+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43281 | |||||||||
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Title | Cryo-EM of tail-tip of bacteriophage Chi | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Flagellotropic 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 | |||||||||
Biological species | Chivirus chi | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Sonani RR / Esteves NC / Scharf BE / Egelman EH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43281.map.gz | 777.7 MB | EMDB map data format | |
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Header (meta data) | emd-43281-v30.xml emd-43281.xml | 23.4 KB 23.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_43281_fsc.xml | 20 KB | Display | FSC data file |
Images | emd_43281.png | 64.7 KB | ||
Masks | emd_43281_msk_1.map | 824 MB | Mask map | |
Filedesc metadata | emd-43281.cif.gz | 8 KB | ||
Others | emd_43281_additional_1.map.gz emd_43281_half_map_1.map.gz emd_43281_half_map_2.map.gz | 763.3 MB 764.7 MB 764.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43281 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43281 | HTTPS FTP |
-Validation report
Summary document | emd_43281_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_43281_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_43281_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | emd_43281_validation.cif.gz | 37.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43281 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43281 | HTTPS FTP |
-Related structure data
Related structure data | 8vjhMC 8vhxC 8vjaC 8vjiC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_43281.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_43281_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_43281_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_43281_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_43281_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Chivirus chi
Entire | Name: Chivirus chi |
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Components |
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-Supramolecule #1: Chivirus chi
Supramolecule | Name: 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
Macromolecule | Name: Minor tail protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chivirus chi |
Molecular weight | Theoretical: 143.342531 KDa |
Sequence | String: 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 |
-Macromolecule #2: Distal tail protein
Macromolecule | Name: Distal tail protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chivirus chi |
Molecular weight | Theoretical: 63.032605 KDa |
Sequence | String: 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 |
-Macromolecule #3: Baseplate hub 1 protein, gp27
Macromolecule | Name: Baseplate hub 1 protein, gp27 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chivirus chi |
Molecular weight | Theoretical: 29.348869 KDa |
Sequence | String: 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 |
-Macromolecule #4: Tail Tube
Macromolecule | Name: Tail Tube / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Chivirus chi |
Molecular weight | Theoretical: 40.375363 KDa |
Sequence | String: 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 |
-Macromolecule #5: Tape measure
Macromolecule | Name: Tape measure / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chivirus chi |
Molecular weight | Theoretical: 153.960453 KDa |
Sequence | String: 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 |
-Macromolecule #6: Tail assembly protein 1
Macromolecule | Name: Tail assembly protein 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Chivirus chi |
Molecular weight | Theoretical: 8.278664 KDa |
Sequence | String: MWWALAMLVA SVLINAALAP KPASAKPATI QDFDIPQVKE GTPQSVVFGE VWTADWQVLG FGNFRTKAVK AKQAKK UniProtKB: Tail assembly protein 1 |
-Macromolecule #7: FE (III) ION
Macromolecule | Name: FE (III) ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: FE |
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Molecular weight | Theoretical: 55.845 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
Details | Tail-tip of bacteriophage Chi |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |