[English] 日本語
Yorodumi
- EMDB-29512: Structure of tail-neck junction of Agrobacterium phage Milano -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-29512
TitleStructure of tail-neck junction of Agrobacterium phage Milano
Map data
Sample
  • Virus: Agrobacterium phage Milano (virus)
    • Protein or peptide: Collar sheath protein, gp13
    • Protein or peptide: Tail sheath protein
    • Protein or peptide: Tail-tube, gp21
    • Protein or peptide: Tail-terminator protein, gp18
KeywordsMyophage / redox trigger / VIRUS
Function / homologyBacterial Ig domain / Virion-associated protein / Tail sheath protein / Virion-associated protein / Virion-associated protein
Function and homology information
Biological speciesAgrobacterium phage Milano (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.49 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 23, 2023-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_29512.png

Downloads & links

-
Map

FileDownload / File: emd_29512.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.5269742 - 0.9227731
Average (Standard dev.)-0.00043561085 (±0.04304067)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #1

Fileemd_29512_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_29512_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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: Tail sheath protein
    • Protein or peptide: Tail-tube, gp21
    • Protein or peptide: Tail-terminator protein, gp18

-
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)

-
Macromolecule #1: Collar sheath protein, gp13

MacromoleculeName: Collar sheath protein, gp13 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / 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

-
Macromolecule #2: Tail sheath protein

MacromoleculeName: Tail sheath protein / type: protein_or_peptide / ID: 2 / 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

-
Macromolecule #3: Tail-tube, gp21

MacromoleculeName: Tail-tube, gp21 / type: protein_or_peptide / ID: 3 / 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

-
Macromolecule #4: Tail-terminator protein, gp18

MacromoleculeName: Tail-terminator protein, gp18 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS 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: 2.2 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

-
Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10216
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more