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- EMDB-69208: The composite Cryo-EM structure of bacteriophage RAN69 pre-ejecto... -

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Basic information

Entry
Database: EMDB / ID: EMD-69208
TitleThe composite Cryo-EM structure of bacteriophage RAN69 pre-ejectosome-portal complex
Map data
Sample
  • Virus: Klebsiella phage RAN69 (virus)
    • Protein or peptide: gp11
    • Protein or peptide: gp12
    • Protein or peptide: gp10
    • Protein or peptide: portal gp19
    • Protein or peptide: gp20
Keywordsbacteriophage / RAN69 / pre-ejectosome-portal complex / VIRUS
Biological speciesKlebsiella phage RAN69 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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 China
Other governmentA2402025 China
National Natural Science Foundation of China (NSFC)32371285 China
CitationJournal: Structure / Year: 2026
Title: Near-complete cryo-EM structure of the Klebsiella pneumoniae podophage RAN69 reveals tail fiber-spike interface and a divergent pre-ejectosome.
Authors: Zhiyang Ruan / Hongli Hu / Aohan Wang / Qianqian Shao / Xiangyun Li / Linlin Xie / Zhuo Sun / Jiaxin Yu / Qianglin Fang /
Abstract: Carbapenem-resistant Klebsiella pneumoniae is a critical-priority pathogen, underscoring the need for alternatives to antibiotics. Bacteriophages are promising agents, yet high-resolution structures ...Carbapenem-resistant Klebsiella pneumoniae is a critical-priority pathogen, underscoring the need for alternatives to antibiotics. Bacteriophages are promising agents, yet high-resolution structures of K. pneumoniae phages are scarce. Here, we report near-complete cryo-electron microscopic reconstructions of the K. pneumoniae podophage RAN69 at 3.0-3.4 Å resolution, enabling atomic models for 12 structural components. Complete in situ structures of the long tail fiber (gp9 trimer) and distal tail spike (gp1 trimer) are resolved, revealing a previously unknown binding interface in which the gp1 N-terminal arm wedges between spike-binding domains of gp9. The pre-ejectosome forms a conserved double-layered assembly (gp10 tetramer over gp11 octamer), tethered to the portal by an octameric gp12 that inserts long helices into the portal barrel, with gp20 reinforcing gp11 interfaces. Divergent folds in gp10 and a lysozyme-like gp11 peripheral domain suggest adaptation to host envelopes. These structures advance our understanding of podophage assembly.
History
DepositionFeb 15, 2026-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_69208.png

Downloads & links

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Map

FileDownload / File: emd_69208.map.gz / Format: CCP4 / Size: 91.1 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 288 pix.
= 342.72 Å		1.19 Å/pix.
x 288 pix.
= 342.72 Å		1.19 Å/pix.
x 288 pix.
= 342.72 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: 2.5
Minimum - Maximum-7.6155715 - 13.135126
Average (Standard dev.)-0.061112106 (±0.98286486)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 342.72003 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: gp11
    • Protein or peptide: gp12
    • Protein or peptide: gp10
    • Protein or peptide: portal gp19
    • Protein or peptide: gp20

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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: gp11

MacromoleculeName: gp11 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage RAN69 (virus)
Molecular weightTheoretical: 96.890922 KDa
SequenceString: MPVIQPTRQG LNIGGVQLQS NEVQLPSSAG EVAVDASKAN RLAALSGFVQ DFGVGFEEGI KENAAAATVR GAMDAQGAVD AMASKDEAV QKQNIFVREA YQDGYVSAAA YDSLAKWRTD SIARAKKAAE AGLTDEEFQQ QEQEHVQSMS DKLGMYLPEM S KQSATAVL ...String:
MPVIQPTRQG LNIGGVQLQS NEVQLPSSAG EVAVDASKAN RLAALSGFVQ DFGVGFEEGI KENAAAATVR GAMDAQGAVD AMASKDEAV QKQNIFVREA YQDGYVSAAA YDSLAKWRTD SIARAKKAAE AGLTDEEFQQ QEQEHVQSMS DKLGMYLPEM S KQSATAVL QQLRATSMAN YTAFQKGRAA FAVAQADRAL DRGLSSSGDE FYQRLQAGQG AAAQMSIKTG LDSILAAEHL DK SKKLDRA KQYLVSVAQQ TQDPLVINQL QELATKELGV NSVDVNAALY QEFKRAGAQI ETQARFEISD AISSLEGQTP EQQ EQTMAR IRSRVIELSA SDVLSAGTSM EFWNKAQTIR EKAADTQALR TAITGNMPSS TLAGMYKGDL GKARNELLKS FPDT PEGNL QLLAYGSNSK DAWAVNEAHK RMSSDMARTL TTLDQLGEDG EVSRENVSSI NLWAQAYSTS TDLGKMALLS EVPSE WQGV VQKAIAQNPS NASNTILDDL RRQARNKASG RYSNIQSNPT DKMVDPSGTS NWFSFFGTAD AQRQEARAAM EEEYRY TYS HNPESLVGKD PDDINTMLKG NIQARKLELD ISGAPRHVYL PAGTSIQSLM GDYRGDQEQF KVSLQQQIQN QVNALID PS NLERVVVQAA TAGNSAQNMT ITTFDKKGTF QTMSVNLRDV QVAAQDAYDK ALSGEMKIGS DQVGIRPATF YDHDNGRA V SVQVNGRNGA GVEPSLFSEI LANTMQFEGF REGKGKGSVG FGLHINSGMP VPKKVTIDDG ISILKSSLEQ QYIPNVNKQ LRGQGLSASA DAMKVMVDLN YHGGNGSSGP VAEAMAAVRK SKDSAGAALY SIPQASAAAL TILRQQPAYK EAQPKRKQYL EQHLQAWIF EVTH

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Macromolecule #2: gp12

MacromoleculeName: gp12 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage RAN69 (virus)
Molecular weightTheoretical: 20.921416 KDa
SequenceString: MGMWWAAAAL AGSKLLGAGA QIEVSKARNK AVIQQTAKQL NDIALQRAQS RDRTEVSLFN IQQQKLQAQS QVGLQAASSG TMGASVKDA VATVNTVAGR QEASVRDQQA TQEEGFRMLV DKTVDSGLAN MDMESGYDKM FNMALSVGGQ MLGQYVGNKL S ETTPEPSA ...String:
MGMWWAAAAL AGSKLLGAGA QIEVSKARNK AVIQQTAKQL NDIALQRAQS RDRTEVSLFN IQQQKLQAQS QVGLQAASSG TMGASVKDA VATVNTVAGR QEASVRDQQA TQEEGFRMLV DKTVDSGLAN MDMESGYDKM FNMALSVGGQ MLGQYVGNKL S ETTPEPSA PSVEPTAQNS FLYDLWGSKG DSKVHTW

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Macromolecule #3: gp10

MacromoleculeName: gp10 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage RAN69 (virus)
Molecular weightTheoretical: 135.202531 KDa
SequenceString: MAQFLNQEPN PQEKDSAKGA TLKPAPASVD WNDADDGGVS ALERASLMAQ AKTPATSAGD SFAAGVGNSI VAAAIRKASA PAFMPEQGF DAKKYLGTDS RTKLYTPSAE EIEYLHGAAS REEYDYRVQD MLTQRNRDRM MSDNVAVGVA GMLLGDSPFI L APMAAGGI ...String:
MAQFLNQEPN PQEKDSAKGA TLKPAPASVD WNDADDGGVS ALERASLMAQ AKTPATSAGD SFAAGVGNSI VAAAIRKASA PAFMPEQGF DAKKYLGTDS RTKLYTPSAE EIEYLHGAAS REEYDYRVQD MLTQRNRDRM MSDNVAVGVA GMLLGDSPFI L APMAAGGI AGRTGLAVRS AIRAGDVATA VYAQDQLGQS AGVTALIAGV SGIDQLWDMS RAAKAAAKLR TGREPAFDPD AP TTRTARD TNVTGVGERT LDSIMDEVLA EPITVQAKNV AGVSLKAHHV TQYLRSTGTL TRGQEVLLDA IEPVVRDVDF TLM AGTDRV VARSRYTFNP DNLTAPGTVA LRAPAAAEGS TWNTVGDALR AADAETRGAA LHELIHAATS RALDADPSLV ERLK PIQEH LQQTANLKGE LKYLASDPHE MLAGLANNSD WVQLLSRTPS QTAGKSVLRQ LGEAVLQAFG ITARGSSLDD VLNTF EAAV KWSADNTRAA QYEFRSDIMR EAAESALREQ NEFLKAKAMM EGTKKAFARN FALYDNIAQG SEDLARLLVS DATSVG ARR PSVVDYKRNL TLEMDASAVI VEDAILSALK ARNIGPLSRF FHRSNFRAAR ADLESRLGHY LDSAYDAQLN GRAVPVP EA DIAPLVEAYK RSGWAGRWHD HMSAAGLLDD ADVLKSDYYF PRQYSYDKLR QGLLEGRTLD NYRDLFRQAL RDIYPNIE P EVVQQVAKEM VDGIYNGRAA GRGPMWRQLI NGMSEDELLG AMRNAGVSDS AINSFAAANL RSSGATNPAR NLRHRNRFN MSKEYMVDGQ AMRMQDLMDT NVPKVMHGYT NRMSGRVGMA YAGVSDLKTL ETMINASKHS VANPEKWERV VDDTIDFILG GMPADANLP DMLRAAGNIA NATMLKNSGL YQLTDTALSL KTFGMTRVAR SMAEQPWFKE GAVVFGSKDM SERLDSILRG G VQRDMRFR WFNTYADDNL DLTRQAPWFN VTQNVGQAAR HVNGMSMVHR LQVNLNSGIV ADELKQMFKG DSEAFKRLEK FG LDRDVAD RAIAAEKANP GAVFDPELQM QIEVVGVRMM DYLVQQIRTG ETSHFAQFNP VGKLIVGFQS FAVAATNKIL RRE LNDAGW IGLAHIMAYQ FPLMLLATKA KHSMDGKDTD TRRLVTEAVM GMSAIGGISL LQDIFTGDSP RHSLASMGYV TGLL GAVQD LATGNMDIKT FTKQVPLIQE FAPTRAIINN FGDD

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Macromolecule #4: portal gp19

MacromoleculeName: portal gp19 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / 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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Macromolecule #5: gp20

MacromoleculeName: gp20 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage RAN69 (virus)
Molecular weightTheoretical: 8.741618 KDa
SequenceString:
MSGGLGKLLG KATDMLGLTD NAGLEAQQRL AEQQASAAKQ QAALEANSAA DNIAEIDPAG AASASADAIT SEQKKRRQAG QSNPLGL

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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 correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 25878
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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