+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38242 | |||||||||
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Title | Tail tip complex of bacteriophage lambda in the open state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Bacteriophage / caudovirales / siphoviridae / phage lambda / host recognition / LamB / cryo-EM / VIRUS | |||||||||
Function / homology | Function and homology information symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / 4 iron, 4 sulfur cluster binding / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / virion attachment to host cell / metal ion binding Similarity search - Function | |||||||||
Biological species | Escherichia phage Lambda (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.46 Å | |||||||||
Authors | Ge XF / Wang JW | |||||||||
Funding support | China, 2 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural mechanism of bacteriophage lambda tail's interaction with the bacterial receptor. Authors: Xiaofei Ge / Jiawei Wang / Abstract: Bacteriophage infection, a pivotal process in microbiology, initiates with the phage's tail recognizing and binding to the bacterial cell surface, which then mediates the injection of viral DNA. ...Bacteriophage infection, a pivotal process in microbiology, initiates with the phage's tail recognizing and binding to the bacterial cell surface, which then mediates the injection of viral DNA. Although comprehensive studies on the interaction between bacteriophage lambda and its outer membrane receptor, LamB, have provided rich information about the system's biochemical properties, the precise molecular mechanism remains undetermined. This study revealed the high-resolution cryo-electron microscopy (cryo-EM) structures of the bacteriophage lambda tail complexed with its irreversible Shigella sonnei 3070 LamB receptor and the closed central tail fiber. These structures reveal the complex processes that trigger infection and demonstrate a substantial conformational change in the phage lambda tail tip upon LamB binding. Providing detailed structures of bacteriophage lambda infection initiation, this study contributes to the expanding knowledge of lambda-bacterial interaction, which holds significance in the fields of microbiology and therapeutic development. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38242.map.gz | 118 MB | EMDB map data format | |
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Header (meta data) | emd-38242-v30.xml emd-38242.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_38242_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_38242.png | 193.8 KB | ||
Filedesc metadata | emd-38242.cif.gz | 6.4 KB | ||
Others | emd_38242_half_map_1.map.gz emd_38242_half_map_2.map.gz | 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38242 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38242 | HTTPS FTP |
-Validation report
Summary document | emd_38242_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_38242_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_38242_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | emd_38242_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38242 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38242 | HTTPS FTP |
-Related structure data
Related structure data | 8xcgMC 8xciC 8xcjC 8xckC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_38242.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0742 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_38242_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_38242_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Bacteriophage lambda tail with LamB
Entire | Name: Bacteriophage lambda tail with LamB |
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Components |
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-Supramolecule #1: Bacteriophage lambda tail with LamB
Supramolecule | Name: Bacteriophage lambda tail with LamB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Escherichia phage Lambda (virus) |
-Macromolecule #1: Tail tip protein M
Macromolecule | Name: Tail tip protein M / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage Lambda (virus) |
Molecular weight | Theoretical: 12.547373 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKTFRWKVKP GMDVASVPSV RKVRFGDGYS QRAPAGLNAN LKTYSVTLSV PREEATVLES FLEEHGGWKS FLWTPPYEWR QIKVTCAKW SSRVSMLRVE FSAEFEQVVN UniProtKB: Tail tip protein M |
-Macromolecule #2: Tip attachment protein J
Macromolecule | Name: Tip attachment protein J / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage Lambda (virus) |
Molecular weight | Theoretical: 124.550625 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 LLEKVELTED NASRLEEFSK EWKDASDKWN AMWAVKIEQT KDGKHYVAGI GLSMEDTEE GKLSQFLVAA NRIAFIDPAN GNETPMFVAQ GNQIFMNDVF LKRLTAPTIT SGGNPPAFSL TPDGKLTAKN A DISGSVNA NSGTLSNVTI AENCTINGTL RAEKIVGDIV KAASAAFPRQ RESSVDWPSG TRTVTVTDDH PFDRQIVVLP LT FRGSKRT VSGRTTYSMC YLKVLMNGAV IYDGAANEAV QVFSRIVDMP AGRGNVILTF TLTSTRHSAD IPPYTFASDV QVM VIKKQA LGISVV UniProtKB: Tip attachment protein J |
-Macromolecule #3: Tail tip assembly protein I
Macromolecule | Name: Tail tip assembly protein I / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage Lambda (virus) |
Molecular weight | Theoretical: 23.14659 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAATHTLPLA SPGMARICLY GDLQRFGRRI DLRVKTGAEA IRALATQLPA FRQKLSDGWY QVRIAGRDVS TSGLTAQLHE TLPDGAVIH IVPRVAGAKS GGVFQIVLGA AAIAGSFFTA GATLAAWGAA IGAGGMTGIL FSLGASMVLG GVAQMLAPKA R TPRIQTTD ...String: MAATHTLPLA SPGMARICLY GDLQRFGRRI DLRVKTGAEA IRALATQLPA FRQKLSDGWY QVRIAGRDVS TSGLTAQLHE TLPDGAVIH IVPRVAGAKS GGVFQIVLGA AAIAGSFFTA GATLAAWGAA IGAGGMTGIL FSLGASMVLG GVAQMLAPKA R TPRIQTTD NGKQNTYFSS LDNMVAQGNV LPVLYGEMRV GSRVVSQEIS TADEGDGGQV VVIGR UniProtKB: Tail tip assembly protein I |
-Macromolecule #4: Tail tip protein L
Macromolecule | Name: Tail tip protein L / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage Lambda (virus) |
Molecular weight | Theoretical: 25.730578 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #5: IRON/SULFUR CLUSTER
Macromolecule | Name: IRON/SULFUR CLUSTER / type: ligand / ID: 5 / Number of copies: 3 / Formula: SF4 |
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Molecular weight | Theoretical: 351.64 Da |
Chemical component information | ChemComp-FS1: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |