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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Cyanophage Pam3 neck | |||||||||
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![]() | Cyanophage Pam3 != uncultured cyanophage Cyanophage Pam3
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Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Yang F / Jiang YL / Zhou CZ | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Fine structure and assembly pattern of a minimal myophage Pam3. Authors: Feng Yang / Yong-Liang Jiang / Jun-Tao Zhang / Jie Zhu / Kang Du / Rong-Cheng Yu / Zi-Lu Wei / Wen-Wen Kong / Ning Cui / Wei-Fang Li / Yuxing Chen / Qiong Li / Cong-Zhao Zhou / ![]() Abstract: The myophage possesses a contractile tail that penetrates its host cell envelope. Except for investigations on the bacteriophage T4 with a rather complicated structure, the assembly pattern and tail ...The myophage possesses a contractile tail that penetrates its host cell envelope. Except for investigations on the bacteriophage T4 with a rather complicated structure, the assembly pattern and tail contraction mechanism of myophage remain largely unknown. Here, we present the fine structure of a freshwater cyanophage Pam3, which has an icosahedral capsid of ~680 Å in diameter, connected via a three-section neck to an 840-Å-long contractile tail, ending with a three-module baseplate composed of only six protein components. This simplified baseplate consists of a central hub-spike surrounded by six wedge heterotriplexes, to which twelve tail fibers are covalently attached via disulfide bonds in alternating upward and downward configurations. In vitro reduction assays revealed a putative redox-dependent mechanism of baseplate assembly and tail sheath contraction. These findings establish a minimal myophage that might become a user-friendly chassis phage in synthetic biology. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 96.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.5 KB 17.5 KB | Display Display | ![]() |
Images | ![]() | 172.3 KB | ||
Others | ![]() ![]() | 79.4 MB 79.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hdrMC ![]() 7yfwC ![]() 7yfzC ![]() 8hdsC ![]() 8hdtC ![]() 8hdwC M: atomic model generated by this map C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.013 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_34678_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34678_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Cyanophage Pam3
Entire | Name: Cyanophage Pam3 |
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Components |
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-Supramolecule #1: uncultured cyanophage
Supramolecule | Name: uncultured cyanophage / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 215796 / Sci species name: uncultured cyanophage / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() |
-Macromolecule #1: pam3 tube protein
Macromolecule | Name: pam3 tube protein / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 15.293298 KDa |
Sequence | String: MAMKAYSMLN VTATLDGRRV IGLMDGDDAI TTSPGVDVGT MLVGADGSWL FSQTADKSAT VVIKLKPNSP THRQLTEKWM AQRAGRLVG FPFDFIDSAS NEGGTGAEFF IQKAPDDSKG NNAVVREWTI VTGEWTPTIP TLL |
-Macromolecule #2: Pam3 connector protein
Macromolecule | Name: Pam3 connector protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 12.023414 KDa |
Sequence | String: MIDVAIAIDA ESVEVTWRNR SGGSYDSRGN ATGASWADTQ IRAAIQPVSG RELQDLPEGV RSKVTLVAWT RSEVAENDQI IYLGDAYRV YAARPRPMDG FTRIALGKVS P |
-Macromolecule #3: Pam3 terminator protein
Macromolecule | Name: Pam3 terminator protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 17.682719 KDa |
Sequence | String: MRRITGITVI KDHQSEDRPA LPYGVVELAN FRDLHQQVRT IHYEDIEDSD NGEGFPEVQA TPEVEQEWVF LVQVYGPGGL DYLRKVAAA FHVNQVNDLP GSLVIHEVAQ INSIPEFLGE RWEKRAQTNI TLRGMSTDGF KVDVIEQHVI NVTGERA |
-Macromolecule #4: Pam3 sheath protein
Macromolecule | Name: Pam3 sheath protein / type: protein_or_peptide / ID: 4 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 41.91509 KDa |
Sequence | String: MAKLPYSRVT NVTLTRTDNF PTRRGFGTQL ILTHTAVSGQ VDATKRTKLY ASLAEVEADY PANTSVYKAA LSAFSQNPRP IRLKVGYAA TPTGGDDAAK KADFITSLGA ILNYDQAFYQ ITLDAALRDQ PYLDGLVEWV EAQPKIAMID SNAAGHEDPA N TTVIAARH ...String: MAKLPYSRVT NVTLTRTDNF PTRRGFGTQL ILTHTAVSGQ VDATKRTKLY ASLAEVEADY PANTSVYKAA LSAFSQNPRP IRLKVGYAA TPTGGDDAAK KADFITSLGA ILNYDQAFYQ ITLDAALRDQ PYLDGLVEWV EAQPKIAMID SNAAGHEDPA N TTVIAARH KGTVERTAVF YHTDSTEYLA ASMAAYMSTR VFDDANSAYT LKFKKAPGVR AIDKGSAVVT AITGFVEQTG QS ESAGHCA NTLIDIGDQE FLVEGSTLTQ NVFLDEIHAT DWIIARTEEE MLSLFLNNDR VPFTDQGMQQ LASVPRAIMQ LAA RAGIVA LDLNPLTGAY EPAYTITVPS VFDIPESQRK ARIAPAIQVR FRYAGAVHYS VINYTMTF |
-Macromolecule #5: Pam3 adaptor protein
Macromolecule | Name: Pam3 adaptor protein / type: protein_or_peptide / ID: 5 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.871434 KDa |
Sequence | String: MNPIPAASDL KTRYPEFTGV SDAVVNAIIA EVNGMVDDGW EVSDQKPAVL ALAAHMLSRE GYPGRATNPN SFDPTNRPIL SRKVGDVST TFGRTDGGAA EGGANSYNYS STVYGQTFLR LLRLNAPAVG LV |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 300 K |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Initial angle assignment | Type: RANDOM ASSIGNMENT |
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Final angle assignment | Type: RANDOM ASSIGNMENT |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 117851 |