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Open data
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Basic information
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Title | Neck structure of Agrobacterium phage Milano, C3 symmetry | |||||||||
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![]() | Myophage / redox trigger / ![]() | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Sonani RR / Wang F / Esteves NC / Kelly RJ / Sebastian A / Kreutzberger MAB / Leiman PG / Scharf BE / Egelman EH | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Neck and capsid architecture of the robust Agrobacterium phage Milano. Authors: Ravi R Sonani / Nathaniel C Esteves / Abigail A Horton / Rebecca J Kelly / Amanda L Sebastian / Fengbin Wang / Mark A B Kreutzberger / Petr G Leiman / Birgit E Scharf / Edward H Egelman / ![]() Abstract: Large gaps exist in our understanding of how bacteriophages, the most abundant biological entities on Earth, assemble and function. The structure of the "neck" region, where the DNA-filled capsid is ...Large gaps exist in our understanding of how bacteriophages, the most abundant biological entities on Earth, assemble and function. The structure of the "neck" region, where the DNA-filled capsid is connected to the host-recognizing tail remains poorly understood. We describe cryo-EM structures of the neck, the neck-capsid and neck-tail junctions, and capsid of the Agrobacterium phage Milano. The Milano neck 1 protein connects the 12-fold symmetrical neck to a 5-fold vertex of the icosahedral capsid. Comparison of Milano neck 1 homologs leads to four proposed classes, likely evolved from the simplest one in siphophages to more complex ones in myo- and podophages. Milano neck is surrounded by the atypical collar, which covalently crosslinks the tail sheath to neck 1. The Milano capsid is decorated with three types of proteins, a minor capsid protein (mCP) and two linking proteins crosslinking the mCP to the major capsid protein. The extensive network of disulfide bonds within and between neck, collar, capsid and tail provides an exceptional structural stability to Milano. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 322.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.9 KB 18.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.8 KB | Display | ![]() |
Images | ![]() | 129.9 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() | 317.9 MB 317.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8fweMC ![]() 8fwbC ![]() 8fwcC ![]() 8fwgC ![]() 8fwmC ![]() 8fxpC ![]() 8fxrC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_29503_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29503_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Agrobacterium phage Milano
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Agrobacterium phage Milano
Supramolecule | Name: Agrobacterium phage Milano / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2557550 / Sci species name: Agrobacterium phage Milano / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: ![]() |
-Macromolecule #1: Collar sheath protein, gp13
Macromolecule | Name: Collar sheath protein, gp13 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.490402 KDa |
Sequence | String: MYFFSVDPRN GASKSGDVCG SCCCESISAR PGEVNGVMVS YAAWSAPLRG HGLTNKTTFE IDGVSVTPPK VSNAFGRTKV GVVFEGTLS DLFPNPEGEQ VEYEISELNG PSNGVVELGA NGAFTYTPGA LFTGVDRFWF SINGNIGEYV ISVDPTTSEL P QPPFTTPV ...String: MYFFSVDPRN GASKSGDVCG SCCCESISAR PGEVNGVMVS YAAWSAPLRG HGLTNKTTFE IDGVSVTPPK VSNAFGRTKV GVVFEGTLS DLFPNPEGEQ VEYEISELNG PSNGVVELGA NGAFTYTPGA LFTGVDRFWF SINGNIGEYV ISVDPTTSEL P QPPFTTPV YVPAARRSVD PRTHVLKFVL GVSPAAIPGD VYRLTVRQVA IDCDGNEFVH ISCYDISIGS CG UniProtKB: Virion-associated protein |
-Macromolecule #2: Portal protein, gp7
Macromolecule | Name: Portal protein, gp7 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 45.840844 KDa |
Sequence | String: MLGIPLLTRK AALTPPAPSA NPAKIFIRRF FSAGVAKNVV SYSNVMAAQR AMEHPVAFRC LDKLGLTVQS VKWDVGKDPQ NTQVGDGGM SASQRKALQQ ILQRPNPTMS GAQLRYSAAL SWACFGRMAF KVSVMSDGSV NAIWPLGIPF LKQKFDRYGD V ESFQYGDE ...String: MLGIPLLTRK AALTPPAPSA NPAKIFIRRF FSAGVAKNVV SYSNVMAAQR AMEHPVAFRC LDKLGLTVQS VKWDVGKDPQ NTQVGDGGM SASQRKALQQ ILQRPNPTMS GAQLRYSAAL SWACFGRMAF KVSVMSDGSV NAIWPLGIPF LKQKFDRYGD V ESFQYGDE AGKETIPSFT KVEKNDKGRP IKNYAFMIVK PSINGAMNFD VQNTPLQAIG VPVALYDALM ARAIDSADGT PN SKWLVTA SRDLDDGQAK EVKEGIEETK PGGDNGGEII FIAGTDVKVQ EMKNDLSDIH SKVPLDDQAR TIAGNFGIPI ALL GFAGAD GSKFANNYDE SRKAFFEDTI EPGYLTPLED GFSMFLCGAG YRVIFDRDSI PALRKSRADI AATYDKVTFI TEEE KREVT GWPAKKEGQT QNDDA UniProtKB: Portal protein |
-Macromolecule #3: Neck 2 protein, gp15
Macromolecule | Name: Neck 2 protein, gp15 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 16.052353 KDa |
Sequence | String: MRTADRKHRV IVCSQQSDVD DEGRLLITRA GVIQGWAAIA PVKAIRFSQD GVSMQKDTMQ PTHDITMNYN PDVNVSVSAW VYEHRLKSP PRWFKVLSVV NVDECSRYMK IRCRLVETSD DVTPPVEEEK NSFGAVKIDI PL UniProtKB: Head completion protein |
-Macromolecule #4: Tail-terminator protein, gp18
Macromolecule | Name: Tail-terminator protein, gp18 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 20.268541 KDa |
Sequence | String: METKLTYGNR VTLPEFAKYI VAPAFHEIEG RAIPVTGVDD DASGTQATKL PFVLVGLRQG DTSGPATIAG NSTINLRDDF IVEFNMKKE RYRDRKGGET PFFSYYDYES IRDRLFNSMI EFSGEHGITF EFVSLDISTE GDVVYIEFRF RQNYEWCETV R EADTTIEA GRFSINLQGC UniProtKB: Virion-associated protein |
-Macromolecule #5: Tail-tube, gp21
Macromolecule | Name: Tail-tube, gp21 / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 14.673427 KDa |
Sequence | String: MACNKQNGVK NILITFTDCD TQEVIGPISH EQPDDTLPTY KNCAWTNTAL TNGYVQRSAS NATMTLPVVR DLRVPLAFYQ GCAQVDVQV EKFDGTVMTL TEGAVVEPEE SDGRSVTMNI VASEIDELLP PGSLAAA UniProtKB: Virion-associated protein |
-Macromolecule #6: Neck 1 protein, gp14
Macromolecule | Name: Neck 1 protein, gp14 / type: protein_or_peptide / ID: 6 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 22.255439 KDa |
Sequence | String: MNLDTLLPLQ TIREHAKCDD NPRVTDDLLK LYREAAFEAA ELYTGLSFTP EKTIVEPIRL KGRRGKIILS ATPIAGRPVV FYGGGLGSP LELIPRPGSN VLFFPYGSPD RFQTWGDCHT CDVESQLMAT YVTGRRCENS VPAGIIIGIL KLIAWNINNP G DEVMSVRN ...String: MNLDTLLPLQ TIREHAKCDD NPRVTDDLLK LYREAAFEAA ELYTGLSFTP EKTIVEPIRL KGRRGKIILS ATPIAGRPVV FYGGGLGSP LELIPRPGSN VLFFPYGSPD RFQTWGDCHT CDVESQLMAT YVTGRRCENS VPAGIIIGIL KLIAWNINNP G DEVMSVRN TLNANAQGLI GGTNNGAVIS GAQDEWFRYR RVLL UniProtKB: Head-to-tail connector complex protein |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |