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- EMDB-29540: Structure of capsid of Agrobacterium phage Milano -

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Basic information

Entry
Database: EMDB / ID: EMD-29540
TitleStructure of capsid of Agrobacterium phage Milano
Map data
Sample
  • Virus: Agrobacterium phage Milano (virus)
    • Protein or peptide: Linking protein 1, gp16
  • Protein or peptide: Minor capsid protein, gp10
  • Protein or peptide: Linking protein 2, gp128
  • Protein or peptide: Major capsid protein, gp9
KeywordsMyophage / redox trigger / VIRUS
Function / homology: / Phage capsid / Phage capsid family / virion component / Virion-associated protein / Virion-associated protein / Major capsid protein
Function and homology information
Biological speciesAgrobacterium phage Milano (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.04 Å
AuthorsSonani RR / Wang F / Esteves NC / Kelly RJ / Sebastian A / Kreutzberger MAB / Leiman PG / Scharf BE / Egelman EH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: 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
DepositionJan 25, 2023-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29540.png

Downloads & links

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Map

FileDownload / File: emd_29540.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.44 Å/pix.
x 768 pix.
= 1105.92 Å		1.44 Å/pix.
x 768 pix.
= 1105.92 Å		1.44 Å/pix.
x 768 pix.
= 1105.92 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.42859972 - 1.1197127
Average (Standard dev.)0.0060864636 (±0.08670141)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 1105.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_29540_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_29540_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Agrobacterium phage Milano

EntireName: Agrobacterium phage Milano (virus)
Components
  • Virus: Agrobacterium phage Milano (virus)
    • Protein or peptide: Linking protein 1, gp16
  • Protein or peptide: Minor capsid protein, gp10
  • Protein or peptide: Linking protein 2, gp128
  • Protein or peptide: Major capsid protein, gp9

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Supramolecule #1: Agrobacterium phage Milano

SupramoleculeName: 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
Host (natural)Organism: Agrobacterium fabrum str. C58 (bacteria)

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Macromolecule #1: Linking protein 1, gp16

MacromoleculeName: Linking protein 1, gp16 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 22.913605 KDa
SequenceString: 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

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Macromolecule #2: Minor capsid protein, gp10

MacromoleculeName: Minor capsid protein, gp10 / type: protein_or_peptide / ID: 2 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 14.54829 KDa
SequenceString:
MNFNVGVDFP SFIAWDGEES FPVKVDGFNQ FGFTFKTIAA LTAATTFNIF YHEPSDADPC VPGPAIRVPE VPFCDTVLLS EDGLAAVTL PETVTPDSFC AGTVPCMNGQ WISIAPATGS ETNAANVQIT VTMKGATR

UniProtKB: Virion-associated protein

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Macromolecule #3: Linking protein 2, gp128

MacromoleculeName: Linking protein 2, gp128 / type: protein_or_peptide / ID: 3 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 3.942762 KDa
SequenceString:
MVKLNCRPLC QAPTASRLVS PPCFICRGVA PSAPVTPG

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Macromolecule #4: Major capsid protein, gp9

MacromoleculeName: Major capsid protein, gp9 / type: protein_or_peptide / ID: 4 / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 52.037324 KDa
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15740
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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