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- EMDB-63689: Cryo-EM structure of bacteriophage NF5 tail-associated lysin -

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Basic information

Entry
Database: EMDB / ID: EMD-63689
TitleCryo-EM structure of bacteriophage NF5 tail-associated lysin
Map data
Sample
  • Complex: Brochothrix phage NF5
    • Protein or peptide: Gp16
Keywordsphage / Viral gene product / 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 bacteriophage NF5
Authors: Peng YN / Liu HR
History
DepositionMar 10, 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_63689.png

Downloads & links

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Map

FileDownload / File: emd_63689.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: 0.25
Minimum - Maximum-0.6582246 - 1.3909355
Average (Standard dev.)-0.0010237494 (±0.053460985)
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_63689_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63689_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_63689_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: Gp16

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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: Gp16

MacromoleculeName: Gp16 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Brochothrix phage NF5 (virus)
Molecular weightTheoretical: 101.291891 KDa
SequenceString: MSVYFFDNKQ QLIKIKNSRT LLQCLQEKEI ASDKSDLMKD VLTVSCLHDV ELEQCDFMAV RENKGVYSLY KILEEEIDAE IMNFKGVNF GAEELNNYVV SDARPVKKTI TEIVKQILTY TDDEWLMTGG VNKIGSANFY YASVKEALKT VQQLGCELLF F CDIDGEGI ...String:
MSVYFFDNKQ QLIKIKNSRT LLQCLQEKEI ASDKSDLMKD VLTVSCLHDV ELEQCDFMAV RENKGVYSLY KILEEEIDAE IMNFKGVNF GAEELNNYVV SDARPVKKTI TEIVKQILTY TDDEWLMTGG VNKIGSANFY YASVKEALKT VQQLGCELLF F CDIDGEGI SSKWVEVREK IGKESDDRYE VGSTAIKVVK TKDRTNIVTS LVGRGKGEEV GDGYGRRLQF DSIEWTQPVP KP KGQSFIE IKELTEKYGI PTKKGKMRKR EQVVIFEDIE DKNELLNATY QTLLENSRPL VQFSSEVIGA SSIGDMVTIH DYD KNYHYE TRVFAIKNDI LNNKIESSLG DNLKGSSASN QLSKASSGIS ELKSMKMNFY DSTEISKWQS DIIRGAKGGS VLLM SPWDT NKGQSREPYQ MVIMNKGSLK ESNHFLVMNS EGIGFIDGDF DKDKFETAWT IDGTFNAKFI RAGVLSGILI KGNII KSSD EGDFQIVLDG GELTFEKKYD SEDINDQHGH PMLTMKALYT DDKLNGISMV QIPNYSFGIN SGGLMVSKPV IEIPKE STI DSRKLNLFGE VRVVGDFYVN DVKIDSNGGS GGSGGGSGGW NGQYPPEITS DVDKRAWAIW STSRGLGYSK AAAAAKL GN IQGESGPQMN PDTEQVGGPA YGLVQWDGSA YPLVGQPTNN GREYVQRLMK AANITDDYRT IVPQVNLIEW SMKNGQWI G AVEPKTVSGF KASISPRTAA RAFLYNFERP ATGHPEREDY AQAWYDKFKD LKQPGGKYGM PVGPGYQITS WFGNRDNPT DPGNIETHKG MDFADKIGSP IFAVEKGEVF ASLSTGSSGG FGEYIVIKHE DGNFTGYAHM TLRMLETGAK VSKGQQIGTL GSTGESTGP HLHFSVGDGL FGNYQDPAPY LGLKRP

UniProtKB: UNIPROTKB: D7RWE0

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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: 37938
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
FSC plot (resolution estimation)

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