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- EMDB-64470: Cryo-EM structure of in vitro assembly product of untagged D13, T... -

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Basic information

Entry
Database: EMDB / ID: EMD-64470
TitleCryo-EM structure of in vitro assembly product of untagged D13, Twister
Map data
Sample
  • Complex: in vitro assembly product of untagged D13 (Twister)
    • Protein or peptide: VACV scaffold protein D13
KeywordsVaccinia virus / Immature virion / D13 scaffold protein assembly / Cryo-EM / VIRAL PROTEIN
Biological speciesVaccinia virus / Orthopoxvirus vaccinia
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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_64470.png

Downloads & links

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Map

FileDownload / File: emd_64470.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 360 pix.
= 478.8 Å		1.33 Å/pix.
x 360 pix.
= 478.8 Å		1.33 Å/pix.
x 360 pix.
= 478.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.33 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.048
Minimum - Maximum-0.09831497 - 0.19399753
Average (Standard dev.)0.00041621557 (±0.011998158)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 478.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64470_msk_1.map
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Additional map: #1

Fileemd_64470_additional_1.map
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Half map: #2

Fileemd_64470_half_map_1.map
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Half map: #1

Fileemd_64470_half_map_2.map
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Sample components

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Entire : in vitro assembly product of untagged D13 (Twister)

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

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Supramolecule #1: in vitro assembly product of untagged D13 (Twister)

SupramoleculeName: in vitro assembly product of untagged D13 (Twister) / 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
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
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: 50.0 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: 2.4 µm / Nominal defocus min: 1.4000000000000001 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

Particle selectionNumber selected: 1500729
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104933
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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