+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29500 | |||||||||
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Title | Portal assembly of Agrobacterium phage Milano | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Myophage / redox trigger / VIRUS | |||||||||
Function / homology | Bacteriophage/Gene transfer agent portal protein / Phage portal protein / symbiont entry into host cell / Portal protein Function and homology information | |||||||||
Biological species | Agrobacterium phage Milano (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.14 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_29500.map.gz | 322.2 MB | EMDB map data format | |
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Header (meta data) | emd-29500-v30.xml emd-29500.xml | 13.9 KB 13.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29500_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_29500.png | 106.3 KB | ||
Filedesc metadata | emd-29500.cif.gz | 5.2 KB | ||
Others | emd_29500_half_map_1.map.gz emd_29500_half_map_2.map.gz | 317.7 MB 317.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29500 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29500 | HTTPS FTP |
-Related structure data
Related structure data | 8fwbMC 8fwcC 8fweC 8fwgC 8fwmC 8fxpC 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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-Map
File | Download / File: emd_29500.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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_29500_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29500_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: 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: Agrobacterium fabrum str. C58 (bacteria) |
-Macromolecule #1: Portal protein, gp7
Macromolecule | Name: Portal protein, gp7 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Agrobacterium phage Milano (virus) |
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 |
-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
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 |