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- EMDB-65449: Cyanopodophage Pan3 capsid -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-65449
TitleCyanopodophage Pan3 capsid
Map data
Sample
  • Virus: Pseudanabaena phage Pan3 (virus)
    • Protein or peptide: Major capsid protein
KeywordsCyanophage / Virus / Capsid / Major capsid protein
Function / homology:
Function and homology information
Biological speciesPseudanabaena phage Pan3 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHou P / Zhou CZ / Jiang YL
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32430001 China
National Natural Science Foundation of China (NSFC)92451302 China
CitationJournal: To Be Published
Title: Cryo-EM structure of cyanopodophage Pan3 reveals a new host recognition mode
Authors: Hou P / Zhou CZ / Jiang YL
History
DepositionJul 21, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65449.png

Downloads & links

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Map

FileDownload / File: emd_65449.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 700 pix.
= 749. Å		1.07 Å/pix.
x 700 pix.
= 749. Å		1.07 Å/pix.
x 700 pix.
= 749. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.09058769 - 0.14414333
Average (Standard dev.)0.0012205818 (±0.0074485485)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 749.00006 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65449_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_65449_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 : Pseudanabaena phage Pan3

EntireName: Pseudanabaena phage Pan3 (virus)
Components
  • Virus: Pseudanabaena phage Pan3 (virus)
    • Protein or peptide: Major capsid protein

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Supramolecule #1: Pseudanabaena phage Pan3

SupramoleculeName: Pseudanabaena phage Pan3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2981586 / Sci species name: Pseudanabaena phage Pan3 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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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: Pseudanabaena phage Pan3 (virus)
Molecular weightTheoretical: 39.866551 KDa
SequenceString: MADTTPATGL VVQQWEDKFF QEYLHDGGFK ALMGTDENAV IQVKEDLSKK AGDSITIALV NRLNNAAVTG ASTLEGNEED MTSRSLRIY VDKRRNAVRI AEISEQRSAI SLRNAARATL LDWAMEDTRD LIIEALGSLN GTRFVDRTAA IADAWLVDNL D RVYFGAGV ...String:
MADTTPATGL VVQQWEDKFF QEYLHDGGFK ALMGTDENAV IQVKEDLSKK AGDSITIALV NRLNNAAVTG ASTLEGNEED MTSRSLRIY VDKRRNAVRI AEISEQRSAI SLRNAARATL LDWAMEDTRD LIIEALGSLN GTRFVDRTAA IADAWLVDNL D RVYFGAGV GSGTDLSADL AQLDTSADLF NVAALDGMIL KAKTCNPKIR PMRDPGNGKR YYVAFANPHA FKNLRDSMDN EY LSNTVVQ MQASKLFEGG DLMWNGVIVK ETDNIPIYEN LGAGGTAEVT PVYLCGAQAL AVAYAKRWKT VTEEFDYGDK YGV AVDGIY GVRKIIFGSG SGDTDDLKDH GVVTGFFATT GAATVAAAAA AEN

UniProtKB: UNIPROTKB: A0AA49CM87

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 191214
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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