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- EMDB-64469: Subtomogram averaging of in vitro assembly product of untagged D1... -

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Basic information

Entry
Database: EMDB / ID: EMD-64469
TitleSubtomogram averaging of in vitro assembly product of untagged D13, Twister
Map datasigma level is 2.
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
Methodsubtomogram averaging / cryo EM / Resolution: 13.0 Å
AuthorsKim SM / Jang YT
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
DepositionMay 2, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64469.png

Downloads & links

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Map

FileDownload / File: emd_64469.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsigma level is 2.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.72 Å/pix.
x 168 pix.
= 456.96 Å		2.72 Å/pix.
x 168 pix.
= 456.96 Å		2.72 Å/pix.
x 168 pix.
= 456.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00228
Minimum - Maximum-0.009893982 - 0.010498157
Average (Standard dev.)0.00005282118 (±0.0011384294)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-84-84-84
Dimensions168168168
Spacing168168168
CellA=B=C: 456.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64469_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sigma level is 2.

Fileemd_64469_additional_1.map
Annotationsigma level is 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64469_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_64469_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 : 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
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

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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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1620
ExtractionNumber tomograms: 5 / Number images used: 3499
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7vfd


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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