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- EMDB-43281: Cryo-EM of tail-tip of bacteriophage Chi -

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Basic information

Entry
Database: EMDB / ID: EMD-43281
TitleCryo-EM of tail-tip of bacteriophage Chi
Map data
Sample
  • Virus: Chivirus chi
    • Protein or peptide: Minor tail protein
    • Protein or peptide: Distal tail protein
    • Protein or peptide: Baseplate hub 1 protein, gp27
    • Protein or peptide: Tail Tube
    • Protein or peptide: Tape measure
    • Protein or peptide: Tail assembly protein 1
  • Ligand: FE (III) ION
KeywordsFlagellotropic bacteriophage / Siphophage / Tail-tip / VIRUS
Function / homology
Function and homology information


Tape measure protein N-terminal / Tape measure protein / Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Phage conserved hypothetical protein BR0599 / 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. / Tip attachment protein J ...Tape measure protein N-terminal / Tape measure protein / Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Phage conserved hypothetical protein BR0599 / 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. / Tip attachment protein J / Putative phage tail protein / Invasin/intimin cell-adhesion fragments / Immunoglobulin-like fold
Similarity search - Domain/homology
Distal tail protein / Tail assembly protein 1 / Major tail protein / Bacteriophage phiJL001 Gp84 C-terminal domain-containing protein / Tape measure / Minor tail protein
Similarity search - Component
Biological speciesChivirus chi
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 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 6, 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_43281.png

Downloads & links

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Map

FileDownload / File: emd_43281.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.14918783 - 0.5389372
Average (Standard dev.)0.00026434305 (±0.017732145)
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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Mask #1

Fileemd_43281_msk_1.map
Projections & Slices
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Additional map: #1

Fileemd_43281_additional_1.map
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Half map: #1

Fileemd_43281_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_43281_half_map_2.map
Projections & Slices
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Sample components

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Entire : Chivirus chi

EntireName: Chivirus chi
Components
  • Virus: Chivirus chi
    • Protein or peptide: Minor tail protein
    • Protein or peptide: Distal tail protein
    • Protein or peptide: Baseplate hub 1 protein, gp27
    • Protein or peptide: Tail Tube
    • Protein or peptide: Tape measure
    • Protein or peptide: Tail assembly protein 1
  • Ligand: FE (III) ION

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Supramolecule #1: Chivirus chi

SupramoleculeName: Chivirus chi / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 / 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: Minor tail protein

MacromoleculeName: Minor tail protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chivirus chi
Molecular weightTheoretical: 143.342531 KDa
SequenceString: MGSKSKKVTV GYKYYMGLFM GLFRGPVNEI TEIRVGDRTA WTGSITGNTT IQINKESLFG GTKAEGGIDG PLEVYMGAPT QTVSQKLKN MLGGRQPEFR GVVTAYFDGL ICAMNPYPKQ WKFKARRSTA GWTGGVWYPE KCLVKMQGYD GQGNQHEIHA M NPAHILYE ...String:
MGSKSKKVTV GYKYYMGLFM GLFRGPVNEI TEIRVGDRTA WTGSITGNTT IQINKESLFG GTKAEGGIDG PLEVYMGAPT QTVSQKLKN MLGGRQPEFR GVVTAYFDGL ICAMNPYPKQ WKFKARRSTA GWTGGVWYPE KCLVKMQGYD GQGNQHEIHA M NPAHILYE CQSNYEWGRG LSRTLIDDTT FRLAADTLFN ENFGLCIRWN RQDTLESFMQ LILDHIGGAM YVSKVTGKLS LR LIRKDYD FDTLPIFDTD SGLLSIQEAT NASPANLVNE VVVTYHNPVM DEDQQVRSHN LAQIQNQGCL NSNTIEYLGI PTG KLAMQV AQRDLRAAST NVRRFTVICD RRAWNVQPGD VLKVRDPKQR GLTEVVIRVG TVEDGTLPDG KIKVVALQDQ FAFQ LNTFN QVEPPAGYEP NLTPAIARRI VYEMPYVDLV QQLPDGELNA VGPNDAFINS QAEKPTDMSA AYDMGIMAEG ESGFD VRGN GDFGAFGSLA SDIDYLSTQI VLSEMTDMWD DVQPGFVARI AKPVLDGQRT QMEIAEEFVR IDAINGNVIT VARGVL DTI PFRHQKSEML WVTTYDGGTD WQKYAGNESI DIKILPWTLG GGRFPIEDAP IDHLDMDFRQ IRPYPPGNVQ HYLASTS TL QRWYVPSALT YTANAGETPD TYTLTWAHRD RVLQGDKPVP HIDGDIGPEP GTSYTIRVYN QEGTLVRTES GINGTTWN W PYATAAADMN VEASLFDPVL ATLRLTSARN GRESWEYYEM KVSVYKKPPQ FVYDASLMQF AAQPYNATSD PNPPTPPMD GPYVSSLMQF AAQPDGSEDF GPAESMNGPN VALLPHQVTQ TSSIITPLDT LLYETPYIQL SRDGRDLNTS KVSAYVARSS DRTVDSYTL FTKHETDANY TSSGTQPWTP WGMSTVGLGF FTDEVTIDPT SDKDGVPVAP AKVGDLLLID QELVSITAIN G RTYKIGRG VADTIPAQHY SSRPVWLISV GFGYSDMAFG DNEKAMVIIR PDTYGTDIPL SKLYPLQLQM QYRPKRPYPP GL MMIGGQP FFNTASGLAD DFNPYDNLKA KDVVCTYAHR NRVSQSTTAR DHFAVGITPE PGVKYRVRIG YAYWSQSGSG FSL LSQFET EDAGFIMRAA DLERWGRQAG YAQDAGGYST LNVTVNAIRD GMLNWQGYTM TVRVPSFPLP PGQKPGGGDG PWNP PGGGN TGGTTPPTEP PDRPDPSEPG TTDPSEPTKP DEPEEPQPPV DPEDPDTDPP EPPEPPVDPT NVPGWSLSWD HGWAM TLPD FRYVPPADEE PE

UniProtKB: Minor tail protein

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Macromolecule #2: Distal tail protein

MacromoleculeName: Distal tail protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chivirus chi
Molecular weightTheoretical: 63.032605 KDa
SequenceString: MALSGLRPAR EQFNQAIYDA LNGAYQLYVQ DAFGQAAANQ TYYMAKWMKL KAGTYTAVMY VDDSGTLSID HAVVATAAIG TNPNSGEFT VAADGVYRFD CIYSNVPADT PAYMAYQLIR DGQTVEVSRA NDFIADIVPI PDKALGPKPP YSDDVRLTYP V FLPLPNWK ...String:
MALSGLRPAR EQFNQAIYDA LNGAYQLYVQ DAFGQAAANQ TYYMAKWMKL KAGTYTAVMY VDDSGTLSID HAVVATAAIG TNPNSGEFT VAADGVYRFD CIYSNVPADT PAYMAYQLIR DGQTVEVSRA NDFIADIVPI PDKALGPKPP YSDDVRLTYP V FLPLPNWK DGVTERIEWQ TDVMISESGA EQRRPIRLHP RRSFEATFLR WEENRTLLDT TIAGVGQSPL LLPLWHDMTA TE NNAPAGS VDIFGQFRVK DFNVGDVVMF NRGTTWDYET NIIAGLDIDA GHMTLTFGLQ SDTPKGTRLY PVRVAQIREA MNG QQMTDS VSQTQVRFFC TENYDLTPSW SDFPIYTRTG LHIFVLPEDW GSSNEITSDR LTYNFDNQSG PVVVVDPGGQ NYGT VKKSY TIKGRTADRQ FRQILFALRG RTKTFHLPLD TNDFILSRDI NPADGALVVR RCGYTQYIGG TQETKRDIMV ELYDG TRIP TTIISSRIVG DEEWLFLSQS IPATSRNDVR RIGYIPVARL DVDGIEIKRL TDSAGVSQVS LTFKFFDDRR IATPLP LS

UniProtKB: Distal tail protein

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Macromolecule #3: Baseplate hub 1 protein, gp27

MacromoleculeName: Baseplate hub 1 protein, gp27 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chivirus chi
Molecular weightTheoretical: 29.348869 KDa
SequenceString: MSYNIIETSN DNGRPVFMYE FRLLDKYWRY TSADAKVSAL GSIWEPMGVS DDGIKQTGEA KTDALNLTLP NSNPVVGLFI GTPPGSPVT LTIRRMHLDD NDPVVCYVGT VDSINQGENP TVATVTCSTL SATMDRNGLR LSWSRGCPHA LYDGQCRVNK E AFRVDATI ...String:
MSYNIIETSN DNGRPVFMYE FRLLDKYWRY TSADAKVSAL GSIWEPMGVS DDGIKQTGEA KTDALNLTLP NSNPVVGLFI GTPPGSPVT LTIRRMHLDD NDPVVCYVGT VDSINQGENP TVATVTCSTL SATMDRNGLR LSWSRGCPHA LYDGQCRVNK E AFRVDATI LTVGAGTVTA AAYATRPDGY FAGGFIEWID PVYGVERRGI ETHTGNTITI FGTVDGLAGG YILKTYPGCP RT SAACDTI FNNLANFGGI PSLPDRSPFD GNPIF

UniProtKB: Bacteriophage phiJL001 Gp84 C-terminal domain-containing protein

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Macromolecule #4: Tail Tube

MacromoleculeName: Tail Tube / type: protein_or_peptide / ID: 4 / 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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Macromolecule #5: Tape measure

MacromoleculeName: Tape measure / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chivirus chi
Molecular weightTheoretical: 153.960453 KDa
SequenceString: MANSKDVELR IRARDYSQKP LKAVTSAIEQ MAKAQDEQRK AAERGEISTR DLEAAYKKLE SAGSQLLKLN SLIEVFKRQN QAMTEATAK TEGLRQKQAD LQKTYDSTEK VTQKQERALA RVTRQVEAAT RAEANQAERV NRATRDLERY GIETSKVGAA Q AGIVTSVA ...String:
MANSKDVELR IRARDYSQKP LKAVTSAIEQ MAKAQDEQRK AAERGEISTR DLEAAYKKLE SAGSQLLKLN SLIEVFKRQN QAMTEATAK TEGLRQKQAD LQKTYDSTEK VTQKQERALA RVTRQVEAAT RAEANQAERV NRATRDLERY GIETSKVGAA Q AGIVTSVA QVNRVLERQD EIISTSAAAA AQAKVIRGLQ QQADQAMATA RGYQTLGRVV QQATGQLGPL GTQIQTIVSP AE AARRTLS GLENQVHGVT AELARNSKEV ENVAQKVRML NEANKTVSAL AQQIDLYRQQ VATLRNARTE YQQARQDVIK LAQ QMRTAT TDTGALGIQM QAAQQRLSAA ATAMRNTATA ARSTQAALRA AQVDTRNLSD AEARLISTSQ QSAAALNTLS TATN RNSQA ARDGSKAWSL FRDEGRTTLS FLQRIRGEVL ALTTTYVGFQ GAISLAGGAI DAYKNRQQAM VKIANVVGNS QAAIN KEWE YMVGLANTLG IDITTLSQSY TKFAVSAKAV GLSLQDSKFI FESVAKAGRV FHLSQDDMEG VFRALEQMLS KGQVYA EEL RGQLGERLPA AFALFAKGMD MTTAELMKAM ENGEVTGEAV INFAREQAKA IDAQLATAQK GVDAMEARAR NAMNAFQ LA LADAGFIEAY VQMLNKITDF LNSEDGRAAA VKLGEAFGML ADAVTWCIEN VDTLITALSI LAGLKVVQFI GGMISGLK N LLPLFNTLSK IGAGIITVLE GVAARMIAAE GAIGLLGVAL KGLTRLIPIV GWALLAYDIG AIMYDQSQTF REAVNAVIR DFKNLGNQLA AVVDTIPALL YDLAVSVLRP ITTMFADTTQ AIIKWIADVL KLIPGVGQGL SEWATSIGDD LTKEQRGFLE STGRIWDNV NKQWVKLNDD MVAKNADATD KIRGQVNQLA ADMAAITKGE GFQFTQDPGT GVTKRSREIA GLTKELNKME E AAKKADVA SRKAEQRKNL SGRLAIIDEE FAPQYARAKS IGGSEGDALT KRLDAVVAAR KKAETTLFNS QQRTTGGIKK QE NALQALI NKYNELNAAV GVKEVKIDPN ATFDDRLAAK LAAVNTQYDQ LIAKSKKLGT GGENLAGQFE DLRKRNLEYA TTQ AKLEEL KRIQDQLNAQ QETRKNLLDE INAKRQAGII SEDEAVSQTV ALYQNMNAGI ASSAEQLDVF AQKIKDTMSP EEFS RIMAQ IAAVKAGLVD VTGTFTTMDT TVVQGVLDGM STALSSIVDE MALVVAGSQS IGDAFSNLGV AVARFFADFL QKIAM AILQ QMALNALASM GGGIGSAAVA LGGTVAKHNG GTVGSKTTGG TQMKGGISPA MFANAPRFHD GGLPGLRSDE VPTILQ KGE QVLSKDDPNN VLNQSRGGGQ TAQSPQGLRF VLVDDRSKVP EAMNTPEGEK AVMQILQRNV PTLKNLVG

UniProtKB: Tape measure

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Macromolecule #6: Tail assembly protein 1

MacromoleculeName: Tail assembly protein 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chivirus chi
Molecular weightTheoretical: 8.278664 KDa
SequenceString:
MWWALAMLVA SVLINAALAP KPASAKPATI QDFDIPQVKE GTPQSVVFGE VWTADWQVLG FGNFRTKAVK AKQAKK

UniProtKB: Tail assembly protein 1

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Macromolecule #7: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 7 / 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: 8
VitrificationCryogen name: ETHANE
DetailsTail-tip 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 reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2159
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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