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- EMDB-11225: negative staining 3D reconstruction of p2 virion baseplate in act... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11225 | |||||||||
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Title | negative staining 3D reconstruction of p2 virion baseplate in activated conformation (3D class with closed Tal trimer) | |||||||||
![]() | negative staining 3D reconstruction of p2 virion baseplate bound to VHH5 (3D class with closed Tal trimer) | |||||||||
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![]() | lactococcal siphophage p2 / baseplate / receptor-binding protein / Distal Tail protein / Tail-associated lysin / VIRAL PROTEIN | |||||||||
Function / homology | ![]() symbiont genome ejection through host cell envelope, long flexible tail mechanism / virus tail, baseplate / virus tail / entry receptor-mediated virion attachment to host cell / cell adhesion / symbiont entry into host cell / virion attachment to host cell Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 42.2 Å | |||||||||
![]() | Spinelli S / Cambillau C | |||||||||
![]() | ![]() Title: Structural Insights into Lactococcal Siphophage p2 Baseplate Activation Mechanism. Authors: Silvia Spinelli / Denise Tremblay / Sylvain Moineau / Christian Cambillau / Adeline Goulet / ![]() ![]() Abstract: Virulent phages infecting , an industry-relevant bacterium, pose a significant risk to the quality of the fermented milk products. Phages of the Skunavirus genus are by far the most isolated ...Virulent phages infecting , an industry-relevant bacterium, pose a significant risk to the quality of the fermented milk products. Phages of the Skunavirus genus are by far the most isolated lactococcal phages in the cheese environments and phage p2 is the model siphophage for this viral genus. The baseplate of phage p2, which is used to recognize its host, was previously shown to display two conformations by X-ray crystallography, a rested state and an activated state ready to bind to the host. The baseplate became only activated and opened in the presence of Ca. However, such an activated state was not previously observed in the virion. Here, using nanobodies binding to the baseplate, we report on the negative staining electron microscopy structure of the activated form of the baseplate directly observed in the p2 virion, that is compatible with the activated baseplate crystal structure. Analyses of this new structure also established the presence of a second distal tail (Dit) hexamer as a component of the baseplate, the topology of which differs largely from the first one. We also observed an uncoupling between the baseplate activation and the tail tip protein (Tal) opening, suggesting an infection mechanism more complex than previously expected. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.2 KB 13.2 KB | Display Display | ![]() |
Images | ![]() | 122.5 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zigMC ![]() 6zihC ![]() 6zjjC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | negative staining 3D reconstruction of p2 virion baseplate bound to VHH5 (3D class with closed Tal trimer) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.46 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Lactococcus virus P2
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Lactococcus virus P2
Supramolecule | Name: Lactococcus virus P2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 254252 / Sci species name: Lactococcus virus P2 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() |
-Macromolecule #1: Receptor binding protein
Macromolecule | Name: Receptor binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 28.668057 KDa |
Sequence | String: MTIKNFTFFS PNSTEFPVGS NNDGKLYMML TGMDYRTIRR KDWSSPLNTA LNVQYTNTSI IAGGRYFELL NETVALKGDS VNYIHANID LTQTANPVSL SAETANNSNG VDINNGSGVL KVCFDIVTTS GTGVTSTKPI VQTSTLDSIS VNDMTVSGSI D VPVQTLTV ...String: MTIKNFTFFS PNSTEFPVGS NNDGKLYMML TGMDYRTIRR KDWSSPLNTA LNVQYTNTSI IAGGRYFELL NETVALKGDS VNYIHANID LTQTANPVSL SAETANNSNG VDINNGSGVL KVCFDIVTTS GTGVTSTKPI VQTSTLDSIS VNDMTVSGSI D VPVQTLTV EAGNGLQLQL TKKNNDLVIV RFFGSVSNIQ KGWNMSGTWV DRPFRPAAVQ SLVGHFAGRD TSFHIDINPN GS ITWWGAN IDKTPIATRG NGSYFIK UniProtKB: Receptor binding protein |
-Macromolecule #2: Distal tail protein
Macromolecule | Name: Distal tail protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 34.511992 KDa |
Sequence | String: MVRQYKIHTN LDGTDDKVWD VTNGKVRFYQ PSNLGLQSTN NIWQSNGIGV MGTRSITQPQ IEFKLETFGE SLEENYQLMK DFVNDILSK KFVTLEYQTE IFQVYADLAL ADVTKTEGYG KNGTFSEKIT FDIITKWYTY ENLTFDKIQN GKVIAGMSKI Y GGTAPGNY ...String: MVRQYKIHTN LDGTDDKVWD VTNGKVRFYQ PSNLGLQSTN NIWQSNGIGV MGTRSITQPQ IEFKLETFGE SLEENYQLMK DFVNDILSK KFVTLEYQTE IFQVYADLAL ADVTKTEGYG KNGTFSEKIT FDIITKWYTY ENLTFDKIQN GKVIAGMSKI Y GGTAPGNY KYIKGTSYTY YGESDIDRLS RWDIKEEIFS FMGILYPKLP KTPAGVRFLD DIGNEYTAIV FKTEQVQDYI LI NTDVNDE TYQGWKGTTA LNLFPVMDFE RYRTRIIEKG QMELINLSKA EFKIKRKADF V UniProtKB: Distal tail protein |
-Macromolecule #3: Baseplate protein gp16
Macromolecule | Name: Baseplate protein gp16 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 42.883266 KDa |
Sequence | String: MLEANVYDNF NPNYYNISDF SMPNGKKEKR GLPIPKARCQ VINYELWETG YLYTSSATLT VSVEVGDIVQ ILFPEVVPIE EALGKKKKL NLDMVYLVTD VDESNKATLK NYFWAMIESL DVPNAITKTT NFAIIDYLID PNKNNLMSYG YFFNSSIFAG K ATINRKAE ...String: MLEANVYDNF NPNYYNISDF SMPNGKKEKR GLPIPKARCQ VINYELWETG YLYTSSATLT VSVEVGDIVQ ILFPEVVPIE EALGKKKKL NLDMVYLVTD VDESNKATLK NYFWAMIESL DVPNAITKTT NFAIIDYLID PNKNNLMSYG YFFNSSIFAG K ATINRKAE TSSAHDVAKR IFSKVQFQPT TTIQHAPSET DPRNLLFINF ASRNWNRKRI TTRVDIKQSV TMDTETIVER SA YNFAVVF VKNKATDDYT DPPKMYIAKN NGDVIDYSTY HGDGTDLPDV RTAKTLFYDR DDHGNPPELS TIKVEISPST IVT RLIFNQ NELLPLYVND LVDIWYEGKL YSGYIADRVK TEFNDRLIFV ESGDKPNVI UniProtKB: Baseplate protein gp16 |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Staining | Type: NEGATIVE / Material: uranyl acetate |
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Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Image recording | Film or detector model: OTHER / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Tecnai Spirit / Image courtesy: FEI Company |