[English] 日本語
![](img/lk-miru.gif)
- EMDB-15968: Cryo-EM structure of the proximal end of bacteriophage T5 tail, a... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the proximal end of bacteriophage T5 tail, after interaction with its receptor : p142 tail terminator protein hexamer and pb6 tail tube protein trimer | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | Bacteriophage / Siphophage / T5 / tail terminator / Trp / VIRAL PROTEIN | |||||||||
Function / homology | ![]() virus tail, tube / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / viral release from host cell by cytolysis Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.05 Å | |||||||||
![]() | Linares R / Effantin G / Breyton C / Darnault C / Epalle N / Boeri Erba E / Schoehn G | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Cryo-EM structure of the proximal end of bacteriophage T5 tail, in its native state and after interaction with its bacterial receptor Authors: Linares R / Effantin G / Breyton C | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 2 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 21 KB 21 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 5.1 KB | Display | ![]() |
Images | ![]() | 101.1 KB | ||
Masks | ![]() | 10.5 MB | ![]() | |
Filedesc metadata | ![]() | 6.4 KB | ||
Others | ![]() ![]() ![]() | 7.9 MB 7.9 MB 7.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 793.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 793.3 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 14.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bcuMC ![]() 8bcpC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.351 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: #1
File | emd_15968_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_15968_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_15968_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Escherichia virus T5
Entire | Name: ![]() |
---|---|
Components |
|
-Supramolecule #1: Escherichia virus T5
Supramolecule | Name: Escherichia virus T5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all Details: Pure T5 tails obtained by infecting E. coli F strain with the amber mutant phage T5D20am30d, incubated with the bacterial receptor FhuA reconstituted in nanodiscs NCBI-ID: 2695836 / Sci species name: Escherichia virus T5 / Sci species strain: T5D20am30d / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
---|---|
Host (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Tail tube terminator protein p142
Macromolecule | Name: Tail tube terminator protein p142 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 18.378643 KDa |
Sequence | String: MDHRTSIAQA MVDRISKQMD GSQPDEYFNN LYGNVSRQTY KFEEIREFPY VAVHIGTETG QYLPSGQQWM FLELPILVYD KEKTDIQEQ LEKLVADIKT VIDTGGNLEY TVSKPNGSTF PCEATDMIIT SVSTDEGLLA PYGLAEINVT VRYQPPRRSL R R UniProtKB: Tail tube terminator protein p142 |
-Macromolecule #2: Tail tube protein
Macromolecule | Name: Tail tube protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 50.459215 KDa |
Sequence | String: MSLQLLRNTR IFVSTVKTGH NKTNTQEILV QDDISWGQDS NSTDITVNEA GPRPTRGSKR FNDSLNAAEW SFSTYILPYK DKNTSKQIV PDYMLWHALS SGRAINLEGT TGAHNNATNF MVNFKDNSYH ELAMLHIYIL TDKTWSYIDS CQINQAEVNV D IEDIGRVT ...String: MSLQLLRNTR IFVSTVKTGH NKTNTQEILV QDDISWGQDS NSTDITVNEA GPRPTRGSKR FNDSLNAAEW SFSTYILPYK DKNTSKQIV PDYMLWHALS SGRAINLEGT TGAHNNATNF MVNFKDNSYH ELAMLHIYIL TDKTWSYIDS CQINQAEVNV D IEDIGRVT WSGNGNQLIP LDEQPFDPDQ IGIDDETYMT IQGSYIKNKL TILKIKDMDT NKSYDIPITG GTFTINNNIT YL TPNVMSR VTIPIGSFTG AFELTGSLTA YLNDKSLGSM ELYKDLIKTL KVVNRFEIAL VLGGEYDDER PAAILVAKQA HVN IPTIET DDVLGTSVEF KAIPSDLDAG DEGYLGFSSK YTRTTINNLI VNGDGATDAV TAITVKSAGN VTTLNRSATL QMSV EVTPS SARNKEVTWA ITAGDAATIN ATGLLRADAS KTGAVTVEAT AKDGSGVKGT KVITVTAGG UniProtKB: Tail tube protein pb6 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 8 Component:
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Grid | Model: Quantifoil R2/1 / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 25 mA | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV Details: 3 uL of T5 tails + FhuA-nanodisc sample were deposited on a freshly glow discharged EM grid and plunge-frozen in nitrogen-cooled liquid ethane using a ThermoFisher Mark IV Vitrobot device ...Details: 3 uL of T5 tails + FhuA-nanodisc sample were deposited on a freshly glow discharged EM grid and plunge-frozen in nitrogen-cooled liquid ethane using a ThermoFisher Mark IV Vitrobot device (100 percent humidity, 20 Celsius degrees, 5 s blotting time, blot force 0). | |||||||||||||||
Details | Pure T5 tails obtained by infecting E. coli F strain with the amber mutant phage T5D20am30d, incubated with the bacterial receptor FhuA reconstituted in nanodiscs |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
+
Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: BACKBONE TRACE / Overall B value: 120 |
---|---|
Output model | ![]() PDB-8bcu: |