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- EMDB-43243: Cryo-EM of neck of bacteriophage Chi -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-43243
TitleCryo-EM of neck of bacteriophage Chi
Map data
Sample
  • Virus: Chivirus chi
    • Protein or peptide: Neck 1
    • Protein or peptide: Tail terminator
    • Protein or peptide: Portal
    • Protein or peptide: Neck 2
    • Protein or peptide: Tail Tube
KeywordsFlagellotropic bacteriophage / Siphophage / Neck / VIRUS
Function / homology
Function and homology information


viral portal complex / virion assembly / viral life cycle / symbiont entry into host cell / structural molecule activity / DNA binding
Similarity search - Function
Head-to-tail joining protein W / Head-to-tail joining protein W superfamily / gpW / Phage portal protein, lambda family / Phage portal protein, lambda family / Bacterial Ig-like domain (group 1) / Bacterial Ig-like domain (group 1) / Big-1 (bacterial Ig-like domain 1) domain / Big-1 (bacterial Ig-like domain 1) domain profile. / Invasin/intimin cell-adhesion fragments / Immunoglobulin-like fold
Similarity search - Domain/homology
Transposase / Uncharacterized protein / Portal protein / Uncharacterized protein / Major tail protein
Similarity search - Component
Biological speciesChivirus chi
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSonani RR / Esteves NC / 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: Structure / Year: 2024
Title: Cryo-EM structure of flagellotropic bacteriophage Chi.
Authors: Ravi R Sonani / Nathaniel C Esteves / Birgit E Scharf / Edward H Egelman /
Abstract: The flagellotropic bacteriophage χ (Chi) infects bacteria via the flagellar filament. Despite years of study, its structural architecture remains partly characterized. Through cryo-EM, we unveil ...The flagellotropic bacteriophage χ (Chi) infects bacteria via the flagellar filament. Despite years of study, its structural architecture remains partly characterized. Through cryo-EM, we unveil χ's nearly complete structure, encompassing capsid, neck, tail, and tail tip. While the capsid and tail resemble phage YSD1, the neck and tail tip reveal new proteins and their arrangement. The neck shows a unique conformation of the tail tube protein, forming a socket-like structure for attachment to the neck. The tail tip comprises four proteins, including distal tail protein (DTP), two baseplate hub proteins (BH1P and BH2P), and tail tip assembly protein (TAP) exhibiting minimal organization compared to other siphophages. Deviating from the consensus in other siphophages, DTP in χ forms a trimeric assembly, reducing tail symmetry from 6-fold to 3-fold at the tip. These findings illuminate the previously unexplored structural organization of χ's neck and tail tip.
History
DepositionJan 2, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43243.png

Downloads & links

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Map

FileDownload / File: emd_43243.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.)
0.82 Å/pix.
x 600 pix.
= 492. Å		0.82 Å/pix.
x 600 pix.
= 492. Å		0.82 Å/pix.
x 600 pix.
= 492. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.47532558 - 0.9406138
Average (Standard dev.)-0.0049098637 (±0.041095797)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 492.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43243_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_43243_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 : Chivirus chi

EntireName: Chivirus chi
Components
  • Virus: Chivirus chi
    • Protein or peptide: Neck 1
    • Protein or peptide: Tail terminator
    • Protein or peptide: Portal
    • Protein or peptide: Neck 2
    • Protein or peptide: Tail Tube

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Supramolecule #1: Chivirus chi

SupramoleculeName: Chivirus chi / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1541887 / Sci species name: Chivirus chi / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Neck 1

MacromoleculeName: Neck 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chivirus chi
Molecular weightTheoretical: 9.431688 KDa
SequenceString:
MTPEECRAQY RLMLKEAMDA YHQLNLGGSV RVVVDQNSER VEYTAANRQS LWAYIVRLQN AINSDNPCAA FMGLPSSPAG FLFP

UniProtKB: Uncharacterized protein

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Macromolecule #2: Tail terminator

MacromoleculeName: Tail terminator / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chivirus chi
Molecular weightTheoretical: 18.804584 KDa
SequenceString:
MSQRLDILKA LTAHLEQITI ANGYAYDLKG KVYRGRDRFG ADFTSRLPIV SILEAKATDY GSFANEEQTV RMDDWVLLVQ GWVKDDPRN PTDPAYELLA EVEKRLAMLV AKDEQGQPMY PALYRLGGKI AKLTLAQPVV RPPEDGLSDT AFFFLPVRVG L KVDIRNP

UniProtKB: Transposase

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Macromolecule #3: Portal

MacromoleculeName: Portal / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chivirus chi
Molecular weightTheoretical: 62.333262 KDa
SequenceString: MTEKKRSTTQ RAKKAAKTAD VATLDATPQN PSALGGGLEG AERNTREMFR WTPAIISPDQ QIAQDGTLAL SRAQDIVQND GYAFGAVAI HRDSVVGSQY KLNSKPNSLV LGAPEGWAEE FQEVVEARFN MVAESPENWF DARRMNTLTG LVRLAVGGFI M TGEVLASC ...String:
MTEKKRSTTQ RAKKAAKTAD VATLDATPQN PSALGGGLEG AERNTREMFR WTPAIISPDQ QIAQDGTLAL SRAQDIVQND GYAFGAVAI HRDSVVGSQY KLNSKPNSLV LGAPEGWAEE FQEVVEARFN MVAESPENWF DARRMNTLTG LVRLAVGGFI M TGEVLASC EWMKPNGTRM QRRPFGTAIQ MISPYRLSNP DNIMDDKYLR SGVKLDEMGA PIGYWLRKAF PGDPTDLEQW RW EYQPARF DWGRRRMIHI IEALLPGQTR GISEMVAALK QMKMTRNFQE VTLQNAIVNA TYAAAIESEL PSDVVFNQMG MGQ TPFGDI LKTYMGSLAE YIAGSKNIAI DGAKIPHLFP GTKLKMQPAG TPGGVGTDYE ESLLRNIAAS LGLSYEQFSR DYTK TNYSS ARASMAETWK YMESRKKLVA DRFASMIYTL WLEEEVNAGN VPLPPGFTWR DFYDPMKRDA LCNAEWIGAS RGQID EKKE TEAAILRIKN GLSTYEAEIA RLGGDFREVF KQRAREEGII KDLGLDFSGK MVEGTEASGS TGSTGSDNNN EEDTKE

UniProtKB: Portal protein

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Macromolecule #4: Neck 2

MacromoleculeName: Neck 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chivirus chi
Molecular weightTheoretical: 13.39921 KDa
SequenceString:
MASNFAAIKA KARRDVHASL SVPARYENYS QDVIVEDLSV RWHNKIAIMG DLENGGYANI VEGIERIIFT REELAVKGVV LSEGDSIIM TAEGYENARL VLKTQEPIVG PVEVVWQVAR AD

UniProtKB: Uncharacterized protein

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Macromolecule #5: Tail Tube

MacromoleculeName: Tail Tube / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chivirus chi
Molecular weightTheoretical: 40.375363 KDa
SequenceString: MNDNYQNNYV VGRGTVYFDR FQDGTNRKTG EMYFGNTPEF TINTDSETLD HYSSDHGMRV MDASVLLEAS QGGTFTCDNI NADNLALWF LGEVSNTTQT QQTDAKEVFN PIMRGRYYQL GTTDDNPTGV RGVTNFQMVK ADASIAISVG SGDITSIVGA T VVNPAGNY ...String:
MNDNYQNNYV VGRGTVYFDR FQDGTNRKTG EMYFGNTPEF TINTDSETLD HYSSDHGMRV MDASVLLEAS QGGTFTCDNI NADNLALWF LGEVSNTTQT QQTDAKEVFN PIMRGRYYQL GTTDDNPTGV RGVTNFQMVK ADASIAISVG SGDITSIVGA T VVNPAGNY EIDLEAGRIY IEPDSTDLSG NVQIAVQYDV DAQKRTLVIG KSNMVYGALR MISDNPVGLN KNYYFPKVSI AP DGDYALK GDDWQVMSFT FKAMQLNNIT QRVYIDIVEA AAAVDPTAQR TIEITPASTT ATTGGAGVVC TVTVRDGTGT AVQ GDAVTF TTVAGATVTP NSATTGATGT ATTTVNRAAA GTATVTATLA NGKAATTGTI TFSAP

UniProtKB: Major tail 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: 8
VitrificationCryogen name: ETHANE
DetailsNeck region of bacteriophage Chi

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Electron microscopy

MicroscopeFEI TITAN 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: 2.4 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 17766
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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