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- EMDB-63666: Cryo-EM structure of bacteriophage NF5 neck -

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Basic information

Entry
Database: EMDB / ID: EMD-63666
TitleCryo-EM structure of bacteriophage NF5 neck
Map data
Sample
  • Complex: Brochothrix phage NF5
    • Protein or peptide: Gp7
    • Protein or peptide: Gp10
    • Protein or peptide: Gp8
Keywordsphage / Viral gene product / VIRAL PROTEIN
Function / homology: / : / :
Function and homology information
Biological speciesBrochothrix phage NF5 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsPeng YN / 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: structure of bacteriophage NF5
Authors: Peng YN / Liu HR
History
DepositionMar 7, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63666.png

Downloads & links

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Map

FileDownload / File: emd_63666.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 320 pix.
= 384. Å		1.2 Å/pix.
x 320 pix.
= 384. Å		1.2 Å/pix.
x 320 pix.
= 384. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.8979194 - 1.7970935
Average (Standard dev.)-0.0054449406 (±0.067921184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 384.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63666_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63666_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_63666_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 : Brochothrix phage NF5

EntireName: Brochothrix phage NF5 (virus)
Components
  • Complex: Brochothrix phage NF5
    • Protein or peptide: Gp7
    • Protein or peptide: Gp10
    • Protein or peptide: Gp8

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Supramolecule #1: Brochothrix phage NF5

SupramoleculeName: Brochothrix phage NF5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Brochothrix phage NF5 (virus)

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Macromolecule #1: Gp7

MacromoleculeName: Gp7 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Brochothrix phage NF5 (virus)
Molecular weightTheoretical: 13.248909 KDa
SequenceString:
MSVLEDVKML LSGKTDEQLE IINRRTTERV VSLIGLESDN EKYKEVIAAV DTIIYEVSLK RFNRIGNEGM QSYSQEGLSI SFPDSDFDE YKDEISRWRK KLSDDQKGAF ATVFLL

UniProtKB: UNIPROTKB: D7RWD1

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Macromolecule #2: Gp10

MacromoleculeName: Gp10 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Brochothrix phage NF5 (virus)
Molecular weightTheoretical: 14.799645 KDa
SequenceString:
MIKTRDQSIF DEVFKQCQSL GYTTYDYKPM NEVGYPFVEI EGTTTNHVAN KTDIKGSVEL TLSVWGLQQK RKQVSDMASN VLYCSSLIQ ATDGFYWSLD YNQSTIQLMD DTTTNTPLKR ARLTLTFTVR

UniProtKB: UNIPROTKB: D7RWD4

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Macromolecule #3: Gp8

MacromoleculeName: Gp8 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Brochothrix phage NF5 (virus)
Molecular weightTheoretical: 12.049663 KDa
SequenceString:
MRCIDEVTFV KKGERHYDTE KGEWIEGAKT ETVATLNVTD LGTDRSLVIF GAITQGAKVV RTLPLFNVPD FDYVIIDGKT YEHLTFRSP LYRNSMIFKE VTIEDE

UniProtKB: UNIPROTKB: D7RWD2

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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

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.2 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21058
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
FSC plot (resolution estimation)

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