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- EMDB-82614: Cryo-electron tomogram of in vitro assembly product of untagged D... -

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Basic information

Entry
Database: EMDB / ID: EMD-82614
TitleCryo-electron tomogram of in vitro assembly product of untagged D13, Twister
Map data
Sample
  • Complex: in vitro assembly product of VACV D13
    • Protein or peptide: VACV scaffold protein D13
KeywordsVaccinia virus / Immature virion / D13 scaffold protein assembly / Cryo-EM / VIRAL PROTEIN
Biological speciesVaccinia virus / Orthopoxvirus vaccinia
Methodelectron tomography / cryo EM
AuthorsKim SM / Jang YT / Hyun JK
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Structures of in vitro assembly products of poxvirus scaffolding protein reveal transition from pre-assembly state to fully assembled scaffold
Authors: Jang YT / Kim SM / Lee SN / Ryu BH / Jeong HS / Kang ES / Sul JH / Kim YH / Jo DG / Hyun JK
History
DepositionJul 29, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_82614.png

Downloads & links

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Map

FileDownload / File: emd_82614.map.gz / Format: CCP4 / Size: 1 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.44 Å/pix.
x 512 pix.
= 2785.28 Å		5.44 Å/pix.
x 1024 pix.
= 5570.56 Å		5.44 Å/pix.
x 1024 pix.
= 5570.56 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 5.44 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum0.0 - 255.0
Average (Standard dev.)184.001419999999996 (±4.4904475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions10241024512
Spacing10241024512
CellA: 5570.56 Å / B: 5570.56 Å / C: 2785.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : in vitro assembly product of VACV D13

EntireName: in vitro assembly product of VACV D13
Components
  • Complex: in vitro assembly product of VACV D13
    • Protein or peptide: VACV scaffold protein D13

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Supramolecule #1: in vitro assembly product of VACV D13

SupramoleculeName: in vitro assembly product of VACV D13 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vaccinia virus

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Macromolecule #1: VACV scaffold protein D13

MacromoleculeName: VACV scaffold protein D13 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Orthopoxvirus vaccinia
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AMNNTIINSL IGGDDSIKRS NVFAVDSQIP TLYMPQYISL SGVMTNDGPD NQAIASFEIR DQYITALNHL VLSLELPEVK GMGRFGYVPY VGYKCINHVS ISSCNGVIWE IEGEELYNNC INNTIALKHS GYSSELNDIS IGLTPNDTIK EPSTVYVYIK TPFDVEDTFS ...String:
AMNNTIINSL IGGDDSIKRS NVFAVDSQIP TLYMPQYISL SGVMTNDGPD NQAIASFEIR DQYITALNHL VLSLELPEVK GMGRFGYVPY VGYKCINHVS ISSCNGVIWE IEGEELYNNC INNTIALKHS GYSSELNDIS IGLTPNDTIK EPSTVYVYIK TPFDVEDTFS SLKLSDSKIT VTVTFNPVSD IVIRDSSFDF ETFNKEFVYV PELSFIGYMV KNVQIKPSFI EKPRRVIGQI NQPTATVTEV HAATSLSVYT KPYYGNTDNK FISYPGYSQD EKDYIDAYVS RLLDDLVIVS DGPPTGYPES AEIVEVPEDG IVSIQDADVY VKIDNVPDNM SVYLHTNLLM FGTRKNSFIY NISKKFSAIT GTYSDATKRT IFAHISHSIN IIDTSIPVSL WTSQRNVYNG DNRSAESKAK DLFINDPFIK GIDFKNKTDI ISRLEVRFGN DVLYSENGPI SRIYNELLTK SNNGTRTLTF NFTPKIFFRP TTITANVSRG KDKLSVRVVY STMDVNHPIY YVQKQLVVVC NDLYKVSYDQ GVSITKIMGD NN

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Gold fiducials (AURION) / Diameter: 10 nm

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 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: 2.5 µm / Nominal magnification: 59000
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

Final reconstructionAlgorithm: FOURIER SPACE / Software - Name: EMAN2 / Number images used: 41
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION

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