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- EMDB-37151: Cyanophage A-1(L) baseplate-initiators -

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Basic information

Entry
Database: EMDB / ID: EMD-37151
TitleCyanophage A-1(L) baseplate-initiators
Map data
Sample
  • Virus: unclassified Caudoviricetes (virus)
    • Protein or peptide: hub
    • Protein or peptide: central spike
    • Protein or peptide: tmp
    • Protein or peptide: baseplate gp16
    • Protein or peptide: tube initiator
    • Protein or peptide: sheath initiator
    • Protein or peptide: wedge protein gp31
    • Protein or peptide: wedge protein gp32
Keywordsbaseplate / virus / viral protein
Biological speciesunclassified Caudoviricetes (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsYu RC / Li Q / Zhou CZ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U19A2020 China
CitationJournal: Nat Commun / Year: 2024
Title: Structure of the intact tail machine of Anabaena myophage A-1(L).
Authors: Rong-Cheng Yu / Feng Yang / Hong-Yan Zhang / Pu Hou / Kang Du / Jie Zhu / Ning Cui / Xudong Xu / Yuxing Chen / Qiong Li / Cong-Zhao Zhou /
Abstract: The Myoviridae cyanophage A-1(L) specifically infects the model cyanobacteria Anabaena sp. PCC 7120. Following our recent report on the capsid structure of A-1(L), here we present the high-resolution ...The Myoviridae cyanophage A-1(L) specifically infects the model cyanobacteria Anabaena sp. PCC 7120. Following our recent report on the capsid structure of A-1(L), here we present the high-resolution cryo-EM structure of its intact tail machine including the neck, tail and attached fibers. Besides the dodecameric portal, the neck contains a canonical hexamer connected to a unique pentadecamer that anchors five extended bead-chain-like neck fibers. The 1045-Å-long contractile tail is composed of a helical bundle of tape measure proteins surrounded by a layer of tube proteins and a layer of sheath proteins, ended with a five-component baseplate. The six long and six short tail fibers are folded back pairwise, each with one end anchoring to the baseplate and the distal end pointing to the capsid. Structural analysis combined with biochemical assays further enable us to identify the dual hydrolytic activities of the baseplate hub, in addition to two host receptor binding domains in the tail fibers. Moreover, the structure of the intact A-1(L) also helps us to reannotate its genome. These findings will facilitate the application of A-1(L) as a chassis cyanophage in synthetic biology.
History
DepositionAug 11, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37151.png

Downloads & links

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Map

FileDownload / File: emd_37151.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.014255267 - 0.032564063
Average (Standard dev.)0.0003209453 (±0.0020603822)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 479.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37151_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_37151_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 : unclassified Caudoviricetes

EntireName: unclassified Caudoviricetes (virus)
Components
  • Virus: unclassified Caudoviricetes (virus)
    • Protein or peptide: hub
    • Protein or peptide: central spike
    • Protein or peptide: tmp
    • Protein or peptide: baseplate gp16
    • Protein or peptide: tube initiator
    • Protein or peptide: sheath initiator
    • Protein or peptide: wedge protein gp31
    • Protein or peptide: wedge protein gp32

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Supramolecule #1: unclassified Caudoviricetes

SupramoleculeName: unclassified Caudoviricetes / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2788787 / Sci species name: unclassified Caudoviricetes / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)

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Macromolecule #1: hub

MacromoleculeName: hub / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: unclassified Caudoviricetes (virus)
Molecular weightTheoretical: 98.390594 KDa
SequenceString: MQDPIIKILI GNDTFLLGQE IIDLDFQIGE GKKQNNINFT IFDKDGFFAD KYISTSYAQG GIDLPIDFLE NPDDAKDTNS ASTATEVDS VGNGTVSRSG VFTPKIRAFL DTIASKETAP GTALNIEGYR SVSGSSTLFD ESEMVAGGFP RSQGSKNIGR Y QFTVIDYN ...String:
MQDPIIKILI GNDTFLLGQE IIDLDFQIGE GKKQNNINFT IFDKDGFFAD KYISTSYAQG GIDLPIDFLE NPDDAKDTNS ASTATEVDS VGNGTVSRSG VFTPKIRAFL DTIASKETAP GTALNIEGYR SVSGSSTLFD ESEMVAGGFP RSQGSKNIGR Y QFTVIDYN HARSKYPNIN NYSPQNQDLL AYFKLQHRNV LPYLLRDDLD NAIDKASYEW ASFPGIGKPQ GQFNQVQSGT TI ASLKSYY ETRLAYYRSL EAGSDFQASA PKDTTNNQYA GKEYKTIRTL SNSTTASFYG YNDGFDSSDL TANGERFNPE GIT AAHESL PFGTLVKVTW AVNNKSVVVR INDRGAFVRL GRQIDLSYGA AKALSSPGND AIAAGLLTVK LEVVELRTPI GENL KESAK NQIAENLEKI KKNQKELATP EISAKGTQIT LEVSIDRSAI AVFSFLHTGT KHNAIISDTT TFTGQSVNWV LNRRV KNTR YTGVTLKGLA ATITRQYGLD LDMSEEGEMI ENISQVSQTD WQFLEKMTAI QGFGMRTVGK VLQIYKITVN AKKLNY TIS VVDNVKSLIV TDQAQTDATG SSQKIEHYGG RMTTVVDADS GSLIKVDKDN KREAGSAART FTTGVDVPQP QIQKQYS NP RPEGASVKEF QLQLELHTSQ SDLENLTPDT ALYIENTLPF IVGKSWFIES VRHSFSEGIF TSQVSAYIPV APKAIATD S GEQNSVVFDN SQSASQGVGK LPVYEILSYR SGRTVKKITS LQQSYEHWRG TGGYTAYKQL SGFSSPVSYM KGRPNQLVY DFILQQNGNQ SCPVPSPASG RVVATGGSNG MVKIDTGGGE VRLLHMSNIR VKPGQNVIRG TILGTQASVG GTSTGTHLHI EANQFILES YVQSLVTGNW

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Macromolecule #2: central spike

MacromoleculeName: central spike / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: unclassified Caudoviricetes (virus)
Molecular weightTheoretical: 29.607072 KDa
SequenceString: MIVDEFSSVY ECLLYCYKMV KRSEQLNGRR VFPILSVVTN NNDPEGRRRV KIADPLFGNL IESNWIRPIR VSQNQDNPLP QINQMVIVW FVDGDSEKGY YLPIINDANP SREKDDPVND SAVRIEGNNT IRIDKNDSET VGGNQTVAIA GEQNINVDGN L IENIGGDI ...String:
MIVDEFSSVY ECLLYCYKMV KRSEQLNGRR VFPILSVVTN NNDPEGRRRV KIADPLFGNL IESNWIRPIR VSQNQDNPLP QINQMVIVW FVDGDSEKGY YLPIINDANP SREKDDPVND SAVRIEGNNT IRIDKNDSET VGGNQTVAIA GEQNINVDGN L IENIGGDI DQNVTGKIEV RSESTILIDA DGTIIIKNDS GAFISLGGNG EVLIQDSQGR KIRLGGAFNS TWDLNGLPMA FI NATSVTI AGKQIATVGA VDTRGDTIVN KGW

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Macromolecule #3: tmp

MacromoleculeName: tmp / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: unclassified Caudoviricetes (virus)
Molecular weightTheoretical: 73.969227 KDa
SequenceString: MANRQHVISV DLRLLTGNFD SSLNYIQGRL NGVFGVVSDN ATNSFFGNGG FLSSYLWNQA FNAIQMAGIA AFRAIGNEVK RAISYQDNL ISMATSYKGL LNLTTKEAFG LARESNIIFQ QRNVGLPTFG NFGTQLRAQY GDDFLSAFYD QNNMKGSLER T ADMIGRTT ...String:
MANRQHVISV DLRLLTGNFD SSLNYIQGRL NGVFGVVSDN ATNSFFGNGG FLSSYLWNQA FNAIQMAGIA AFRAIGNEVK RAISYQDNL ISMATSYKGL LNLTTKEAFG LARESNIIFQ QRNVGLPTFG NFGTQLRAQY GDDFLSAFYD QNNMKGSLER T ADMIGRTT VLLGSISGVT NYQRTSFLSN FLSDDFKKLQ RLEVFRNSPQ LQRAFNSQVD SIGGEQGFNA LTRKDRLLLL EN IAAIAVD DDIIKAYKDS LGGVLSRLGQ ELFGDIGIFS FTRDLIFGLP NTSILNSITF FMKEVFAPDG VFGLIKPALQ GIV DTVLIG TKFILDRTSF IFMGLNALAR VLQPIAPLIY ATSSALTVLA AVGLANTIKS AVQGYLISSG AAMLGGRMGM AAMF GMGGD LVGLKTLGTL GLGKLIAPLG FLTMGLDKLA DVGWLAISGG FAKAALGIKT FGMSLWAIVA NPAFLTIAGI VGAIA LAGY TLWKYWEPIG DFLQGFWIGF KAGLPILDQI ESVLQSIGQA LSPITEGFKN MASAMQPVLD GFTKFFNLQQ EKGGEN YVK QGVNFGDAAS GVTRTILSNP LINPFSGFFG LFGNPAQNKA DGDPQSVMSA INDERRKMPS GASLVIANSS ENVFTRS QT QQLASAGRGS TVINNTFNIS GADPQAIAKQ IADIINSQWQ GTLTDYA

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Macromolecule #4: baseplate gp16

MacromoleculeName: baseplate gp16 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: unclassified Caudoviricetes (virus)
Molecular weightTheoretical: 17.151273 KDa
SequenceString:
MTTQEFLSKN KTIESELLDL LIKPNTDDSI LTRNKQAIAD RDLFDIEWEP GQSLNKLATE YLGDSFAWQI IADANGIDPT KEIDIGAGL KVPDQKALEN SIKKFIVNSP TGKQLISDAK QSILNLIGVG DSNTEFSKTL KDCIGKVVNF SFDNTQ

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Macromolecule #5: tube initiator

MacromoleculeName: tube initiator / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: unclassified Caudoviricetes (virus)
Molecular weightTheoretical: 31.966795 KDa
SequenceString: MSKFLKNRAV VNGLPVIKNP GKYQHCYLIE YEDSTNVKQT PTENKNKQQQ GFPVYLFMMN PENITYNLPI NYQEIAIPFT AKNQLNYSN GGNIVMTMSN LILDTMDEKR SLQPLIDRLI ALREPTVKKG LKSHPKILAF KWGSNTFAPC VLTNISFDVT R WIDGYPTK ...String:
MSKFLKNRAV VNGLPVIKNP GKYQHCYLIE YEDSTNVKQT PTENKNKQQQ GFPVYLFMMN PENITYNLPI NYQEIAIPFT AKNQLNYSN GGNIVMTMSN LILDTMDEKR SLQPLIDRLI ALREPTVKKG LKSHPKILAF KWGSNTFAPC VLTNISFDVT R WIDGYPTK ARVNMSLKEI QKPSSDSKAL EEAKKKVKVE TVQNGNLKKT LSEKQLIDGV KRVTEYLKKN ISFQPRTIQN IL SDPKSVI KIDKDTGQVS LFNGNGEFAA LVGTYNGDIF SPSRQ

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Macromolecule #6: sheath initiator

MacromoleculeName: sheath initiator / type: protein_or_peptide / ID: 6 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: unclassified Caudoviricetes (virus)
Molecular weightTheoretical: 12.997665 KDa
SequenceString:
MYVYPPRIIN GTLYKSTDLA EYTRGKILQT LSIVRGELVA DPFFGVPLRL FSNINDYQSD VSKIQIILEE EITEAQFIVT GDLKNNGIV SLTVYWAYLG TENIENFEID TSNIF

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Macromolecule #7: wedge protein gp31

MacromoleculeName: wedge protein gp31 / type: protein_or_peptide / ID: 7 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: unclassified Caudoviricetes (virus)
Molecular weightTheoretical: 42.385879 KDa
SequenceString: MTTDLNAPQL VVDDYEQLII DSLVHTNVVS NGEFTDLDAS GFMRPFAGTM AYAGSELLYK ANLASIAAAK SFFKNVLGVP EDTGTKATT TLQFGLSASL STDFIVPINF QVSDLSGTLR FYTIGNLVIP AGATFGTIEA IAEDIGEKYN VSANFIDQYS T PLTYLQYV ...String:
MTTDLNAPQL VVDDYEQLII DSLVHTNVVS NGEFTDLDAS GFMRPFAGTM AYAGSELLYK ANLASIAAAK SFFKNVLGVP EDTGTKATT TLQFGLSASL STDFIVPINF QVSDLSGTLR FYTIGNLVIP AGATFGTIEA IAEDIGEKYN VSANFIDQYS T PLTYLQYV TNIRPATNGR SGETIDNLIE RCAQIIRIRN PVSALDFEQL AELTMGEGSR CKAIGLLGIN KIVTDPQPGV VH LFLLDVN GNPADPVTIS TVGATLQPRI MLGTRLLISP MEVLNIELEL IALSDSSKTF QQLADDILEA LKVFFNPANL TPG EPVLIE EVKFAIRSVG GLSISYLQMN DNAINIPMPN QWTIPRFSYI GFELTDSEGT VYRDNVVTVT NPEE

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Macromolecule #8: wedge protein gp32

MacromoleculeName: wedge protein gp32 / type: protein_or_peptide / ID: 8 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: unclassified Caudoviricetes (virus)
Molecular weightTheoretical: 22.423377 KDa
SequenceString:
MSKDAFTAWN VDRRPIYSRM PKEQVGTSYH DYIATDWLTA YWDKIFIECY DKLEDLPRQF DPLQCDEEYL DFLAPLCGWT APYWSGDYP PESKRVLLAN SYSLIWRDKG SLTVLSFVLN ALFINHRIFV PGSFILGQSQ VSEDTLGAAG WEFEILLPRD Y AENGYEFR LTLKIASLFS PLWCKYRVRY DNL

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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 / Chamber humidity: 100 % / Chamber temperature: 300 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k 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: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 41062

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