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- EMDB-19908: Human Picobirnavirus Reassembled VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-19908
TitleHuman Picobirnavirus Reassembled VLP
Map dataHuman Picobirnavirus Reassembled VLPs - Cryosparc Refinement (sharpened map)
Sample
  • Virus: Human Picobirnavirus Reassembled VLP (human)
    • Protein or peptide: Capsid protein precursor
KeywordsPicobirnavirus / CryoEM / Assembly / VLP / VIRUS LIKE PARTICLE
Function / homology: / : / Picobirnavirus, Capsid protein / T=3 icosahedral viral capsid / Capsid protein precursor
Function and homology information
Biological speciesHomo sapiens (human) / Human Picobirnavirus Reassembled VLP (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsRodriguez-Espinosa MJ / Novoa G / Martinez-Romero JM / de Pablo PJ / Caston JR
Funding support Spain, 1 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-113287RB-I00 Spain
CitationJournal: To Be Published
Title: Human Picobirnavirus CP Reassembled VLP
Authors: Rodriguez-Espinosa MJ / Novoa G / Martinez-Romero JM / de Pablo PJ / Caston JR
History
DepositionMar 22, 2024-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19908.png

Downloads & links

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Map

FileDownload / File: emd_19908.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman Picobirnavirus Reassembled VLPs - Cryosparc Refinement (sharpened map)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 400 pix.
= 548. Å		1.37 Å/pix.
x 400 pix.
= 548. Å		1.37 Å/pix.
x 400 pix.
= 548. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-2.3836496 - 5.40348
Average (Standard dev.)0.04679481 (±0.37248677)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 548.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Human Picobirnavirus Reassembled VLPs - Cryosparc Refinement (sharpened...

Fileemd_19908_additional_1.map
AnnotationHuman Picobirnavirus Reassembled VLPs - Cryosparc Refinement (sharpened map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Human Picobirnavirus Reassembled VLPs - Cryosparc Refinement (sharpened...

Fileemd_19908_half_map_1.map
AnnotationHuman Picobirnavirus Reassembled VLPs - Cryosparc Refinement (sharpened map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Human Picobirnavirus Reassembled VLPs - Cryosparc Refinement (sharpened...

Fileemd_19908_half_map_2.map
AnnotationHuman Picobirnavirus Reassembled VLPs - Cryosparc Refinement (sharpened 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 : Human Picobirnavirus Reassembled VLP

EntireName: Human Picobirnavirus Reassembled VLP (human)
Components
  • Virus: Human Picobirnavirus Reassembled VLP (human)
    • Protein or peptide: Capsid protein precursor

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Supramolecule #1: Human Picobirnavirus Reassembled VLP

SupramoleculeName: Human Picobirnavirus Reassembled VLP / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 9606 / Sci species name: Human Picobirnavirus Reassembled VLP / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Molecular weightTheoretical: 7.44 MDa
Virus shellShell ID: 1 / Diameter: 380.0 Å / T number (triangulation number): 1

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Macromolecule #1: Capsid protein precursor

MacromoleculeName: Capsid protein precursor / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.225707 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: VAWYARYPHI LEEATRLPFA YPIGQYYDTG YSVASATEWS KYVDTSLTIP GVMCVNFTPT PGESYNKNSP INIAAQNVYT YVRHMNSGH ANYEQADLMM YLLAMDSLYI FHSYVRKILA ISKLYTPVNK YFPRALLVAL GVDPEDVFAN QAQWEYFVNM V AYRAGAFA ...String:
VAWYARYPHI LEEATRLPFA YPIGQYYDTG YSVASATEWS KYVDTSLTIP GVMCVNFTPT PGESYNKNSP INIAAQNVYT YVRHMNSGH ANYEQADLMM YLLAMDSLYI FHSYVRKILA ISKLYTPVNK YFPRALLVAL GVDPEDVFAN QAQWEYFVNM V AYRAGAFA APASMTYYER HAWMSNGLYV DQDVTRAQIY MFKPTMLWKY ENLGTTGTKL VPLMMPKAGD NRKLVDFQVL FN NLVSTML GDEDFGIMSG DVFKAFGADG LVKLLAVDST TMTLPTYDPL ILAQIHSARA VGAPILETST LTGFPGRQWQ ITQ NPDVNN GAIIFHPSFG YDGQDHEELS FRAMCSNMIL NLPGEAHSAE MIIEATRLAT MFQVKAVPAG DTSKPVLYLP NGFG TEVVN DYTMISVDKA TPHDLTIHTF FNNILVPNAK ENYVANLELL NNIIQFDWAP QLYLTYGIAQ ESFGPFAQLN DWTIL TGET LARMHEVCVT SMFDVPQ

UniProtKB: Capsid protein precursor

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

BufferpH: 7.5 / Component:
ConcentrationName
25.0 mMTris-HCl
50.0 mMNaCl
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: OTHER / Average electron dose: 45.76 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm

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Image processing

Particle selectionNumber selected: 41048
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 40192
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9eqw:
Human Picobirnavirus CP Reassembled VLP

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