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- EMDB-52006: pT=3 virus-like particle of ssRNA phage Beihai26 coat protein -

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Basic information

Entry
Database: EMDB / ID: EMD-52006
TitlepT=3 virus-like particle of ssRNA phage Beihai26 coat protein
Map dataMap
Sample
  • Complex: virus like particles of ssRNA phage Beihai26
    • Protein or peptide: Capsid protein
Keywordsvirus like particle / ssRNA phage / coat protein
Function / homologyBacteriophage RNA-type, capsid / Capsid protein
Function and homology information
Biological speciesLeviviridae sp. (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKalnins G
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography.
Authors: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams /
Abstract: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.
History
DepositionNov 5, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52006.png

Downloads & links

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Map

FileDownload / File: emd_52006.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.78 Å/pix.
x 512 pix.
= 400.896 Å		0.78 Å/pix.
x 512 pix.
= 400.896 Å		0.78 Å/pix.
x 512 pix.
= 400.896 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.783 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.005966441 - 0.014230856
Average (Standard dev.)0.00013314917 (±0.0007392102)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 400.896 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1

Fileemd_52006_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_52006_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 : virus like particles of ssRNA phage Beihai26

EntireName: virus like particles of ssRNA phage Beihai26
Components
  • Complex: virus like particles of ssRNA phage Beihai26
    • Protein or peptide: Capsid protein

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Supramolecule #1: virus like particles of ssRNA phage Beihai26

SupramoleculeName: virus like particles of ssRNA phage Beihai26 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Leviviridae sp. (virus)

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 180 / Enantiomer: LEVO
Source (natural)Organism: Leviviridae sp. (virus)
Molecular weightTheoretical: 12.896364 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
AARSSIVLTD GTTPVTLTPV GGGVGQTLYR ATAEALSAAN PSLSFGYRFT DGGTNRQSLS YKQPITAVDS TTSETLVRGQ CVVDINIVI PRVATATDRA EAIKRAFDVL NALNAELITG EGQW

UniProtKB: Capsid 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

Concentration2 mg/mL
BufferpH: 8 / Component - Concentration: 20.0 mM / Component - Name: Tris-HCl / Details: 20 mM Tris-HCl, pH 8.0
GridModel: Quantifoil Active R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
TemperatureMax: 70.0 K
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 1 / Number real images: 2714 / Average exposure time: 4.0 sec. / Average electron dose: 1.6 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 28843
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 28843
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 1 / Avg.num./class: 2714 / Software - Name: RELION
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: AB INITIO MODEL / Overall B value: 110.094
Output model

PDB-9hat:
pT=3 virus-like particle of ssRNA phage Beihai26 coat protein

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