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- EMDB-82742: Cryo-EM structure of bacteriophage A1002 mature capsid -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-82742
TitleCryo-EM structure of bacteriophage A1002 mature capsid
Map data
Sample
  • Complex: Cryo-EM structure of bacteriophage A1002 mature capsid
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Structural protein
Keywordshead / phage / VIRAL PROTEIN / STRUCTURAL PROTEIN
Function / homologyProtein of unknown function DUF4043 / Phage capsid protein / viral capsid / Major capsid protein / Structural protein
Function and homology information
Biological speciesPseudomonas phage (virus) / Pseudomonas phage KPP25 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsChen Y / 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: The in stiu structure of the mature capsid of bacteriophage A1002
Authors: Chen Y / Liu HR
History
DepositionAug 5, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_82742.png

Downloads & links

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Map

FileDownload / File: emd_82742.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 600 pix.
= 498. Å		0.83 Å/pix.
x 600 pix.
= 498. Å		0.83 Å/pix.
x 600 pix.
= 498. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.34785202 - 0.6965269
Average (Standard dev.)-0.0016712333 (±0.03114358)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-300-300-300
Dimensions600600600
Spacing600600600
CellA=B=C: 498.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_82742_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_82742_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 : Cryo-EM structure of bacteriophage A1002 mature capsid

EntireName: Cryo-EM structure of bacteriophage A1002 mature capsid
Components
  • Complex: Cryo-EM structure of bacteriophage A1002 mature capsid
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Structural protein

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Supramolecule #1: Cryo-EM structure of bacteriophage A1002 mature capsid

SupramoleculeName: Cryo-EM structure of bacteriophage A1002 mature capsid
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Pseudomonas aeruginosa phage A1002
Source (natural)Organism: Pseudomonas phage (virus)

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage KPP25 (virus)
Molecular weightTheoretical: 41.531879 KDa
SequenceString: MPLPVQGNYT NFARLTNEQK TVWSLQFWRQ ARNAAFINMF LGTDANSMIQ QITELRRDEK GARAVITLIA DMVGDGVVGD NQLEGNEEA LTAFDTVIQL DQMRAANVHE GRMADQRSIV NFRTTSRDML AYWLADRMDQ LAFLSLAGVS YAYRTNGALR G SSPFPNLT ...String:
MPLPVQGNYT NFARLTNEQK TVWSLQFWRQ ARNAAFINMF LGTDANSMIQ QITELRRDEK GARAVITLIA DMVGDGVVGD NQLEGNEEA LTAFDTVIQL DQMRAANVHE GRMADQRSIV NFRTTSRDML AYWLADRMDQ LAFLSLAGVS YAYRTNGALR G SSPFPNLT FAADVTPPSA NRRLRWDGTN KVLVPNAATS DVTAADTPSY ALLVNLKAYA KTKYIRGLRG DGGEEMYHVF LD PLAMAKL KLDPDYIANL RSGYTRGNVN PLFKGGIVTV DGLVIHEFRH VYNTRGMAPG AKWGASGNVD GCSMLFCGAQ ALG FADIGN PRWVEKEFDY DNKHGISVAK ILGFLKPQFP SIYEDGNTED FGVINVYVAA

UniProtKB: Major capsid protein

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Macromolecule #2: Structural protein

MacromoleculeName: Structural protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage KPP25 (virus)
Molecular weightTheoretical: 14.715539 KDa
SequenceString:
MATLENTARQ YPLFIEQTLD FSDLVDGQAA TLTLELQNGA ILVPEISKLL VTTASNAAGA ATLDIGVIEP GLAADPDGIA ADLDLKTTG AKVLAPAKLT YPNGAVITFT ATASTGGTAG KFKFLLAYIV EGRGNETYGS PAYN

UniProtKB: Structural 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 POLARA 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 10233
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
FSC plot (resolution estimation)

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