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- EMDB-47685: In situ cryoEM structure of bacteriophage Ur-lambda tail tip complex -

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Basic information

Entry
Database: EMDB / ID: EMD-47685
TitleIn situ cryoEM structure of bacteriophage Ur-lambda tail tip complex
Map dataBacteriophage Ur-lambda tail tip complex full map
Sample
  • Virus: Escherichia phage Ur-lambda (virus)
    • Protein or peptide: Tape measure protein
    • Protein or peptide: Tail tip assembly protein I
    • Protein or peptide: Tail tip assembly protein I
    • Protein or peptide: Tip attachment protein J
    • Protein or peptide: Tail tip protein L
    • Protein or peptide: Tail fiber protein
    • Protein or peptide: Tail tip protein M
    • Protein or peptide: Tail tube protein
  • Ligand: IRON/SULFUR CLUSTER
Keywordsbacteriophage / tail tip complex / VIRAL PROTEIN
Function / homology
Function and homology information


virus tail, tube / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail, fiber / virus tail / adhesion receptor-mediated virion attachment to host cell / 4 iron, 4 sulfur cluster binding / entry receptor-mediated virion attachment to host cell / host cell cytoplasm / receptor-mediated virion attachment to host cell ...virus tail, tube / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail, fiber / virus tail / adhesion receptor-mediated virion attachment to host cell / 4 iron, 4 sulfur cluster binding / entry receptor-mediated virion attachment to host cell / host cell cytoplasm / receptor-mediated virion attachment to host cell / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / metal ion binding
Similarity search - Function
Lambda-like tail fibre protein, N-terminal / Prophage tail fibre N-terminal / Bacteriophage lambda, Tail fiber protein, repeat-1 / Phage tail fibre repeat / Bacteriophage lambda, Tail fiber protein, repeat-2 / Phage tail fibre repeat / Bacteriophage tail tape measure, C-terminal / Bacteriophage tail tape measure, N-terminal / Tape measure protein / Prophage tail length tape measure protein ...Lambda-like tail fibre protein, N-terminal / Prophage tail fibre N-terminal / Bacteriophage lambda, Tail fiber protein, repeat-1 / Phage tail fibre repeat / Bacteriophage lambda, Tail fiber protein, repeat-2 / Phage tail fibre repeat / Bacteriophage tail tape measure, C-terminal / Bacteriophage tail tape measure, N-terminal / Tape measure protein / Prophage tail length tape measure protein / Lambda phage tail tape-measure protein (Tape_meas_lam_C) / Bacteriophage lambda, Tail tip protein L / Bacteriophage lambda, Tail tip protein M / Bacteriophage lambda tail assembly I / Phage minor tail protein L / Phage minor tail protein / Bacteriophage lambda tail assembly protein I / Phage tail collar domain superfamily / : / Phage tail collar domain / Domain of unknown function DUF3672 / : / Phage Tail Collar Domain / Tip attachment protein J, C-terminal receptor binding domain / Tip attachment protein J, Ig-like domain / Tip attachment protein J second Ig-like domain / : / Tip attachment protein J,FNIII-A domain / : / Domain of unknown function DUF1983 / Bacteriophage tail tip fiber protein / Lambda phage tail tube protein / Lambda phage tail tube protein, TTP / Tip attachment protein J / Putative phage tail protein / Carboxypeptidase-like, regulatory domain superfamily / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Beta-grasp domain superfamily / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Tail tip assembly protein I / Tail tube protein / Tape measure protein / Tail tip protein M / Tail tip protein L / Tip attachment protein J / Tail fiber protein
Similarity search - Component
Biological speciesEscherichia phage Lambda (virus) / Escherichia phage Ur-lambda (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsYu H / Liu J / Molineux IJ
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)124378 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)110243 United States
CitationJournal: Sci Adv / Year: 2025
Title: Structural basis of bacteriophage Ur-lambda infection initiation.
Authors: Huaxin Yu / Chunyan Wang / Jian Yue / Wangbiao Guo / Ian J Molineux / Jun Liu /
Abstract: Bacteriophages must recognize host receptors and penetrate the host cell envelope to initiate infection. How the classic phage λ initiates infection is not yet understood. Here, we combine cryo- ...Bacteriophages must recognize host receptors and penetrate the host cell envelope to initiate infection. How the classic phage λ initiates infection is not yet understood. Here, we combine cryo-electron microscopy and tomography to visualize infection initiation by Ur-λ, the original λ isolate that uses side fibers to adsorb rapidly to . We determine the structure of Ur-λ, resolving the full-length central and side fibers, thus providing a structural basis for host recognition. We show that Ur-λ contains six copies of its tape measure protein. We capture intermediates of the tail tip complex during infection initiation, revealing how extensive conformational changes enable adsorption, and visualize the trans-envelope channel required for genome ejection.
History
DepositionNov 3, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47685.png

Downloads & links

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Map

FileDownload / File: emd_47685.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacteriophage Ur-lambda tail tip complex full map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 448 pix.
= 491.904 Å		1.1 Å/pix.
x 448 pix.
= 491.904 Å		1.1 Å/pix.
x 448 pix.
= 491.904 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.098 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.32790124 - 1.1059334
Average (Standard dev.)0.00005379641 (±0.023330418)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 491.90402 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Bacteriophage Ur-lambda tail tip complex half B map

Fileemd_47685_half_map_1.map
AnnotationBacteriophage Ur-lambda tail tip complex half B map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Bacteriophage Ur-lambda tail tip complex half A map

Fileemd_47685_half_map_2.map
AnnotationBacteriophage Ur-lambda tail tip complex half A 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 Ur-lambda

EntireName: Escherichia phage Ur-lambda (virus)
Components
  • Virus: Escherichia phage Ur-lambda (virus)
    • Protein or peptide: Tape measure protein
    • Protein or peptide: Tail tip assembly protein I
    • Protein or peptide: Tail tip assembly protein I
    • Protein or peptide: Tip attachment protein J
    • Protein or peptide: Tail tip protein L
    • Protein or peptide: Tail fiber protein
    • Protein or peptide: Tail tip protein M
    • Protein or peptide: Tail tube protein
  • Ligand: IRON/SULFUR CLUSTER

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Supramolecule #1: Escherichia phage Ur-lambda

SupramoleculeName: Escherichia phage Ur-lambda / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#8 / NCBI-ID: 2681611 / Sci species name: Escherichia phage Ur-lambda / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Tape measure protein

MacromoleculeName: Tape measure protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 3.471985 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
IGPAALKAVY DMARKGARDE IQTQMRDGGL FS

UniProtKB: Tape measure protein

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Macromolecule #2: Tail tip assembly protein I

MacromoleculeName: Tail tip assembly protein I / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 9.322579 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
GGMTGILFSL GASMVLGGVA QMLAPKARTP RIQTTDNGKQ NTYFSSLDNM VAQGNVLPVL YGEMRVGSRV VSQEISTADE GDGGQVVVI G

UniProtKB: Tail tip assembly protein I

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Macromolecule #3: Tail tip assembly protein I

MacromoleculeName: Tail tip assembly protein I / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 9.308553 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
GGMTGVLFSL GASMVLGGVA QMLAPKARTP RIQTTDNGKQ NTYFSSLDNM VAQGNVLPVL YGEMRVGSRV VSQEISTADE GDGGQVVVI G

UniProtKB: Tail tip assembly protein I

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Macromolecule #4: Tip attachment protein J

MacromoleculeName: Tip attachment protein J / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 92.362289 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MGKGSSKGHT PREAKDNLKS TQLLSVIDAI SEGPIEGPVD GLKSVLLNST PVLDTEGNTN ISGVTVVFRA GEQEQTPPEG FESSGSETV LGTEVKYDTP ITRTITSANI DRLRFTFGVQ ALVETTSKGD RNPSEVRLLV QIQRNGGWVT EKDITIKGKT T SQYLASVV ...String:
MGKGSSKGHT PREAKDNLKS TQLLSVIDAI SEGPIEGPVD GLKSVLLNST PVLDTEGNTN ISGVTVVFRA GEQEQTPPEG FESSGSETV LGTEVKYDTP ITRTITSANI DRLRFTFGVQ ALVETTSKGD RNPSEVRLLV QIQRNGGWVT EKDITIKGKT T SQYLASVV MGNLPPRPFN IRMRRMTPDS TTDQLQNKTL WSSYTEIIDV KQCYPNTALV GVQVDSEQFG SQQVSRNYHL RG RILQVPS NYNPQTRQYS GIWDGTFKPA YSNNMAWCLW DMLTHPRYGM GKRLGAADVD KWALYVIGQY CDQSVPDGFG GTE PRITCN AYLTTQRKAW DVLSDFCSAM RCMPVWNGQT LTFVQDRPSD KTWTYNRSNV VMPDDGAPFR YSFSALKDRH NAVE VNWID PNNGWETATE LVEDTQAIAR YGRNVTKMDA FGCTSRGQAH RAGLWLIKTE LLETQTVDFS VGAEGLRHVP GDVIE ICDD DYAGISTGGR VLAVNSQTRT LTLDREITLP SSGTALISLV DGSGNPVSVE VQSVTDGVKV KVSRVPDGVA EYSVWE LKL PTLRQRLFRC VSIRENDDGT YAITAVQHVP EKEAIVDNGA HFDGEQSGTV NGVTPPAVQH LTAEVTADSG EYQVLAR WD TPKVVKGVSF LLRLTVTADD GSERLVSTAR TTETTYRFTQ LALGNYRLTV RAVNAWGQQG DPASVSFRIA APAAPSRI E LTPGYFQITA TPHLAVYDPT VQFEFWFSEK QIADIRQVET STRYLGTALY WIAASINIKP GHDYYFYIRS VNTVGKSAF VEAVGRASDD AEGYLDFFKG KITESHLGKE LLEKV

UniProtKB: Tip attachment protein J

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Macromolecule #5: Tail tip protein L

MacromoleculeName: Tail tip protein L / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 25.730578 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MQDIRQETLN ECTRAEQSAS VVLWEIDLTE VGGERYFFCN EQNEKGEPVT WQGRQYQPYP IQGSGFELNG KGTSTRPTLT VSNLYGMVT GMAEDMQSLV GGTVVRRKVY ARFLDAVNFV NGNSYADPEQ EVISRWRIEQ CSELSAVSAS FVLSTPTETD G AVFPGRIM ...String:
MQDIRQETLN ECTRAEQSAS VVLWEIDLTE VGGERYFFCN EQNEKGEPVT WQGRQYQPYP IQGSGFELNG KGTSTRPTLT VSNLYGMVT GMAEDMQSLV GGTVVRRKVY ARFLDAVNFV NGNSYADPEQ EVISRWRIEQ CSELSAVSAS FVLSTPTETD G AVFPGRIM LANTCTWTYR GDECGYSGPA VADEYDQPTS DITKDKCSKC LSGCKFRNNV GNFGGFLSIN KLSQ

UniProtKB: Tail tip protein L

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Macromolecule #6: Tail fiber protein

MacromoleculeName: Tail fiber protein / type: protein_or_peptide / ID: 6 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 10.092285 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MAVKISGVLK DGTGKPVQNC TIQLKARRNS TTVVVNTVGS ENPDEAGRYS MDVEYGQYSV ILQVDGFPPS HAGTITVYED SQPGTLNDF LCAMT

UniProtKB: Tail fiber protein

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Macromolecule #7: Tail tip protein M

MacromoleculeName: Tail tip protein M / type: protein_or_peptide / ID: 7 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 12.547373 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MKTFRWKVKP GMDVASVPSV RKVRFGDGYS QRAPAGLNAN LKTYSVTLSV PREEATVLES FLEEHGGWKS FLWTPPYEWR QIKVTCAKW SSRVSMLRVE FSAEFEQVVN

UniProtKB: Tail tip protein M

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Macromolecule #8: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 8 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 16.540227 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
VPNPTMPVKG AGTTLWVYKG SGDPYANPLS DVDWSRLAKV KDLTPGELTA ESYDDSYLDD EDADWTATGQ GQKSAGDTSF TLAWMPGEQ GQQALLAWFN EGDTRAYKIR FPNGTVDVFR GWVSSIGKAV TVITRTVKVT NVGRPSMAED RST

UniProtKB: Tail tube protein

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Macromolecule #9: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 9 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 6517
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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