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- EMDB-29383: Structure of baseplate with receptor binding complex of Agrobacte... -

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Basic information

Entry
Database: EMDB / ID: EMD-29383
TitleStructure of baseplate with receptor binding complex of Agrobacterium phage Milano
Map data
Sample
  • Virus: Agrobacterium phage Milano (virus)
    • Protein or peptide: x 10 types
  • Ligand: x 1 types
KeywordsMyophage / redox trigger / disulfides / VIRUS
Function / homology
Function and homology information


DNA circulation, N-terminal / DNA circularisation protein N-terminus / Baseplate protein J-like / Baseplate J-like protein / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
DNA-circularization protein / Baseplate hub protein / Tail sheath protein / Virion-associated protein / Baseplate protein / Baseplate protein / Tail fiber protein / Virion-associated protein / Virion-associated protein
Similarity search - Component
Biological speciesAgrobacterium phage Milano (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSonani RR / Leiman PG / Wang F / Kreutzberger MAB / Sebastian A / Esteves NC / Kelly RJ / Scharf B / 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: Nat Commun / Year: 2024
Title: An extensive disulfide bond network prevents tail contraction in Agrobacterium tumefaciens phage Milano.
Authors: Ravi R Sonani / Lee K Palmer / Nathaniel C Esteves / Abigail A Horton / Amanda L Sebastian / Rebecca J Kelly / Fengbin Wang / Mark A B Kreutzberger / William K Russell / Petr G Leiman / ...Authors: Ravi R Sonani / Lee K Palmer / Nathaniel C Esteves / Abigail A Horton / Amanda L Sebastian / Rebecca J Kelly / Fengbin Wang / Mark A B Kreutzberger / William K Russell / Petr G Leiman / Birgit E Scharf / Edward H Egelman /
Abstract: A contractile sheath and rigid tube assembly is a widespread apparatus used by bacteriophages, tailocins, and the bacterial type VI secretion system to penetrate cell membranes. In this mechanism, ...A contractile sheath and rigid tube assembly is a widespread apparatus used by bacteriophages, tailocins, and the bacterial type VI secretion system to penetrate cell membranes. In this mechanism, contraction of an external sheath powers the motion of an inner tube through the membrane. The structure, energetics, and mechanism of the machinery imply rigidity and straightness. The contractile tail of Agrobacterium tumefaciens bacteriophage Milano is flexible and bent to varying degrees, which sets it apart from other contractile tail-like systems. Here, we report structures of the Milano tail including the sheath-tube complex, baseplate, and putative receptor-binding proteins. The flexible-to-rigid transformation of the Milano tail upon contraction can be explained by unique electrostatic properties of the tail tube and sheath. All components of the Milano tail, including sheath subunits, are crosslinked by disulfides, some of which must be reduced for contraction to occur. The putative receptor-binding complex of Milano contains a tailspike, a tail fiber, and at least two small proteins that form a garland around the distal ends of the tailspikes and tail fibers. Despite being flagellotropic, Milano lacks thread-like tail filaments that can wrap around the flagellum, and is thus likely to employ a different binding mechanism.
History
DepositionJan 5, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateFeb 7, 2024-
Current statusFeb 7, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29383.png

Downloads & links

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Map

FileDownload / File: emd_29383.map.gz / Format: CCP4 / Size: 736.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.7795086 - 1.4777966
Average (Standard dev.)0.0070742643 (±0.04529745)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions578578578
Spacing578578578
CellA=B=C: 624.24005 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_29383_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_29383_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: Baseplate hub protein, gp26
    • Protein or peptide: Tail-tube, gp21
    • Protein or peptide: Baseplate Wedge 2 protein, gp29
    • Protein or peptide: Baseplate wedge 1, gp28
    • Protein or peptide: Tail sheath protein, gp20
    • Protein or peptide: Baseplate Wedge 3 protein, gp30
    • Protein or peptide: Tail Spike protein, gp124
    • Protein or peptide: Short Tail Fibers, gp31
    • Protein or peptide: Baseplate Centerpiece, gp25
    • Protein or peptide: Baseplate Central Spike, gp27
  • Ligand: FE (III) ION

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Supramolecule #1: Agrobacterium phage Milano

SupramoleculeName: Agrobacterium phage Milano / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#10 / 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: Baseplate hub protein, gp26

MacromoleculeName: Baseplate hub protein, gp26 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 49.701758 KDa
SequenceString: MIKPMRIFIG GEELVTYTSA QLQRTKKQMT GSLTVEIFLD YVPTKPTIVN AVRGKEILVY IMGELAFTGI IDKRRGKSVK KQNRDASGR FAFSGGPGSL SEDAGGDVSV NFSKGNGYSV TLTARGRTKY LIDSSQTHPT GFFKNTSDKK VIETLVKEHN V VLQWDAEE ...String:
MIKPMRIFIG GEELVTYTSA QLQRTKKQMT GSLTVEIFLD YVPTKPTIVN AVRGKEILVY IMGELAFTGI IDKRRGKSVK KQNRDASGR FAFSGGPGSL SEDAGGDVSV NFSKGNGYSV TLTARGRTKY LIDSSQTHPT GFFKNTSDKK VIETLVKEHN V VLQWDAEE IDEPKVTLRD GNRIYNEIFE RCNQNCHFAY ETRDGKLLIT DGTNGTVGED IILGYNILDF SAEQSEDQAN SQ ITVKGHR TQKGVWGNDA IVQPVQTVAD SWVGANIPLT IQHYGDATNE GLQRRAKFEA DRRAAESKSV SVTVFHVAQQ TGT PWDIGT VHYVEIPPEG IFDVLECVSL TYTVDAKSTL ETKLELAPPP SQGISGGAAS GVSGLLSSAN NLLSDLTTKG IARR VQAGV QIIGGQYPSS WTSAALSAIA NPINAITSVV NSLLAKEDEK PPKQPPMRLP PE

UniProtKB: Baseplate hub protein

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Macromolecule #2: Tail-tube, gp21

MacromoleculeName: Tail-tube, gp21 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / 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 #3: Baseplate Wedge 2 protein, gp29

MacromoleculeName: Baseplate Wedge 2 protein, gp29 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 43.322723 KDa
SequenceString: MSCTIQRPDP QDLRNDIATR FSTNVLGGAP IIPESNEFYV VSLEYAMQEE FYAFGEQMWR ERDPRFACCE NLVKMAAERG VYPKPAQFA QGYVRMTGTP GSALNQGLRF QFGNQTYEPA SVVPDQLPAT GILVLRVSAV NPGPSGNARV TDGTLVTPVP G ISSAVTAY ...String:
MSCTIQRPDP QDLRNDIATR FSTNVLGGAP IIPESNEFYV VSLEYAMQEE FYAFGEQMWR ERDPRFACCE NLVKMAAERG VYPKPAQFA QGYVRMTGTP GSALNQGLRF QFGNQTYEPA SVVPDQLPAT GILVLRVSAV NPGPSGNARV TDGTLVTPVP G ISSAVTAY GGNFCGGSDE EECEQFRTRY LQRLQYQPRF TVEWLKSKAA EWPCVTDVFD LGPNCCAVNA LGEVVCPNNF EF YVLFRDT FDCGLAPQCV VDEITDWLFG SPQGLGLGEA EFGICGKVRT AAPVKLDIIL DGLSCATPAQ SRVVEERVTD FVN RLPPST NLTIDQLRFI GLQVLGPSFN FNVAIRSPND AVQPGLRFTS CGDAEIDCDY KACLNSVVVI NNNVTTSGCL

UniProtKB: Baseplate protein

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Macromolecule #4: Baseplate wedge 1, gp28

MacromoleculeName: Baseplate wedge 1, gp28 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 19.318713 KDa
SequenceString:
MTCTVDVADR RKRFWTTQIA ACGTSSDDCG DCARPGLQLM CNGQGQVTVS TDNYAVGLAL NILLTDASKA DTGCGWTPGN RGGFWGDSF RSDNLRSGSK IRQVPTRTSM RETVSLIRAY ALDDLKKLVT YGVAKSVDVD LTYRGSNKID MTVIIQGVDG N ESRVGLTG ERISNAWVWS

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Macromolecule #5: Tail sheath protein, gp20

MacromoleculeName: Tail sheath protein, gp20 / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 53.896094 KDa
SequenceString: MAQDALSDGF VRLCIDPSLN FFGEGCKILV EGQMTDDGSA TPDAVTCVTS ELDIIERFGQ GSVLTESLRK VFCTCKSGVS VYALPREDA AAGVKAVYTL TIAGPATTDG RVQLYMGEAE YAVDIGVDAG DTATDIAAAI VAAISPDFPY AATAAAGVIT L TARNAGTI ...String:
MAQDALSDGF VRLCIDPSLN FFGEGCKILV EGQMTDDGSA TPDAVTCVTS ELDIIERFGQ GSVLTESLRK VFCTCKSGVS VYALPREDA AAGVKAVYTL TIAGPATTDG RVQLYMGEAE YAVDIGVDAG DTATDIAAAI VAAISPDFPY AATAAAGVIT L TARNAGTI GNHLSVIYTN LGSCTSVTPE GVTVTFAQTT AGSVNPTPND YATVVNECCF AVYVLSSDDT DWQENLRDWI RS AWDCSKP QCFGHGYVFN KGTLGQVLAD GDNSAELSRL ALPTTYPVLP YLTNAAYGAL SACSTCNNPE LNIQGQTFGL LSC INMPES CTPGWTFGEV TQLQANGFVV SGPSTTSGQG NYTSPYIYND VTNYLRDEKN RPNATFRDAS SRRLAAATGV ALAE FLQQF NGLAVFTKNT NIRTGIIGTN PRLMLGKIRK WAQDNVGTLF SEFDNINEDI QLLTDFEVQP KCVGQPGIFH LNMRY RPPV RGARINVNMA PALFDNCDR

UniProtKB: Tail sheath protein

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Macromolecule #6: Baseplate Wedge 3 protein, gp30

MacromoleculeName: Baseplate Wedge 3 protein, gp30 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 31.414879 KDa
SequenceString: MNVLIPGIDG MVSAGTLEYT GCCPPSFADV DECTLATAFV GLLPSGPLWD RPKYEAITTI TEAGNCAACW TTDHCPTLVD YAVNVGARL ASVIERTIWP AVRESDPFTA VTSTADWLNR FDWVNCFETS CRSKELGEKT PIEYMTDCGP VYVKITYPPS L QQAFESAL ...String:
MNVLIPGIDG MVSAGTLEYT GCCPPSFADV DECTLATAFV GLLPSGPLWD RPKYEAITTI TEAGNCAACW TTDHCPTLVD YAVNVGARL ASVIERTIWP AVRESDPFTA VTSTADWLNR FDWVNCFETS CRSKELGEKT PIEYMTDCGP VYVKITYPPS L QQAFESAL IKSLERLSMG IIKNLAAINF VIEPLKVRVV PVDTTDACEN ETLCVVLEKT SDFFDGVNAN TCGIPTPVAA YI DRDVMQL PSDLDKYIWP GHMAAECIVR SLLSHVSRFC LIRTEQAPD

UniProtKB: Virion-associated protein

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Macromolecule #7: Tail Spike protein, gp124

MacromoleculeName: Tail Spike protein, gp124 / type: protein_or_peptide / ID: 7 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 61.649805 KDa
SequenceString: MAKLRPLQVG GVPGCANIPG GEDCQCWPEW TADNGYFFGD VVQQGGVLYY ATRDVPPGTP FLAADWAPYR PAATAIPPHN ENSTYFQYQ PVAYNDKLYT ARTDLPPGPF DPANWQEISV EGLVEVVDSA TIDFTGTGAA GDPVSADVKL DPDPDNLLSA T ANGLILTA ...String:
MAKLRPLQVG GVPGCANIPG GEDCQCWPEW TADNGYFFGD VVQQGGVLYY ATRDVPPGTP FLAADWAPYR PAATAIPPHN ENSTYFQYQ PVAYNDKLYT ARTDLPPGPF DPANWQEISV EGLVEVVDSA TIDFTGTGAA GDPVSADVKL DPDPDNLLSA T ANGLILTA DNIPFPDPSQ ILISEEVTLR VDYVTGDDAT ADGTLAKPFA TVSAAIGVAT TGDRVEIYPG TYIGNFAPKS DV TVVGLEG VVIDGDVTIA AGVSGALVDG LFVDGSVLVN GANGSVTFRN SRVTENVLAT GNNTGVYRFE NCDIETAAIV NGT GNAEFI FSGGVSENDF FLNSPGTMIV ENRSRVKAVL HEAGNMIVQN IGVIESLAST PDNGFLAVMS SSLFDPLTST YGTI SKTGL CPFVFQDFGR DNTDTTALNG PKFIVSNGRD VHGNYDPAFY ALPNGQTLNS HFAGIDAALE TLQEYSPLDR LVPVD LGFS FTGGWTDGET IGAHVVSRST IVPENMAGSV FSTDSSTLDG VLNIVVGPSV VGTVTIVDGI ATFASSSFNL DPGQTV RVV TTSDGTFDYA ALTLVGHREV VYVN

UniProtKB: Tail fiber protein

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Macromolecule #8: Short Tail Fibers, gp31

MacromoleculeName: Short Tail Fibers, gp31 / type: protein_or_peptide / ID: 8 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 31.667646 KDa
SequenceString: MAGIFFSGGL ACNLTVNAAC GIATTGDDCP ALYYPPKCNV QVDPLQMNAV ISEIANAINA FGNTYDCSRL DNLKQVLNRA RNICDLPPF GDAPDMDDRI AGCFDGQSST VTVQQLVNLV LGQVGTLCQL PQIGAIQDDD WLAGCIDGAA RIVPFAAVRS A LGGGGGVI ...String:
MAGIFFSGGL ACNLTVNAAC GIATTGDDCP ALYYPPKCNV QVDPLQMNAV ISEIANAINA FGNTYDCSRL DNLKQVLNRA RNICDLPPF GDAPDMDDRI AGCFDGQSST VTVQQLVNLV LGQVGTLCQL PQIGAIQDDD WLAGCIDGAA RIVPFAAVRS A LGGGGGVI GGVIPQNQLF DSWRAGGFWD VSQSTAGRTA FVFRSRKEGI GITVSELFIA TGGGAYQSIS EWEPSTFAYV PT GETTAID GGRIQAVAIA FKKGNQWYAK AGDIILPLGG DDGVIRVRTP GYQRLQIWDG VQV

UniProtKB: Virion-associated protein

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Macromolecule #9: Baseplate Centerpiece, gp25

MacromoleculeName: Baseplate Centerpiece, gp25 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 43.287 KDa
SequenceString: MAGPCYNPDA EYLPASFKGF SFDADSSDSD HGRNGAEAEF VFGERTGYAD LGIKIKSYQL RARFQTNDHI AQTNAFIAVL ESPGPGLLV HPTRGTVFAA CRSARVTDSK VDAAGVTYVE LDFVEANSVL SGFGLVGNLV ALALAPIITA TEGSFKRHFS P DNIRYYNT ...String:
MAGPCYNPDA EYLPASFKGF SFDADSSDSD HGRNGAEAEF VFGERTGYAD LGIKIKSYQL RARFQTNDHI AQTNAFIAVL ESPGPGLLV HPTRGTVFAA CRSARVTDSK VDAAGVTYVE LDFVEANSVL SGFGLVGNLV ALALAPIITA TEGSFKRHFS P DNIRYYNT EAVVSTMAQA VTQVQNAYLA ISGNDTSQDK WTTVRDFRNV LIDEFTFYSP ANAWNVLRNG FAILDAAATG SD KFNVLRN LINWSSTHSD LDGESGDAEN AIFTAVRVLS AAYLAKAYTE TAATTVNEGL TQYDLIAAVL EQEAQIAKDD CHD NEFFLQ IRAFAVDVAR VMVNRAYNSP SLIVYAFPGT VHGLVAAWEI FGDAKRSRDL EARNNGSPWA VGPKIISERV RA

UniProtKB: DNA-circularization protein

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Macromolecule #10: Baseplate Central Spike, gp27

MacromoleculeName: Baseplate Central Spike, gp27 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage Milano (virus)
Molecular weightTheoretical: 20.720535 KDa
SequenceString:
MTTSKTYDER NRDIQDGFER HVFKGIEHTD TGALVSVKGS GTQEEDVPVI NSGYGFTPAA DTELEVFLHG DGSDASNKFA TMTIPRNKQ RKWPEGAGGV QHPFNADKFV QFDDDSIWLK DGKFTLGNNQ ELTITVSNGL VTLSSNNEVD FRCPKLMHNG V NIGDSHVH PQKPDSGGDS EEDTDPPKRD

UniProtKB: Baseplate protein

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Macromolecule #11: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14856
FSC plot (resolution estimation)

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