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- EMDB-68037: Cryo-EM structure of bacteriophage phi92 neck-tail -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-68037
TitleCryo-EM structure of bacteriophage phi92 neck-tail
Map data
Sample
  • Complex: Escherichia phage phi92
    • Protein or peptide: Phi92_gp130
    • Protein or peptide: Phi92_gp128
    • Protein or peptide: Phi92_gp129
    • Protein or peptide: Phi92_gp131
Keywordsneck / tail / VIRAL PROTEIN
Function / homology
Function and homology information


: / Phage neck terminator protein / Structural protein ORF10, bacteriophage KPP10 / Bacteriophage PhiTE tail tube protein / Protein of unknown function DUF3383 / E217 tail sheath protein gp31-like, N-terminal domain / Bacteriophage SPP1, head-tail adaptor / Phage head completion protein
Similarity search - Domain/homology
Phi92_gp129 / Phi92_gp131 / Phi92_gp128 / Phi92_gp130
Similarity search - Component
Biological speciesEscherichia phage phi92 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsChen Y / Liu HR
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32071209 China
CitationJournal: To Be Published
Title: The in stiu structure of the neck-tail of Bacteriophage phi92
Authors: Chen Y / Liu HR
History
DepositionDec 31, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68037.png

Downloads & links

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Map

FileDownload / File: emd_68037.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 480 pix.
= 528. Å		1.1 Å/pix.
x 480 pix.
= 528. Å		1.1 Å/pix.
x 480 pix.
= 528. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.3
Minimum - Maximum-8.086228999999999 - 13.710457
Average (Standard dev.)-0.013588586 (±0.97488576)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-240-240-240
Dimensions480480480
Spacing480480480
CellA=B=C: 528.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_68037_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_68037_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 : Escherichia phage phi92

EntireName: Escherichia phage phi92 (virus)
Components
  • Complex: Escherichia phage phi92
    • Protein or peptide: Phi92_gp130
    • Protein or peptide: Phi92_gp128
    • Protein or peptide: Phi92_gp129
    • Protein or peptide: Phi92_gp131

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Supramolecule #1: Escherichia phage phi92

SupramoleculeName: Escherichia phage phi92 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage phi92 (virus)

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Macromolecule #1: Phi92_gp130

MacromoleculeName: Phi92_gp130 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage phi92 (virus)
Molecular weightTheoretical: 51.142324 KDa
SequenceString: MATFRDKVVS VTLTYGATSI SETQFDIPLI LTGHNVTGNL VDYFTSSDAL LQAGFGTADP AYKMAKLLFD GLFAPEQVIV GKRDVSKTT LTPVVEDSAT YVITIKANSK SKDFKFVADD TATAQEIVVG LTEMINADVV YKEFFTVSND GSVITVTPVA G KYATMDSS ...String:
MATFRDKVVS VTLTYGATSI SETQFDIPLI LTGHNVTGNL VDYFTSSDAL LQAGFGTADP AYKMAKLLFD GLFAPEQVIV GKRDVSKTT LTPVVEDSAT YVITIKANSK SKDFKFVADD TATAQEIVVG LTEMINADVV YKEFFTVSND GSVITVTPVA G KYATMDSS GFTTKVEYAN DILEDIAKIA DYENSWFWLL SDSHAEQDII DLAGYVEEHD KVYFFSTSQP GVLTKEEDNI LE RLGDMGY NNTCMALWMT NADTVFPEAA VVGSICSATP GTTTLHGKTL VGIEIEKLGQ TAENFIVQQN GNIYRKEHGV LFY RDGFMV SGFYVDYVVH ALWFKARVEE SLFALFKQQS MLGSGVRATS AGLALIRQAV TANPIQVGIN NGSIANEVVT SEET GLLVS LKPTIYIPSR ADMTDAQINA RLVDGMVIEY VYAGFFHYVK VQVNVLTNRT ANSQNSNSST VSS

UniProtKB: Phi92_gp130

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Macromolecule #2: Phi92_gp128

MacromoleculeName: Phi92_gp128 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage phi92 (virus)
Molecular weightTheoretical: 15.747314 KDa
SequenceString:
MLLDQFTLLD LTTYQGRKRT YVQDPDSPIS NMGNTVAYED FTIEAASLQP ISGRTLQALP EGYRSKAQYS FWTKTEIRGI QQGSDQLSD QILIDGQWFS IYSLKDWTRT SFLIHTHCVA ILDDQNNTYS YSEEGGNFG

UniProtKB: Phi92_gp128

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Macromolecule #3: Phi92_gp129

MacromoleculeName: Phi92_gp129 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage phi92 (virus)
Molecular weightTheoretical: 25.059418 KDa
SequenceString: MANIYEQIEL YENTILLNIA KFLQRLVGLP VYVMDKPFVK PTTPYLTLRI VSSDDSGGWS QKYSFSEDAF SYLMDNKYEI ELMAFRGRP MTLLSYVLAA LRGADELKYQ YLYSKGISFL SATNVAQANT VLDGDKTEQR ARIFLTFNTT MVIEDLVTTE I EAINMNIH ...String:
MANIYEQIEL YENTILLNIA KFLQRLVGLP VYVMDKPFVK PTTPYLTLRI VSSDDSGGWS QKYSFSEDAF SYLMDNKYEI ELMAFRGRP MTLLSYVLAA LRGADELKYQ YLYSKGISFL SATNVAQANT VLDGDKTEQR ARIFLTFNTT MVIEDLVTTE I EAINMNIH SFRDDYDDPT PIDLPLDKIY IVAHRSKTYY FTTTDDGSLI KYIPTDNSLE

UniProtKB: Phi92_gp129

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Macromolecule #4: Phi92_gp131

MacromoleculeName: Phi92_gp131 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage phi92 (virus)
Molecular weightTheoretical: 17.335488 KDa
SequenceString:
MDKMLTGVMA YDPSQVILSL GGWEPWGFAA DTKIVINKTN DIINPYSGTD GDVSLALSRN RLGTLTMSLQ RTSPANEVLA AYAQTMYST RQVAFSVYLE DPRGYYISTI GWIQSQPDDT IGETIQENQW VIGLKDASLL RSTVGVGVNA LNSISALTIQ

UniProtKB: Phi92_gp131

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 32158
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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