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- EMDB-63230: SFP21A phage tail fiber (Gp09) -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-63230
TitleSFP21A phage tail fiber (Gp09)
Map datamain EM map
Sample
  • Complex: Trimeric complex of phage tail fiber
    • Protein or peptide: Tail fibers protein
KeywordsShigella flexneri / bacteriophage / tail fiber / Podoviridae / VIRAL PROTEIN
Function / homology
Function and homology information


virus tail / adhesion receptor-mediated virion attachment to host cell / symbiont entry into host cell
Similarity search - Function
Tail spike TSP1/Gp66, N-terminal domain / Tail spike TSP1/Gp66 receptor binding N-terminal domain / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein, N-terminal domain / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily
Similarity search - Domain/homology
Biological speciesShigella flexneri (bacteria) / Shigella phage SFP21A (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBaek Y / Ha N-C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of the tail fiber protein from Podoviridae family bacteriophage infecting Shigella flexneri
Authors: Baek Y / Choi H / Lee J / Ha N-C
History
DepositionJan 21, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63230.png

Downloads & links

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Map

FileDownload / File: emd_63230.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.65634227 - 0.95797503
Average (Standard dev.)0.00037888822 (±0.039356854)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 215.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63230_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_63230_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_63230_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trimeric complex of phage tail fiber

EntireName: Trimeric complex of phage tail fiber
Components
  • Complex: Trimeric complex of phage tail fiber
    • Protein or peptide: Tail fibers protein

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Supramolecule #1: Trimeric complex of phage tail fiber

SupramoleculeName: Trimeric complex of phage tail fiber / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Shigella flexneri (bacteria)
Molecular weightTheoretical: 118 KDa

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Macromolecule #1: Tail fibers protein

MacromoleculeName: Tail fibers protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Shigella phage SFP21A (virus)
Molecular weightTheoretical: 91.293039 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MANTTLTQFP AGQTQYKITF DYLARPFVVV TLVNSNDAAL NRVLTAGNDY LFLNPTTIEI LTSQAGFDIL QIHRFTSTDL LVDFRDGSV LTATDLTNSE LQAIHIAEEG RDQSTGLAKQ YADQAVEAGK DAQDILNQII LLGKNGYTPV GSFENGGTVR L QNDVLQYG ...String:
MANTTLTQFP AGQTQYKITF DYLARPFVVV TLVNSNDAAL NRVLTAGNDY LFLNPTTIEI LTSQAGFDIL QIHRFTSTDL LVDFRDGSV LTATDLTNSE LQAIHIAEEG RDQSTGLAKQ YADQAVEAGK DAQDILNQII LLGKNGYTPV GSFENGGTVR L QNDVLQYG SGTATTHWRW EGTLPKVVPA GSTPTSAGGI GKGKWIDVTD ATLRGQLAGT GGASMVKASD GRTVEQWLVQ SD SASYRAK NMAKLAWVDY QVHNRGSIKS CFLGDSMTAG FDRTSSDVIP PQDGDWATRA SMNYPYRFAS YLAEQSGCTS TVV MRAISG HTAKQAYEQA EWQTNPNCDI VFIMYAINDS GGVAGATLDI YMEYMEKLIR RYIDWGCAVV VQRPSGGGQG AGNP RWLHW AKRLQMVARV YGCPIFDAHE VMLYRHYAAV QSDGTHYNSM GYAIHGEKLA SMLMAGGLLD TYRPVVNEIT VWTGM MSDR VGWCDAMGNI GTFRSDGAFT RSKITGRLPG STRVVTTFSF YLDAEAAHIY GKFVGKMNVI MTNSRWWNNN AQPYYQ YAD DQPHSFGMSL ERTPKSPNDF SGASGSRKFI GRVIGRGWHT LTFFKALDGT DTTESFINSL TIQPIPLGLS TEQMWGQ DE ERRYKVVHTR KLPSPSGQGN NLPQATVLNS FHMRVPQSVL GTGPGALCLP TPYFYNTIPA TLRITDEKGT YIEFLVYN N GSSGLTWTGK VLKSTLAEAS YPTLTAQLAT AKQSVVRAAG QDGTNMPLEN IYDFNGGLQP QNSSASDISW KGGIYFQFT LTWPGTAPTG YWNIELEGSD WFGNSESSFG AF

UniProtKB: Tail fibers protein

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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

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold2 predicted model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146100
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9lna:
SFP21A phage tail fiber (Gp09)

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