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- EMDB-32616: Tail structure of Helicobacter pylori bacteriophage KHP30 -

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Basic information

Entry
Database: EMDB / ID: EMD-32616
TitleTail structure of Helicobacter pylori bacteriophage KHP30
Map data
Sample
  • Virus: Helicobacter phage KHP (virus)
    • Protein or peptide: Portal protein
    • Protein or peptide: Adaptor protein gp12
    • Protein or peptide: Nozzle protein gp25
KeywordsPHAGE / PHAGE TAIL / CRYOEM / VIRUS / VIRAL PROTEIN
Function / homologysymbiont genome ejection through host cell envelope, short tail mechanism / viral capsid / Uncharacterized protein / Phage protein / Portal protein
Function and homology information
Biological speciesHelicobacter phage KHP30 (virus) / Helicobacter phage KHP (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKamiya R / Uchiyama J
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15K18521 Japan
Japan Society for the Promotion of Science (JSPS)18K06154 Japan
CitationJournal: To Be Published
Title: Cryo-EM structure of Helicobacter pylori bacteriophage KHP30
Authors: Kamiya R / Uchiyama J / Matsuzaki S / Murata K / Iwasaki K / Miyazaki N
History
DepositionJan 15, 2022-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32616.png

Downloads & links

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Map

FileDownload / File: emd_32616.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.6 Å/pix.
x 400 pix.
= 639.412 Å		1.6 Å/pix.
x 400 pix.
= 639.412 Å		1.6 Å/pix.
x 400 pix.
= 639.412 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.59853 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.105374776 - 0.17204654
Average (Standard dev.)0.00014185368 (±0.003984008)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 639.41205 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Helicobacter phage KHP

EntireName: Helicobacter phage KHP (virus)
Components
  • Virus: Helicobacter phage KHP (virus)
    • Protein or peptide: Portal protein
    • Protein or peptide: Adaptor protein gp12
    • Protein or peptide: Nozzle protein gp25

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Supramolecule #1: Helicobacter phage KHP

SupramoleculeName: Helicobacter phage KHP / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1208236 / Sci species name: Helicobacter phage KHP / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / Name: Head / Diameter: 700.0 Å / T number (triangulation number): 9

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Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter phage KHP30 (virus)
Molecular weightTheoretical: 69.634734 KDa
SequenceString: MDFTTLQNDF TNDYQKALIA NNEFLEAKKY YNGNQLPQDV LNIILERGQT PIIENMFKVI VNKILGYKIE SISEIRLSPK QEEDRALSD LLNSLLQVFI QQENYDKSMI ERDKNLLIGG LGVIQLWVSQ DKDKNVEIEI KAIKPESFVI DYFSTDKNAL D ARRFHKML ...String:
MDFTTLQNDF TNDYQKALIA NNEFLEAKKY YNGNQLPQDV LNIILERGQT PIIENMFKVI VNKILGYKIE SISEIRLSPK QEEDRALSD LLNSLLQVFI QQENYDKSMI ERDKNLLIGG LGVIQLWVSQ DKDKNVEIEI KAIKPESFVI DYFSTDKNAL D ARRFHKML EVSEQEALLL FGDSVIVNYS NVNHERIASV IESWYKEYNE ETQSYEWNRY LWNRNTGIYK SEKKPFKNGA CP FIVSKLY TDELNNYYGL FRDIKPMQDF INYAENRMGN MMGSFKAMFE EDAVVDVAEF VETMSLDNAI AKVRPNALKD HKI QFMNNQ ADLSALSQKA EQKRQLLRLL AGLNDESLGM AVNRQSGVAI AQRKESGLMG LQTFLKATDD MDRLIFRLAV SFIC EYFTK EQVFKIVDKK LGDRYFKINS NDDNKIRPLK FDLILKSQLK TESRDEKWYN WNELLKILAP IRPDLVPSLV PLMLN DMDS PITNDVLEAI QNANALQQQN AEANAPYNQQ IQALQIQKLQ AEIMELQAKA HKYAEQGALS QTTNESEKIN QAVAIT EMQ QQNANNANNE ESNNKPKKKL KTSDKTTWRK YPSAQNLDY

UniProtKB: Portal protein

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Macromolecule #2: Adaptor protein gp12

MacromoleculeName: Adaptor protein gp12 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter phage KHP30 (virus)
Molecular weightTheoretical: 22.609309 KDa
SequenceString: MIEVSEVIAK VRERLNDNEV GNYEILDSVL VENINQALLK ICLEFRLKKA ITRSLITEEE RFLTLNNLLG IESVKLDKKE IESRNTIEK DTGELELLIL SDRISVTPFK IGELEVVYYT YEEIRNILET IKLPKICLDV LVYSVLCNLL EIPNNETNFS V LANYKQLL ...String:
MIEVSEVIAK VRERLNDNEV GNYEILDSVL VENINQALLK ICLEFRLKKA ITRSLITEEE RFLTLNNLLG IESVKLDKKE IESRNTIEK DTGELELLIL SDRISVTPFK IGELEVVYYT YEEIRNILET IKLPKICLDV LVYSVLCNLL EIPNNETNFS V LANYKQLL KLAKDNLTNY LSLMYSKNIH FSKVVRV

UniProtKB: Phage protein

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Macromolecule #3: Nozzle protein gp25

MacromoleculeName: Nozzle protein gp25 / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter phage KHP30 (virus)
Molecular weightTheoretical: 29.741775 KDa
SequenceString: MDTTRFIRNF ILFKDALQKQ NFNNKDLNTT SMQAALQSEQ LALSEESQYL QSEQVRAKMQ IDFLGMQANL QNAKAETLNK LIQCQAMLK SLKDNAMINR ANALVSLLQV QANAANGITT SNFEAAFKII AQIGSEYNQI TLNNGNVSVQ EKEQTNELKT I LNSLSKEL ...String:
MDTTRFIRNF ILFKDALQKQ NFNNKDLNTT SMQAALQSEQ LALSEESQYL QSEQVRAKMQ IDFLGMQANL QNAKAETLNK LIQCQAMLK SLKDNAMINR ANALVSLLQV QANAANGITT SNFEAAFKII AQIGSEYNQI TLNNGNVSVQ EKEQTNELKT I LNSLSKEL EKLNQQSEVN SIQIFSDKLE VLKDAPARLW GFSTLSNAKE GFYNEANEQI ASGSVCLFRS DKVRKHTITF KA INTKTSL SKNITISVIA NKLKERMS

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: 7.2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 2.5 sec. / 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 / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 32655
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 27422
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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