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- EMDB-29541: Structure of neck with portal vertex of capsid of Agrobacterium p... -

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Basic information

Entry
Database: EMDB / ID: EMD-29541
TitleStructure of neck with portal vertex of capsid of Agrobacterium phage Milano
Map data
Sample
  • Virus: Agrobacterium phage Milano (virus)
    • Protein or peptide: Linking protein 2, gp128
    • Protein or peptide: Neck 1 protein, gp14
    • Protein or peptide: Neck 2 protein, gp15
    • Protein or peptide: Linking protein 1, gp16
    • Protein or peptide: Major capsid protein, gp9
    • Protein or peptide: Minor capsid protein, gp10
    • Protein or peptide: Collar sheath protein, gp13
    • Protein or peptide: Portal protein, gp7
    • Protein or peptide: Tail-terminator protein, gp18
    • Protein or peptide: Tail-tube, gp21
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 / : / Phage capsid / Phage capsid family
Similarity search - Domain/homology
Virion-associated protein / Head completion protein / Virion-associated protein / Virion-associated protein / Major capsid 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: 4.5 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 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29541.png

Downloads & links

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Map

FileDownload / File: emd_29541.map.gz / Format: CCP4 / Size: 824 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 600 pix.
= 648. Å		1.08 Å/pix.
x 600 pix.
= 648. Å		1.08 Å/pix.
x 600 pix.
= 648. 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: 0.125
Minimum - Maximum-0.26988322 - 0.48266962
Average (Standard dev.)-0.0010759807 (±0.03429753)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 648.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_29541_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_29541_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: Linking protein 2, gp128
    • Protein or peptide: Neck 1 protein, gp14
    • Protein or peptide: Neck 2 protein, gp15
    • Protein or peptide: Linking protein 1, gp16
    • Protein or peptide: Major capsid protein, gp9
    • Protein or peptide: Minor capsid protein, gp10
    • Protein or peptide: Collar sheath protein, gp13
    • Protein or peptide: Portal protein, gp7
    • Protein or peptide: Tail-terminator protein, gp18
    • Protein or peptide: Tail-tube, gp21

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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: No / Virus empty: No
Host (natural)Organism: Agrobacterium fabrum str. C58 (bacteria)

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Macromolecule #1: Linking protein 2, gp128

MacromoleculeName: Linking protein 2, gp128 / type: protein_or_peptide / ID: 1 / Number of copies: 25 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 3.942762 KDa
SequenceString:
MVKLNCRPLC QAPTASRLVS PPCFICRGVA PSAPVTPG

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Macromolecule #2: Neck 1 protein, gp14

MacromoleculeName: Neck 1 protein, gp14 / type: protein_or_peptide / ID: 2 / 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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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: Linking protein 1, gp16

MacromoleculeName: Linking protein 1, gp16 / type: protein_or_peptide / ID: 4 / Number of copies: 5 / 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 #5: Major capsid protein, gp9

MacromoleculeName: Major capsid protein, gp9 / type: protein_or_peptide / ID: 5 / Number of copies: 30 / 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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Macromolecule #6: Minor capsid protein, gp10

MacromoleculeName: Minor capsid protein, gp10 / type: protein_or_peptide / ID: 6 / Number of copies: 40 / 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 #7: Collar sheath protein, gp13

MacromoleculeName: Collar sheath protein, gp13 / type: protein_or_peptide / ID: 7 / 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 #8: Portal protein, gp7

MacromoleculeName: Portal protein, gp7 / type: protein_or_peptide / ID: 8 / 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 #9: Tail-terminator protein, gp18

MacromoleculeName: Tail-terminator protein, gp18 / type: protein_or_peptide / ID: 9 / 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 #10: Tail-tube, gp21

MacromoleculeName: Tail-tube, gp21 / type: protein_or_peptide / ID: 10 / 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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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: PDB ENTRY
PDB model - PDB ID:

8fwg

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10083
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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