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- EMDB-49281: Composite baseplate asymmetric unit of JohannRWettstein (Bas63) -

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Basic information

Entry
Database: EMDB / ID: EMD-49281
TitleComposite baseplate asymmetric unit of JohannRWettstein (Bas63)
Map dataThe final reconstruction is a composite reconstruction of maps under accessions:EMD-49262, EMD-49264 and EMD-49265. Particle number and resolution are reported from the consensus reconstruction used (
Sample
  • Virus: Escherichia phage JohannRWettstein (virus)
    • Protein or peptide: Hub protein (gp020)
    • Protein or peptide: LTF platform protein (gp025)
    • Protein or peptide: Spacer protein (gp019)
    • Protein or peptide: Tape measure protein (gp017)
    • Protein or peptide: Wedge protein 2 (gp023)
  • Protein or peptide: Tube initiator protein (gp018)
  • Protein or peptide: Sheath initiator (gp022)
  • Protein or peptide: Puncture apparatus (gp021)
  • Protein or peptide: Wedge protein 1 (gp024)
Keywordsbaseplate / wedge / hub / puncture apparatus / sheath initiator / tube initiator / tape measure protein / LTF-platform / spacer / phage / bacteriophage / VIRAL PROTEIN
Function / homology
Function and homology information


viral tail assembly
Similarity search - Function
: / Dit-like phage tail protein / : / Cyanophage baseplate Pam3 plug gp18 / Phage protein Gp138 N-terminal domain / Phage protein Gp138 N-terminal domain / Tape measure protein N-terminal / Tape measure protein / Baseplate protein J-like / Baseplate J-like protein barrel domain / Vgr protein, OB-fold domain superfamily
Similarity search - Domain/homology
Cyanophage baseplate Pam3 plug gp18 domain-containing protein / Tail length tape-measure protein / Dit-like phage tail protein N-terminal domain-containing protein / Phage protein / Baseplate wedge subunit / Baseplate protein / Baseplate protein / Baseplate assembly protein / Phage protein
Similarity search - Component
Biological speciesEscherichia phage JohannRWettstein (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.83 Å
AuthorsHodgkinson-Bean J
Funding support Japan, 2 items
OrganizationGrant numberCountry
Ministry of Agriculture, Forestry and Fisheries (MAFF)GD0696J004 Japan
Japan Society for the Promotion of Science (JSPS)21K20645 Japan
CitationJournal: To Be Published
Title: Icosahedral capsid assembly of phage JohannRWettstein (Bas63)
Authors: Hodgkinson-Bean J / Ayala R / McJarrow-Keller K / Cassin L / Rutter GL / Crowe AJM / Wolf M / Bostina M
History
DepositionFeb 18, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49281.png

Downloads & links

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Map

FileDownload / File: emd_49281.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe final reconstruction is a composite reconstruction of maps under accessions:EMD-49262, EMD-49264 and EMD-49265. Particle number and resolution are reported from the consensus reconstruction used (
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.39 Å/pix.
x 400 pix.
= 554.8 Å		1.39 Å/pix.
x 400 pix.
= 554.8 Å		1.39 Å/pix.
x 400 pix.
= 554.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.387 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.78
Minimum - Maximum-8.973017 - 31.048459999999999
Average (Standard dev.)0.01499121 (±1.0438957)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 554.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Escherichia phage JohannRWettstein

EntireName: Escherichia phage JohannRWettstein (virus)
Components
  • Virus: Escherichia phage JohannRWettstein (virus)
    • Protein or peptide: Hub protein (gp020)
    • Protein or peptide: LTF platform protein (gp025)
    • Protein or peptide: Spacer protein (gp019)
    • Protein or peptide: Tape measure protein (gp017)
    • Protein or peptide: Wedge protein 2 (gp023)
  • Protein or peptide: Tube initiator protein (gp018)
  • Protein or peptide: Sheath initiator (gp022)
  • Protein or peptide: Puncture apparatus (gp021)
  • Protein or peptide: Wedge protein 1 (gp024)

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Supramolecule #1: Escherichia phage JohannRWettstein

SupramoleculeName: Escherichia phage JohannRWettstein / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #3, #9, #8, #4, #6 / NCBI-ID: 2852035 / Sci species name: Escherichia phage JohannRWettstein / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Tube initiator protein (gp018)

MacromoleculeName: Tube initiator protein (gp018) / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 28.593939 KDa
SequenceString: MLWDSNMQIK YSGKDGIYFH LRDNVDAFLT LSATENMEFD SPMQVTTQNM QSGQTVTDNV QRAPRTITIS GVVVVGYEGS LLLTRQGQL VENFIDTLES WRDQKQIISV ICKDGIKIDD SIITSFKASK DVGISNGLRV QLTFQEINFK AIVGQTDVSA A TGKTATTN ...String:
MLWDSNMQIK YSGKDGIYFH LRDNVDAFLT LSATENMEFD SPMQVTTQNM QSGQTVTDNV QRAPRTITIS GVVVVGYEGS LLLTRQGQL VENFIDTLES WRDQKQIISV ICKDGIKIDD SIITSFKASK DVGISNGLRV QLTFQEINFK AIVGQTDVSA A TGKTATTN DGGATSKKNT GNTTTSLGNG KLNCQLLFDL DANGVRELTS AEDNALAKCS MSAKTRKGVT TFSDEAERNA GA ALNSTAG NGKALQKHSV NPNKKGTY

UniProtKB: Dit-like phage tail protein N-terminal domain-containing protein

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Macromolecule #2: Sheath initiator (gp022)

MacromoleculeName: Sheath initiator (gp022) / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 15.632561 KDa
SequenceString:
MKTDFALNLG GDYVATLGSD SVYVAHGDLK ITGNQIRIIP EDDKATQVAQ RLHIRCLLRS GEVFFNTSAG FPYLQLAKFK QKTSIFDNY MKAYLVETRD VSNIYNYSSS MDNAQRKVTV NFDATTTTDI LTDITQEVNI

UniProtKB: Baseplate wedge subunit

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Macromolecule #3: Hub protein (gp020)

MacromoleculeName: Hub protein (gp020) / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 37.204172 KDa
SequenceString: MSVKDSTAGA SFRCYQLAVG SETTAFNDKP TSHAKDSMQM DYFDNLQFTC NVSYTSQKNK VTSDDTTFEI YNLNKEMRAK FKTVGATVM LRAGYTTGFK RDANGDLIIE YDNLPLIYLG TIEYAYTYKR GVDMITKVIC SNDKMERTTI KTSISYKAGT T RKNVIRDL ...String:
MSVKDSTAGA SFRCYQLAVG SETTAFNDKP TSHAKDSMQM DYFDNLQFTC NVSYTSQKNK VTSDDTTFEI YNLNKEMRAK FKTVGATVM LRAGYTTGFK RDANGDLIIE YDNLPLIYLG TIEYAYTYKR GVDMITKVIC SNDKMERTTI KTSISYKAGT T RKNVIRDL VNRLGFSLID EDLSSIDGYT YKNGFSVWGS VAEALTKVCE ESSLRWYTFN KQIRVVPFNA KARQLSWEIY PY NVIDSLQ GYYRRTRKVL KKENKTVIKV KTGVRCKIHL DGRIKMGDNV TIRESEDFEG QYRVKGLSHN LDFTGGAWTT ELD LEKVE

UniProtKB: Phage protein

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Macromolecule #4: Tape measure protein (gp017)

MacromoleculeName: Tape measure protein (gp017) / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 80.340586 KDa
SequenceString: MAQYTVDSFI VELGFSEKVV KGLQRVEKMS MQAAQRIERN INKAFDVKPN KSSQEALNRI VKNAQSASGR INKALNSSLN LDSQGVKSL KKLETQAKKT AKGINKSLRD AMKVDGKITI KTGRGRGGQS IPPVGGGAPR GPRVDVAQRQ MERMFNNNFY S GLTRRLET ...String:
MAQYTVDSFI VELGFSEKVV KGLQRVEKMS MQAAQRIERN INKAFDVKPN KSSQEALNRI VKNAQSASGR INKALNSSLN LDSQGVKSL KKLETQAKKT AKGINKSLRD AMKVDGKITI KTGRGRGGQS IPPVGGGAPR GPRVDVAQRQ MERMFNNNFY S GLTRRLET IGGQGNQMAA SFRGSLQGIY NKYKGTGKVG EYEMEVKKLI DVTKRWVIAE NARLKSVKEA AWLQDRANSS LR QLVGGFV SAYALLELSQ KTIEAGVKRQ SAQLASTAIF GADTQQARMF AASFAHQIGQ NYTDTMKQYS NFAAGAQPTL GFQ GTQEFY KNAAMFARIR GATDEDLKGI MVAFQQMASK GKVQAEELRG QLGDRLAGAV QLFADAIGKT PQELDKMMQD GKLL AQDVL PKVSERMAEL VKQAGGMNAV SKQTATSMGQ AKAMWDNTLV ALFNNSSEGI SQLSNSVAMF LQGSLGSTQA LGVVI GNLL KGASNLLDFV TDFMYRTSAL YYYARAWYKD LDNSQQKLIK SAGEFLGTVV TIGGVVAVVS KAVKLLSGLV GGGIFG KIL QRLGVSAAGT AAAGEAAAAA GGVTATRMAL GTVGSALMLR GSTDPNAAKN YSEVTLPKPF ENAVANITNP KRPMFFD EN GQLQFAQYTQ DVEGNRKLID NGLSNWEIIM DKLSTSIDNF ANKFNQTPMM MTPSGLPMQT KQTLNVTFNL DGKQIATK M VDITDKNQED ILLSSSYPEE E

UniProtKB: Tail length tape-measure protein

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Macromolecule #5: Puncture apparatus (gp021)

MacromoleculeName: Puncture apparatus (gp021) / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 23.186848 KDa
SequenceString: MKSPVTRMSG YVSECLDEFR KELYTGLPAI IQSFDSKTQT ATVKPLYSIN GLPMPEITGV PVQFPSGGGA SLTFPVKTND RCWLAFSML PLDDFVVNDK NTQMETNMRR THDISDCVAF VGICTRTQNF KPDPTAVRLH FGDSVLRVTD DGNFYFEGDV H ISKNLYVK ...String:
MKSPVTRMSG YVSECLDEFR KELYTGLPAI IQSFDSKTQT ATVKPLYSIN GLPMPEITGV PVQFPSGGGA SLTFPVKTND RCWLAFSML PLDDFVVNDK NTQMETNMRR THDISDCVAF VGICTRTQNF KPDPTAVRLH FGDSVLRVTD DGNFYFEGDV H ISKNLYVK EEVHGSDFIS DTTGVSFNEH THHYYWTDPA GEADTTEAQ

UniProtKB: Baseplate protein

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Macromolecule #6: Wedge protein 2 (gp023)

MacromoleculeName: Wedge protein 2 (gp023) / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 53.139953 KDa
SequenceString: MAGLTTTGLQ TLRYQEIFDN IKSRLLRDIS PNLDVSEDSQ LGLFLASIAR SLADTHEVLS EIYDGGTIDK AEGFNLDDIT ALNAVYRYV AQATRGQVEF TGTTGATIPS TTRLRSTAGN IFYPVSGITL TPSYCVEAVL EVNSLRTDAN YVIIIDNVIF S YQPKSSDT ...String:
MAGLTTTGLQ TLRYQEIFDN IKSRLLRDIS PNLDVSEDSQ LGLFLASIAR SLADTHEVLS EIYDGGTIDK AEGFNLDDIT ALNAVYRYV AQATRGQVEF TGTTGATIPS TTRLRSTAGN IFYPVSGITL TPSYCVEAVL EVNSLRTDAN YVIIIDNVIF S YQPKSSDT ITVLLTELAD AINGGIVAKA EVINDGSALR VYKDEGDIIA RTNPMVVTAT TFLTFTKITT IHDVVAEEVG AI PALAGTL IEIETTVDGL DSVYNRYDLT TGRNEETDTE LRQRYLESLA VTGVGTLDAI VAAVKRVQGV SDASGVENDT EET SSEGLP PKSFKIVVVG GQNDNVAQAI WDTKPAGIRA YGAIFGTAYD LGNLAHNVYF SRPTPKYAFV KVSYSLYDEE SLTI PEEDI RDSIVQGINA YGRTLKVGND VIPNRIYGYI YDVIKGVEIN EIKVALSNNQ SVPPSDGQYT TARITVDGDQ YTVWE SSQY TIAKE

UniProtKB: Baseplate protein

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Macromolecule #7: Wedge protein 1 (gp024)

MacromoleculeName: Wedge protein 1 (gp024) / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 31.622605 KDa
SequenceString: MFQKIDNVYY KTLDERTVTQ FKDKFIYTSL LKAVTDELQT LEDVSWQMHT ERNIRKAVGQ QLDNIGSLIK VPRPLGADDE TYRAMLYIQ IFLRRSDTTP TFLQNAIMTL YNATFSQIFE HITPMTAGIV VRVNTRNNVI DTAYTLAKIA ATTIGSAVIL R DVTLNGTA ...String:
MFQKIDNVYY KTLDERTVTQ FKDKFIYTSL LKAVTDELQT LEDVSWQMHT ERNIRKAVGQ QLDNIGSLIK VPRPLGADDE TYRAMLYIQ IFLRRSDTTP TFLQNAIMTL YNATFSQIFE HITPMTAGIV VRVNTRNNVI DTAYTLAKIA ATTIGSAVIL R DVTLNGTA WTPVEVADSA LAIVDDKDNW FVTDANKGLV TNNTGGSLEK NLLGSLADAG VRDAYFKVDR TANSGSVDYL KV NKNYNAT DNYIVGKETV AGGDYGVMAE VAQIIKGRKD KSQQEGSS

UniProtKB: Baseplate assembly protein

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Macromolecule #8: Spacer protein (gp019)

MacromoleculeName: Spacer protein (gp019) / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 13.209922 KDa
SequenceString:
MSQYIPVPDT EWSTQTVTLD GTVFVIELKY KERLDRWFLT LSDVDGNVLL SEKKCLADQS ITGRYVIPSL AGELFVERMY GTDLQPTRN NFGREKAFEL NYYTQEDMRL MENL

UniProtKB: Cyanophage baseplate Pam3 plug gp18 domain-containing protein

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Macromolecule #9: LTF platform protein (gp025)

MacromoleculeName: LTF platform protein (gp025) / type: protein_or_peptide / ID: 9 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 11.093398 KDa
SequenceString:
MAFLNWSTDE VDADGNQLKV LPPPEIQATG LLRGEPMGRQ WFNYILNYLL KKANGTVGEV RSFATEQPDL VANGWNLIKT ETGTASTST KNLYTYEFVG A

UniProtKB: Phage 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: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 49.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC
Details: The final reconstruction is a composite reconstruction of maps under accessions:EMD-49262, EMD-49264 and EMD-49265. Particle number and resolution are reported from the consensus reconstruction used (EMD-49262).
Number images used: 14390
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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