+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29540 | |||||||||
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Title | Structure of capsid of Agrobacterium phage Milano | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Myophage / redox trigger / VIRUS | |||||||||
Function / homology | Phage capsid / Phage capsid family / Virion-associated protein / Virion-associated protein / Major capsid protein Function and homology information | |||||||||
Biological species | Agrobacterium phage Milano (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.04 Å | |||||||||
Authors | Sonani RR / Wang F / Esteves NC / Kelly RJ / Sebastian A / Kreutzberger MAB / Leiman PG / Scharf BE / Egelman EH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Commun Biol / Year: 2023 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 | emd_29540.map.gz | 1.6 GB | EMDB map data format | |
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Header (meta data) | emd-29540-v30.xml emd-29540.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29540_fsc.xml | 25.3 KB | Display | FSC data file |
Images | emd_29540.png | 141.8 KB | ||
Filedesc metadata | emd-29540.cif.gz | 5.7 KB | ||
Others | emd_29540_half_map_1.map.gz emd_29540_half_map_2.map.gz | 1.6 GB 1.6 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29540 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29540 | HTTPS FTP |
-Related structure data
Related structure data | 8fxpMC 8fwbC 8fwcC 8fweC 8fwgC 8fwmC 8fxrC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_29540.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.44 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_29540_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_29540_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Agrobacterium phage Milano
Entire | Name: Agrobacterium phage Milano (virus) |
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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: #1 / 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: Agrobacterium fabrum str. C58 (bacteria) |
-Macromolecule #1: Linking protein 1, gp16
Macromolecule | Name: Linking protein 1, gp16 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Agrobacterium phage Milano (virus) |
Molecular weight | Theoretical: 22.913605 KDa |
Sequence | String: MDCRNLCGAA APSRLVQPGC FICRGVAVSI PPAAPGPATS VFDTPPSTFS LRPDGTIIAG TGIRGDHASV GTDGTIEMFI VPFIGDVTG SELTHPYAVE LQDGEELAIA FGVTLKSGYG ARITEYYDVS LFLENGGNSK ELTLQPANTK SGYVWSDGHG Y NITDSDGD ...String: MDCRNLCGAA APSRLVQPGC FICRGVAVSI PPAAPGPATS VFDTPPSTFS LRPDGTIIAG TGIRGDHASV GTDGTIEMFI VPFIGDVTG SELTHPYAVE LQDGEELAIA FGVTLKSGYG ARITEYYDVS LFLENGGNSK ELTLQPANTK SGYVWSDGHG Y NITDSDGD LHTVQNVTRP VWFEMTEPGI VGVIMEARYK ATGLVSSSIS ITVNVTYAD UniProtKB: Virion-associated protein |
-Macromolecule #2: Minor capsid protein, gp10
Macromolecule | Name: Minor capsid protein, gp10 / type: protein_or_peptide / ID: 2 / Number of copies: 30 / Enantiomer: LEVO |
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Source (natural) | Organism: Agrobacterium phage Milano (virus) |
Molecular weight | Theoretical: 14.54829 KDa |
Sequence | String: MNFNVGVDFP SFIAWDGEES FPVKVDGFNQ FGFTFKTIAA LTAATTFNIF YHEPSDADPC VPGPAIRVPE VPFCDTVLLS EDGLAAVTL PETVTPDSFC AGTVPCMNGQ WISIAPATGS ETNAANVQIT VTMKGATR UniProtKB: Virion-associated protein |
-Macromolecule #3: Linking protein 2, gp128
Macromolecule | Name: Linking protein 2, gp128 / type: protein_or_peptide / ID: 3 / Number of copies: 11 / Enantiomer: LEVO |
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Source (natural) | Organism: Agrobacterium phage Milano (virus) |
Molecular weight | Theoretical: 3.942762 KDa |
Sequence | String: MVKLNCRPLC QAPTASRLVS PPCFICRGVA PSAPVTPG |
-Macromolecule #4: Major capsid protein, gp9
Macromolecule | Name: Major capsid protein, gp9 / type: protein_or_peptide / ID: 4 / Number of copies: 17 / Enantiomer: LEVO |
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Source (natural) | Organism: Agrobacterium phage Milano (virus) |
Molecular weight | Theoretical: 52.037324 KDa |
Sequence | String: MANKESELNG LDDIHSDIEK LSAHVEKFSD GMDEKYKELT ARFDGVKGDN DAIRKAVADA TKEYAELSAK HQFFTEELAA MKARLDTPI MRSQAELDDH DRKTAIQLQR NMHEFRGGDP KEFVADESNL VDLKAYRSAV RKMLKVGIES KERVIASMTD V ERKAFEAS ...String: MANKESELNG LDDIHSDIEK LSAHVEKFSD GMDEKYKELT ARFDGVKGDN DAIRKAVADA TKEYAELSAK HQFFTEELAA MKARLDTPI MRSQAELDDH DRKTAIQLQR NMHEFRGGDP KEFVADESNL VDLKAYRSAV RKMLKVGIES KERVIASMTD V ERKAFEAS TIGPAFFTPQ VLALEVDCNI ECASLLDLYG QIEVSRSTFT YMKIADYGQL GEYTCDAKCD AEFGEPGNIR HL EGKTYDY RGVFCFNRKN LQEANYDFLS FMIGAAQRSH RINRNQALMI GKGVNEPKGW LTENCFPVFQ TLPVDVNGTS TPA FLAQDW RRFVTSFPAE YGEARSVMHQ NVFGYLAAMV DANGRFLFGD GDLTFTPDLV RERIRISNCL PDPTEGNTKG GTGQ DAFAA GSFVAAQAAW KTAFYAVEKR PMFFEQYEGG SSAWCVKYQF GAEDGGFVGC CEHGRILQIG UniProtKB: Major capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |