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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20648 | |||||||||||||||
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Title | CryoEM Structure of Pyocin R2 - postcontracted - baseplate | |||||||||||||||
![]() | Structure of Pyocin R2 - postcontracted - baseplate | |||||||||||||||
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![]() | bacteriocin / pyocin / ANTIMICROBIAL PROTEIN | |||||||||||||||
Function / homology | ![]() Tail protein I / Phage tail protein (Tail_P2_I) / Phage Tail Protein X-like / Baseplate assembly protein J, predicted / : / Phage Tail Protein X / Baseplate protein J-like / Baseplate J-like protein / IraD/Gp25-like / Baseplate wedge protein gp25 ...Tail protein I / Phage tail protein (Tail_P2_I) / Phage Tail Protein X-like / Baseplate assembly protein J, predicted / : / Phage Tail Protein X / Baseplate protein J-like / Baseplate J-like protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / : / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain Similarity search - Domain/homology | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||
![]() | Ge P / Avaylon J | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Action of a minimal contractile bactericidal nanomachine. Authors: Peng Ge / Dean Scholl / Nikolai S Prokhorov / Jaycob Avaylon / Mikhail M Shneider / Christopher Browning / Sergey A Buth / Michel Plattner / Urmi Chakraborty / Ke Ding / Petr G Leiman / Jeff ...Authors: Peng Ge / Dean Scholl / Nikolai S Prokhorov / Jaycob Avaylon / Mikhail M Shneider / Christopher Browning / Sergey A Buth / Michel Plattner / Urmi Chakraborty / Ke Ding / Petr G Leiman / Jeff F Miller / Z Hong Zhou / ![]() ![]() ![]() Abstract: R-type bacteriocins are minimal contractile nanomachines that hold promise as precision antibiotics. Each bactericidal complex uses a collar to bridge a hollow tube with a contractile sheath loaded ...R-type bacteriocins are minimal contractile nanomachines that hold promise as precision antibiotics. Each bactericidal complex uses a collar to bridge a hollow tube with a contractile sheath loaded in a metastable state by a baseplate scaffold. Fine-tuning of such nucleic acid-free protein machines for precision medicine calls for an atomic description of the entire complex and contraction mechanism, which is not available from baseplate structures of the (DNA-containing) T4 bacteriophage. Here we report the atomic model of the complete R2 pyocin in its pre-contraction and post-contraction states, each containing 384 subunits of 11 unique atomic models of 10 gene products. Comparison of these structures suggests the following sequence of events during pyocin contraction: tail fibres trigger lateral dissociation of baseplate triplexes; the dissociation then initiates a cascade of events leading to sheath contraction; and this contraction converts chemical energy into mechanical force to drive the iron-tipped tube across the bacterial cell surface, killing the bacterium. | |||||||||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 261.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20 KB 20 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.9 KB | Display | ![]() |
Images | ![]() | 159.7 KB | ||
Filedesc metadata | ![]() | 6.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6u5kMC ![]() 5cesC ![]() 6pytC ![]() 6u5bC ![]() 6u5fC ![]() 6u5hC ![]() 6u5jC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Structure of Pyocin R2 - postcontracted - baseplate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.041 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 : Pyocin R2 - Postcontracted
Entire | Name: Pyocin R2 - Postcontracted |
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Components |
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-Supramolecule #1: Pyocin R2 - Postcontracted
Supramolecule | Name: Pyocin R2 - Postcontracted / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Sheath PA0622
Macromolecule | Name: Sheath PA0622 / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 |
Molecular weight | Theoretical: 41.247332 KDa |
Sequence | String: MSFFHGVTVT NVDIGARTIA LPASSVIGLC DVFTPGAQAS AKPNVPVLLT SKKDAAAAFG IGSSIYLACE AIYNRAQAVI VAVGVETAE TPEAQASAVI GGISAAGERT GLQALLDGKS RFNAQPRLLV APGHSAQQAV ATAMDGLAEK LRAIAILDGP N STDEAAVA ...String: MSFFHGVTVT NVDIGARTIA LPASSVIGLC DVFTPGAQAS AKPNVPVLLT SKKDAAAAFG IGSSIYLACE AIYNRAQAVI VAVGVETAE TPEAQASAVI GGISAAGERT GLQALLDGKS RFNAQPRLLV APGHSAQQAV ATAMDGLAEK LRAIAILDGP N STDEAAVA YAKNFGSKRL FMVDPGVQVW DSATNAARNA PASAYAAGLF AWTDAEYGFW SSPSNKEIKG VTGTSRPVEF LD GDETCRA NLLNNANIAT IIRDDGYRLW GNRTLSSDSK WAFVTRVRTM DLVMDAILAG HKWAVDRGIT KTYVKDVTEG LRA FMRDLK NQGAVINFEV YADPDLNSAS QLAQGKVYWN IRFTDVPPAE NPNFRVEVTD QWLTEVLDVA UniProtKB: Probable bacteriophage protein |
-Macromolecule #2: Glue PA0627
Macromolecule | Name: Glue PA0627 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 |
Molecular weight | Theoretical: 7.486475 KDa |
Sequence | String: MATTCRTADG DMLDSLCYHV YGHLLGCVEA TLDANPGLAD EQQPFRAGLL ISFPDMPVVN VEQVRLWD UniProtKB: Phage tail protein |
-Macromolecule #3: Tri1a PA0618
Macromolecule | Name: Tri1a PA0618 / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 |
Molecular weight | Theoretical: 31.986117 KDa |
Sequence | String: MIIDLSQLPE PEVIENLDFE TIYQELLGDF REAMAGEWTA EVESDPVLKL LQLAAYRELL LRARINDAAR AVMLAYASGA DLDQIGAGF NVQRLLIRPA QPEAVPPVEA QYESDKSLRN RIQLAFEQLS VAGPRNAYIA HALGADGRVA DASATSPAPC E VLISVLGV ...String: MIIDLSQLPE PEVIENLDFE TIYQELLGDF REAMAGEWTA EVESDPVLKL LQLAAYRELL LRARINDAAR AVMLAYASGA DLDQIGAGF NVQRLLIRPA QPEAVPPVEA QYESDKSLRN RIQLAFEQLS VAGPRNAYIA HALGADGRVA DASATSPAPC E VLISVLGV EGNGQAPEAV LQAVRLALNA EDVRPVADRV TVRSAGIVPY QVKAQLYLFP GPEAELIRAA AEASLRDYIS AQ RRLGRDI RRSALFATLH VEGVQRVELQ EPAADVVLDE TQAAYCTGYA ITLGGVDE UniProtKB: Probable bacteriophage protein |
-Macromolecule #4: Tri2 PA0619
Macromolecule | Name: Tri2 PA0619 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 |
Molecular weight | Theoretical: 20.013682 KDa |
Sequence | String: MSSRLLPPNR SSLERSLGDV LPAELPVPLR ELHDPARCEA ALLPYLAWTR SVDRWDPDWS DEAKRNAVAT SFVLHQRKGT LTALRQVVE PIGALSEVTE WWQRSPTGVP GTFEITVDVS DRGIDEGTVL ELERLLDDVR PVSRHLTRLD LRITPVIRSR H GLAVTDGD TLEIFPWKQ UniProtKB: Probable bacteriophage protein |
-Macromolecule #5: Sheath Initiator PA0617
Macromolecule | Name: Sheath Initiator PA0617 / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 |
Molecular weight | Theoretical: 11.862759 KDa |
Sequence | String: MIGMDRRSGL PLSGLAHLKQ SVEDILTTPL GSRRMRPEYG SKLRRMVDMP VSEGWKSAVQ AEVARSLGRW EPRIGLSAVR VVAVVDGRV DLLLSGVFEG ENINMEVSA UniProtKB: Probable bacteriophage protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 Component:
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Grid | Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Details: unspecified | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 80.0 K / Max: 81.0 K |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: -10 eV / Energy filter - Upper energy threshold: 10 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 3-20 / Number grids imaged: 1 / Number real images: 7331 / Average exposure time: 10.0 sec. / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.4 µm / Calibrated defocus min: 1.1 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.16 µm / Nominal defocus min: 2.16 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-6u5k: |