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- EMDB-63664: Cryo-EM structure of bacteriophage NF5 portal -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-63664
TitleCryo-EM structure of bacteriophage NF5 portal
Map data
Sample
  • Complex: Brochothrix phage NF5
    • Protein or peptide: Gp3
KeywordsComplex / VIRAL PROTEIN
Function / homology:
Function and homology information
Biological speciesBrochothrix phage NF5 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 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 the 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_63664.png

Downloads & links

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Map

FileDownload / File: emd_63664.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 432. Å		1.2 Å/pix.
x 360 pix.
= 432. Å		1.2 Å/pix.
x 360 pix.
= 432. 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: 0.2
Minimum - Maximum-0.6312611 - 1.1472975
Average (Standard dev.)0.0017370679 (±0.049654532)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63664_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63664_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_63664_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: Gp3

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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: Gp3

MacromoleculeName: Gp3 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Brochothrix phage NF5 (virus)
Molecular weightTheoretical: 52.225301 KDa
SequenceString: MDKLEIGFEV FTFPREEEIT IEVIEEFMSL HSKQQPRYER LMKMYKGDAA IFARKAKEPH KPDNRLNVNY AKYITDTFSG FFNGIPSKK NHKNDVVSDA INNFDNEQDM QDEEAELVKL ACVYGHAFEL MYQDEETKTN VKHNSPEDMF IVYDDTVSQK P LFAVRYGL ...String:
MDKLEIGFEV FTFPREEEIT IEVIEEFMSL HSKQQPRYER LMKMYKGDAA IFARKAKEPH KPDNRLNVNY AKYITDTFSG FFNGIPSKK NHKNDVVSDA INNFDNEQDM QDEEAELVKL ACVYGHAFEL MYQDEETKTN VKHNSPEDMF IVYDDTVSQK P LFAVRYGL DREGELCGTL YTEDVDVTLI GKNGTMIFGE ESENVYNDLA VTEFIFNEER MGIYETVTAL IDSYDKAISE KT NDVDYFS DSYLKVVGAM LSPEMIEKIR DTRVINVPEP PHDVSVDIGF LDKPDSDSQT ENLLDRIDKH IYQIAMVANI SDE SFGSSS GVALAYKLQP MSNLAAAFER KFQAALTQRY KMFMSLLTNV SANLSNEWRG IEFRFTRNIP KNVLEEAQTA VQLA TIASQ ETTLSVLSVV PDVRAEMDRI HSERKDDINL LDYQQEVPEK ETVEVVEKED S

UniProtKB: UNIPROTKB: D7RWC6

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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: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40860
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
FSC plot (resolution estimation)

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