ILRDQNDKLV GSGHVRLLRL DVAVRNSGHF DVQVLDTP R DVNWGGELTG ILMNSKELTL GQALRMDLAT ITVPCRTNAD TTEVTLFTEG SMELNVLDIS YILRYNQRRR RI

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Macromolecule #3: tail fiber gp9

MacromoleculeName: tail fiber gp9 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage RAN69 (virus)
Molecular weightTheoretical: 32.818289 KDa
SequenceString: MAYSWQEQIK PAGTQDIQCD IEYLDKSYIH VYLDGVETTG YTWTSSTNIR LNTALTVNTT VLLIRKTERE YLYIEFASGS PFIEVNVDS QNTQFLHLAQ ELVEGRAIPG FYGTISMNGY RITDLANPTN SQDAATKAYV DAADALLGQR IDAEAATRKA A DDALSMRT ...String:
MAYSWQEQIK PAGTQDIQCD IEYLDKSYIH VYLDGVETTG YTWTSSTNIR LNTALTVNTT VLLIRKTERE YLYIEFASGS PFIEVNVDS QNTQFLHLAQ ELVEGRAIPG FYGTISMNGY RITDLANPTN SQDAATKAYV DAADALLGQR IDAEAATRKA A DDALSMRT SALENTFISG VETVSYPWST VLAEATDEVT PGLAFTKAVV EINGVGQIRG YSFEIIDNTI LFAETLPAGT VV AARLGAD VTAGDGFATQ ASVDYLADSL GDLAYLDTAE AVPDATGAGD VVAQLNALLA SLRTSGVLAS

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Macromolecule #4: adaptor gp14

MacromoleculeName: adaptor gp14 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage RAN69 (virus)
Molecular weightTheoretical: 21.286904 KDa
SequenceString:
MRELDAINLT LEALGESRVM DINTSNPSAG LARSALARNR RGLLSTGFWF NVVEREVAPT ADGFIKVPWN QLAVYDAGSD SKYGVRDGN LYDLMEQDQY FDSSVKLKIV LDLDFEDLPE HAAMWVANYT TAQVYLNDLG GDSNYANYAQ EAERYKSMVL R EHLRNQKF STSKTRFARR IRRARFMV

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Macromolecule #5: portal gp19

MacromoleculeName: portal gp19 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage RAN69 (virus)
Molecular weightTheoretical: 58.217703 KDa
SequenceString: MEQKATLAEL FKKDQDAGVL DASEKFAQWT LSTIFTRDDS LDGRRRPLER DYQSTGAQLV NTAATKIVGA LFPQGTSFFR FSKSSDLDE FISSLGSAAT AESKLAEVEN TASQKVFEKD GYAAKLQAVK LLLVTGNALE YIDERTGKSI VYSVRNFTVR R DGSGNVLR ...String:
MEQKATLAEL FKKDQDAGVL DASEKFAQWT LSTIFTRDDS LDGRRRPLER DYQSTGAQLV NTAATKIVGA LFPQGTSFFR FSKSSDLDE FISSLGSAAT AESKLAEVEN TASQKVFEKD GYAAKLQAVK LLLVTGNALE YIDERTGKSI VYSVRNFTVR R DGSGNVLR LIIRERASVQ DLPEDFRGTF YRDKDPYGDV DIYTAACRKV KRTEDGAEVV SYEVYQEADG HRIGDSSTYP EL ELPYNVL VWNLVSGEHY GRGLVEDYAG DFARLSVLSE ALTNYEVESA RLIPLIDASS GLDVDEFSTS ETGEAVQVGG GGS NGNSKS PVTAYEGGSA QKIQWIASNI QMLEQKLSRA FMYTGNSRQG ERVTAYEIRQ NAKEAEAAMG GGFSILSDTW LRKL AYLYT ALVYPRFKLY LSEGVVNINV TVGTSALAKA AAADKLLEAA QSMQLAIPVL EQITPRFNKD ACVDWYFDAY GIVSE PFMY TEEQLQQKQK VQDASADVSA GAAQDQLQGL TAADPTVAGK QLGLLPS

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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 / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 53029
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 / Software - Name: RELION (ver. 4.0) / Number images used: 53029
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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