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- EMDB-29503: Neck structure of Agrobacterium phage Milano, C3 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-29503
TitleNeck structure of Agrobacterium phage Milano, C3 symmetry
Map data
Sample
  • Virus: Agrobacterium phage Milano (virus)
    • Protein or peptide: Collar sheath protein, gp13
    • Protein or peptide: Portal protein, gp7
    • Protein or peptide: Neck 2 protein, gp15
    • Protein or peptide: Tail-terminator protein, gp18
    • Protein or peptide: Tail-tube, gp21
    • Protein or peptide: Neck 1 protein, gp14
KeywordsMyophage / redox trigger / VIRUS
Function / homology
Function and homology information


symbiont entry into host cell
Similarity search - Function
Bacterial Ig domain / Bacteriophage SPP1, head-tail adaptor superfamily / Bacteriophage/Gene transfer agent portal protein / Phage portal protein
Similarity search - Domain/homology
Virion-associated protein / Head completion protein / Portal protein / Virion-associated protein / Virion-associated protein / Head-to-tail connector complex protein
Similarity search - Component
Biological speciesAgrobacterium phage Milano (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 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 21, 2023-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29503.png

Downloads & links

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Map

FileDownload / File: emd_29503.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 448 pix.
= 483.84 Å		1.08 Å/pix.
x 448 pix.
= 483.84 Å		1.08 Å/pix.
x 448 pix.
= 483.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.42088145 - 0.7798062
Average (Standard dev.)-0.0003919592 (±0.04518737)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 483.84003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_29503_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_29503_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

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: Collar sheath protein, gp13
    • Protein or peptide: Portal protein, gp7
    • Protein or peptide: Neck 2 protein, gp15
    • Protein or peptide: Tail-terminator protein, gp18
    • Protein or peptide: Tail-tube, gp21
    • Protein or peptide: Neck 1 protein, gp14

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Supramolecule #1: Agrobacterium phage Milano

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

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Macromolecule #1: Collar sheath protein, gp13

MacromoleculeName: Collar sheath protein, gp13 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 24.490402 KDa
SequenceString: 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

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Macromolecule #2: Portal protein, gp7

MacromoleculeName: Portal protein, gp7 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 45.840844 KDa
SequenceString: 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

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Macromolecule #3: Neck 2 protein, gp15

MacromoleculeName: Neck 2 protein, gp15 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 16.052353 KDa
SequenceString:
MRTADRKHRV IVCSQQSDVD DEGRLLITRA GVIQGWAAIA PVKAIRFSQD GVSMQKDTMQ PTHDITMNYN PDVNVSVSAW VYEHRLKSP PRWFKVLSVV NVDECSRYMK IRCRLVETSD DVTPPVEEEK NSFGAVKIDI PL

UniProtKB: Head completion protein

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Macromolecule #4: Tail-terminator protein, gp18

MacromoleculeName: Tail-terminator protein, gp18 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 20.268541 KDa
SequenceString:
METKLTYGNR VTLPEFAKYI VAPAFHEIEG RAIPVTGVDD DASGTQATKL PFVLVGLRQG DTSGPATIAG NSTINLRDDF IVEFNMKKE RYRDRKGGET PFFSYYDYES IRDRLFNSMI EFSGEHGITF EFVSLDISTE GDVVYIEFRF RQNYEWCETV R EADTTIEA GRFSINLQGC

UniProtKB: Virion-associated protein

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Macromolecule #5: Tail-tube, gp21

MacromoleculeName: Tail-tube, gp21 / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 14.673427 KDa
SequenceString:
MACNKQNGVK NILITFTDCD TQEVIGPISH EQPDDTLPTY KNCAWTNTAL TNGYVQRSAS NATMTLPVVR DLRVPLAFYQ GCAQVDVQV EKFDGTVMTL TEGAVVEPEE SDGRSVTMNI VASEIDELLP PGSLAAA

UniProtKB: Virion-associated protein

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Macromolecule #6: Neck 1 protein, gp14

MacromoleculeName: Neck 1 protein, gp14 / type: protein_or_peptide / ID: 6 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 22.255439 KDa
SequenceString: 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

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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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10216
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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