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- EMDB-48599: Connector structure of phage JohannRWettstein (Bas63) -

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Basic information

Entry
Database: EMDB / ID: EMD-48599
TitleConnector structure of phage JohannRWettstein (Bas63)
Map data
Sample
  • Virus: JohannRWettstein (Bas63) (virus)
  • Protein or peptide: Portal protein
  • Protein or peptide: Head-closure protein
  • Protein or peptide: Tail terminator protein
  • Protein or peptide: Tube protein
  • Protein or peptide: Phage protein
  • Protein or peptide: Structural protein
  • Protein or peptide: Phage protein
  • Protein or peptide: Collar protein
Keywordsconnector / portal / adaptor / head completion / tail terminator / fiber / whisker / collar / tube / sheath / phage / bacteriophage / neck / Bas63 / JohannRWettstein / VIRAL PROTEIN
Function / homology
Function and homology information


: / Phage neck terminator protein / Protein of unknown function DUF935 / Portal protein of Mu bacteriophage / Structural protein ORF10, bacteriophage KPP10 / Protein of unknown function DUF3383 / Bacteriophage PhiTE tail tube protein / Protein of unknown function (DUF3383)
Similarity search - Domain/homology
Uncharacterized protein / Phage neck terminator protein gp12-like domain-containing protein / Head-closure protein / Uncharacterized protein / Portal protein / Structural protein / Phage protein / Phage protein
Similarity search - Component
Biological speciesEscherichia phage JohannRWettstein (virus) / JohannRWettstein (Bas63) (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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: Sci Adv / Year: 2025
Title: C12 local connector reconstruction of phage JohannRWettstein (Bas63)
Authors: Hodgkinson-Bean J / Ayala R / McJarrow-Keller K / Cassin L / Rutter GL / Crowe AJM / Wolf M / Bostina M
History
DepositionJan 10, 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_48599.png

Downloads & links

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Map

FileDownload / File: emd_48599.map.gz / Format: CCP4 / Size: 166.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 422 pix.
= 585.314 Å		1.39 Å/pix.
x 322 pix.
= 446.614 Å		1.39 Å/pix.
x 322 pix.
= 446.614 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.387 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-0.9059245 - 3.5063803
Average (Standard dev.)0.03560856 (±0.15240598)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1-1-101
Dimensions322322422
Spacing322322422
CellA: 446.61398 Å / B: 446.61398 Å / C: 585.31396 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : JohannRWettstein (Bas63)

EntireName: JohannRWettstein (Bas63) (virus)
Components
  • Virus: JohannRWettstein (Bas63) (virus)
  • Protein or peptide: Portal protein
  • Protein or peptide: Head-closure protein
  • Protein or peptide: Tail terminator protein
  • Protein or peptide: Tube protein
  • Protein or peptide: Phage protein
  • Protein or peptide: Structural protein
  • Protein or peptide: Phage protein
  • Protein or peptide: Collar protein

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Supramolecule #1: JohannRWettstein (Bas63)

SupramoleculeName: JohannRWettstein (Bas63) / type: virus / ID: 1 / Parent: 0
Details: Connector structure of phage JohannRWettstein (Bas63).
NCBI-ID: 2852035 / Sci species name: JohannRWettstein (Bas63) / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 55.44702 KDa
SequenceString: MAEITETQES LPPFRMGEVG SLGLKVKNGR IYEEPRQALR FPESIKTFQL MMRDPAVAAS VNIIKMFVRK VNWRFVPPKG KEQDPKMLE RADFFNSLMD DMEHDWADFI NSVMSFCTYG FCVNEKVYKK RQGKKGKYQS KFDDGLIGWA KLPIRNQSTL D KWYFDEDF ...String:
MAEITETQES LPPFRMGEVG SLGLKVKNGR IYEEPRQALR FPESIKTFQL MMRDPAVAAS VNIIKMFVRK VNWRFVPPKG KEQDPKMLE RADFFNSLMD DMEHDWADFI NSVMSFCTYG FCVNEKVYKK RQGKKGKYQS KFDDGLIGWA KLPIRNQSTL D KWYFDEDF RKVTGVRQNL RNVSHIAGAI NLGERPLTRK LPRAKFMLFK YDDEYGNPEG RSPLLNAYVP WKYKVQIEEY EA VGVSRDL VGMPKIGLPP DYLDENAEPE KKAFVQYCKT VVNDMIANDR AGLIWPRYID PDTKEDIFEF SLVSRQGAKA YDT GSIIDR YSKQIMMAFM SDVLAMGQSK YGSFSLADSK TSLLAMSVDI LLKQIKNVIN RDLVAQTYAL NMWDDEEHVQ ITYD DIETP DLEAIGSYIQ KTVAVGALEV DKELSNKLRE HIGLPPADES QPVSEKLSPN SQSRSGDGYK TAGEGTAKTP SAKDP STAN KANK

UniProtKB: Portal protein

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Macromolecule #2: Head-closure protein

MacromoleculeName: Head-closure protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 15.630534 KDa
SequenceString:
MRLLNRHSFV VKRKVSEDGY YNDDGDWVAS QDIVEVNCKG NIQPYIKGSV KNGTQIALPE GIRLTDTRIL YTTYKLRTSD DVEWNESDI VMIDGHEYEV FMTMDWSQQL AHTSHYEYII IRRDKMNAVR NSRT

UniProtKB: Head-closure protein

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Macromolecule #3: Tail terminator protein

MacromoleculeName: Tail terminator protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 22.316256 KDa
SequenceString: MQLETAELEK GLVRTLVDVI GHRLARDKNN RPNVIRAYPS DNSNDKGLKP DQPFITVYCQ DAATPYGWVL DKFVEDDVVC YRIAFQIPV LITVNGKGAH SIMLELKQRL EMSSVRDLIL EETGATVLDT GAIPNDYTYL NTDFENSAPL VVTLVKNSVL K DERGSIIE ...String:
MQLETAELEK GLVRTLVDVI GHRLARDKNN RPNVIRAYPS DNSNDKGLKP DQPFITVYCQ DAATPYGWVL DKFVEDDVVC YRIAFQIPV LITVNGKGAH SIMLELKQRL EMSSVRDLIL EETGATVLDT GAIPNDYTYL NTDFENSAPL VVTLVKNSVL K DERGSIIE RVIVDGELVY EEGQEPPEYT IHLDVDSKGV K

UniProtKB: Phage neck terminator protein gp12-like domain-containing protein

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Macromolecule #4: Tube protein

MacromoleculeName: Tube protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 16.203184 KDa
SequenceString:
MAMYQQYSPK DVVCSWNGIA IEGFAPDSFL RLQRTSPLVT PVVGAGGQVA LTRNADKTGT IEIELMQTSL SNQMLSAIQA KQDNMELEE DISSNFVIYD PSGSVLATGI NAWLQELPQI ELGRDQNSKT WIFGCEKLDY TSTIPASSV

UniProtKB: Uncharacterized protein

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Macromolecule #5: Phage protein

MacromoleculeName: Phage protein / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 11.67307 KDa
SequenceString:
MGTLTIDGKN KILATLTPTT IILHNVDPTA DPTANKVTQP VAIYFSEPDN GLIASEDTVN ITVPASATVS HYSLWDANDK CVATGALSK PQFFAEEGIY VISSVSVDLN K

UniProtKB: Phage protein

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Macromolecule #6: Structural protein

MacromoleculeName: Structural protein / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 48.916574 KDa
SequenceString: MWNPIVNVDI TLNTAGTTRE GFGLPLFLAS TDNFEERVRG YTSLTEVAED FDENTAAYKA AKQLWSQTPK VTQLYIGRRA MQYTVSIPN AVTESTDYSI TVAAGGGISQ PYQYTAQAED TAENVLQQFK TQIEADPTIK DKVSVNVTGS NGSATMIITK A GDNDFVKV ...String:
MWNPIVNVDI TLNTAGTTRE GFGLPLFLAS TDNFEERVRG YTSLTEVAED FDENTAAYKA AKQLWSQTPK VTQLYIGRRA MQYTVSIPN AVTESTDYSI TVAAGGGISQ PYQYTAQAED TAENVLQQFK TQIEADPTIK DKVSVNVTGS NGSATMIITK A GDNDFVKV TTTAQTVYIA STTADTASTA LAAIEAYSTD WYFIAAEDRT QQFVLAMASE IQARKKIFFT ANSDVTALQG TE LASANDV PAQLAKNMYT RTVCLWHHAA AEDYPEMAYI AYGAPYDAGS IAWGNAQLTG VAASLQPSNQ RPLTSIQKSA LDV RHCNFI DLDGGVPVVR RGITSGGEWI DIVRGVDWLE SDLKTSLRDL LINQKGGKIT YDDTGITRIR QVIETSLQRA VNRN FLSSY TVNVPKASQV ALADKKARIL KDVTFAGILA GAILDVDLKG TVAYE

UniProtKB: Structural protein

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Macromolecule #7: Phage protein

MacromoleculeName: Phage protein / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 16.980219 KDa
SequenceString:
MCYTGDPANN PLDRVRILCT DTNNDEILIE QSVLEWFYLE SGKDEKKAAI KALKYLLFQV AKMGDEKVGG VYLRNSSRFK SLKAVYDDL VKSSVSGLPY AGGINQCDID MRRQNPCSVK KYTEYGDAAR YEGRDYCNRV NGVFIIERDE

UniProtKB: Phage protein

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Macromolecule #8: Collar protein

MacromoleculeName: Collar protein / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage JohannRWettstein (virus)
Molecular weightTheoretical: 18.289898 KDa
SequenceString:
MAEVISISNA TRVHSYRGVL IITDKLSVEA GSRASLSGYI SDGGTSDVFT ICRLLDAPMS GKPFISGNCS EIVKIPFDSS CLLGVKLYN CENKRINVNS IEAAFITLDT AFQSPMTVNK DTNRLEYIFS QNDYKVLVKG KVYDMIVNVV DESGNHSTVL K QKVRFN

UniProtKB: Uncharacterized 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
Component:
ConcentrationNameFormula
10.0 mMTris HCL 7.4
10.0 mMmagnesium sulphateMgSO4
0.01 % W/VGelatin

Details: Phage buffer
VitrificationCryogen name: ETHANE-PROPANE
DetailsMature viral particles with packaged genomes

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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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20388
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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