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- EMDB-54288: Penicillium chrysogenum Virus full virions -

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Basic information

Entry
Database: EMDB / ID: EMD-54288
TitlePenicillium chrysogenum Virus full virions
Map data
Sample
  • Virus: Penicillium chrysogenum virus (isolate Caston)
    • Protein or peptide: Capsid protein
    • Protein or peptide: Protein 4 Penicillium chrysogenum Virus
KeywordsCryo-EM / PcV / Virus. / VIRUS
Function / homology: / : / Fungal virus Capsid protein, N-terminal domain / Fungal virus Capsid protein, C-terminal domain / T=1 icosahedral viral capsid / Uncharacterized protein p4 / Capsid protein
Function and homology information
Biological speciesPenicillium chrysogenum (fungus) / Penicillium chrysogenum virus (isolate Caston)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.14 Å
AuthorsGil-Cantero D / Novoa Benavides G / Luque D / Ruiz Caston J
Funding support Spain, 1 items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2023-146143NB-I00 Spain
CitationJournal: To Be Published
Title: Penicillium chrysogenum Virus full virions
Authors: Gil-Cantero D / Novoa Benavides G / Luque D / Ruiz Caston J
History
DepositionJul 8, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54288.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 454 pix.
= 481.24 Å		1.06 Å/pix.
x 454 pix.
= 481.24 Å		1.06 Å/pix.
x 454 pix.
= 481.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.5524098 - 3.2787683
Average (Standard dev.)0.035959605 (±0.18233249)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-227-227-227
Dimensions454454454
Spacing454454454
CellA=B=C: 481.23996 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_54288_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54288_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 : Penicillium chrysogenum virus (isolate Caston)

EntireName: Penicillium chrysogenum virus (isolate Caston)
Components
  • Virus: Penicillium chrysogenum virus (isolate Caston)
    • Protein or peptide: Capsid protein
    • Protein or peptide: Protein 4 Penicillium chrysogenum Virus

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Supramolecule #1: Penicillium chrysogenum virus (isolate Caston)

SupramoleculeName: Penicillium chrysogenum virus (isolate Caston) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 654932
Sci species name: Penicillium chrysogenum virus (isolate Caston)
Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Penicillium chrysogenum virus (isolate Caston)
Molecular weightTheoretical: 120 kDa/nm

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Penicillium chrysogenum (fungus)
Molecular weightTheoretical: 60.430168 KDa
SequenceString: MRRSLMHEKK QVFAELRREA QALRVAKEAR GKMSVWDPST REGARGYREK VVRFGRQIAS LLQYFENMHS PALDIIACDK FLLKYQIYG DIDRDPAFGE NTMTAEVPVV WDKCEVEVKL YAGPLQKLMS RAKLVGTARE GIPNRNDVAK STGWNQDQVQ K FPDNRMDS ...String:
MRRSLMHEKK QVFAELRREA QALRVAKEAR GKMSVWDPST REGARGYREK VVRFGRQIAS LLQYFENMHS PALDIIACDK FLLKYQIYG DIDRDPAFGE NTMTAEVPVV WDKCEVEVKL YAGPLQKLMS RAKLVGTARE GIPNRNDVAK STGWNQDQVQ K FPDNRMDS LISLLEQMQT GQSKLTRLVK GFLILLEMAE RKEVDFHVGN HIHVTYAIAP VCDSYDLPGR CYVFNSKPTS EA HAAVLLA MCREYPPPQF ASHVSVPADA EDVCIVSQGR QIQPGSAVTL NPGLVYSSIL TYAMDTSCTD LLQEAQIIAC SLQ ENRYFS RIGLPTVVSL YDLMVPAFIA QNSALEGARL SGDLSKAVGR VHQMLGMVAA KDIISATHMQ SRTGFDPSHG IRQY LNSNS RLVTQMASKL TGIGLFDATP QMRIFSEMDT ADYADMLHLT IFEGLWLVQD ASVCIDNGPI SFLVNGEKLL SADRA GYDV LVEELTLANI RIEHHKMPTG AFTTRWVAAK RDSALGLTPR SRTAHRVDMV RECDFNP

UniProtKB: Capsid protein

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Macromolecule #2: Protein 4 Penicillium chrysogenum Virus

MacromoleculeName: Protein 4 Penicillium chrysogenum Virus / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Penicillium chrysogenum (fungus)
Molecular weightTheoretical: 61.985125 KDa
SequenceString: LVEEIDGPVV EKGLISDGEK EIIRHLNVQD KFTINGFRKS VKICHMVSLG ATRQTKRTGT TELDFMGAGP WTLYPSSARA LYSSKESTV HLVDEAQRRM IMSKCPTMAG PTSTGTYMAA IHERLSTPSD LRHLFTKMVL YLYDYTLAVV SKDNTMHTAD D ISFDLRPH ...String:
LVEEIDGPVV EKGLISDGEK EIIRHLNVQD KFTINGFRKS VKICHMVSLG ATRQTKRTGT TELDFMGAGP WTLYPSSARA LYSSKESTV HLVDEAQRRM IMSKCPTMAG PTSTGTYMAA IHERLSTPSD LRHLFTKMVL YLYDYTLAVV SKDNTMHTAD D ISFDLRPH LPSDALLATV INHDMVIDGD LFTPEQISLL CLAGQQYPSV WYAGEGNIYN SCNMVADDLV VVSSGRLTTD SA FTWGSPD KLYNMMWTIA QKLNGVSCLM YALESMRGKC KMMSDIVAKT DCREVNAMIP RSYCMSTAFG QIREKQIVVK MPG YFSTSI GMLSDLMYGM TFKAVASCVA ETLGAMGTIV SSSTPRTNPT INGLMRDYGL QHTNAWDNFM LRNFEMVTRR PTQW DIGQH MKEYALALAE HVMLGYDIEM PSILLTIPAL TAVNTAYGLT RGWYGGGSTL DMDKKQRKES TDALCAVGWM CGLRQ CRPQ VFRNRAGKKQ VMVNAAERKL KAEAGDDCRI RDVEFWLEDT PGGRVDENEE SAPNLYKTEF SGTKCAMVFN Y

UniProtKB: Uncharacterized protein p4

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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: 7.8 / Details: 50mM Tris-HCl pH 7.8; 150 mM NaCl; 5 mM EDTA
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 22 K / Instrument: FEI VITROBOT MARK IV
Details: 3 min incubation in carbon covered grids R2/2 Cu/Rh. Blotted 3 s at force 0.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 83000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2244540
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3j3i

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1269168
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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