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- EMDB-63696: Cryo-EM structure of bacteriophage NF5 C1 RBP -

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Basic information

Entry
Database: EMDB / ID: EMD-63696
TitleCryo-EM structure of bacteriophage NF5 C1 RBP
Map data
Sample
  • Complex: Brochothrix phage NF5
    • Protein or peptide: Gp17
KeywordsRBP / phage / Viral gene product / VIRAL PROTEIN
Function / homology:
Function and homology information
Biological speciesBrochothrix phage NF5 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 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 11, 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_63696.png

Downloads & links

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Map

FileDownload / File: emd_63696.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 307.2 Å		1.2 Å/pix.
x 256 pix.
= 307.2 Å		1.2 Å/pix.
x 256 pix.
= 307.2 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: 0.27
Minimum - Maximum-0.49520028 - 0.99573815
Average (Standard dev.)0.0062801386 (±0.05651375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 307.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63696_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63696_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_63696_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: Gp17

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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: Gp17

MacromoleculeName: Gp17 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Brochothrix phage NF5 (virus)
Molecular weightTheoretical: 71.342992 KDa
SequenceString: MVELDKYLPV NREEAFRNGV NKNFAKIEQG FSQRDAVMNS HQTTQKNAHD TEQILHYLSD KEKDVYYHSA LDLKHYLLLE CSRISNLVL GATTDQSVEL KESRVDLEGK AHITLYGRLL ADFTRLKNAL DKLIELEESF DIPKIEPQFW TELGGIRNVV Q QYFWINKL ...String:
MVELDKYLPV NREEAFRNGV NKNFAKIEQG FSQRDAVMNS HQTTQKNAHD TEQILHYLSD KEKDVYYHSA LDLKHYLLLE CSRISNLVL GATTDQSVEL KESRVDLEGK AHITLYGRLL ADFTRLKNAL DKLIELEESF DIPKIEPQFW TELGGIRNVV Q QYFWINKL NGRVYQTQSD SQAQEGFYIN ELTPSGHFLG TMHIPKGGHG TSLGVEYVNG QMFMWTNVDK RLVKFTFKAD TK LDATLLR DYMPSSVAPV FFAPVSDWKG EKMAFRRSDG IIELRDVNDL NKNIDKVYAQ VTIPLEEREN DYRPMQGVAI SDK NCYWMS GWGTDENIGK VFVYDWHGKL LDTITLDNLT QVTGVGGEEY ASDNHSEPEG LFFTEDKGKK VLFVGFSTGG TRKR HHKIY GFSQRGGLER YSSIVRNGAQ NYPLTRGDGK AHSTPDGLTK LSDLTKVGSY YAQGSDVALL TDLPVEFKGV PLWID NLPA EQHNDVRQVI TRRSTEKSML KFERMINIGK AEQAFSVGSW TVYQSQTTRG EFIDASIYQN KLSNITSPMK MYMTAE QAN LFTDHPVKNG NAGWFYENSG YGVTGEFRQT ITINSSLRYE VYSRMVFADR VSEWFVIAGN QVK

UniProtKB: UNIPROTKB: D7RWE1

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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: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57406
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
FSC plot (resolution estimation)

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