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- EMDB-82617: Cryo-electron tomogram of His6-tagged D13 assembled into scaffold... -

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Basic information

Entry
Database: EMDB / ID: EMD-82617
TitleCryo-electron tomogram of His6-tagged D13 assembled into scaffold-like particles from vaccinia virus
Map data
Sample
  • Complex: Vaccinia virus D13
    • Protein or peptide: Vaccinia virus D13
KeywordsVaccinia virus / Immature virion / D13 scaffold protein assembly / Cryo-EM / VIRAL PROTEIN
Biological speciesVaccinia virus / Orthopoxvirus vaccinia
Methodelectron tomography / cryo EM
AuthorsJang YT / Kim SM / Lee SN / Ryu BH / Jeong HS / Kang ES / Sul JH / Kim YH / Jo DG / 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_82617.png

Downloads & links

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Map

FileDownload / File: emd_82617.map.gz / Format: CCP4 / Size: 4.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10 Å/pix.
x 1057 pix.
= 10570. Å		10 Å/pix.
x 1217 pix.
= 12170. Å		10 Å/pix.
x 865 pix.
= 8650. 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: 10 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-0.37885988 - 0.20205604
Average (Standard dev.)0.04033137 (±0.015156822)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions12178651057
Spacing86512171057
CellA: 8650.0 Å / B: 12170.0 Å / C: 10570.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Vaccinia virus D13

EntireName: Vaccinia virus D13
Components
  • Complex: Vaccinia virus D13
    • Protein or peptide: Vaccinia virus D13

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Supramolecule #1: Vaccinia virus D13

SupramoleculeName: Vaccinia virus D13 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vaccinia virus
Molecular weightTheoretical: 196 KDa

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Macromolecule #1: Vaccinia virus D13

MacromoleculeName: Vaccinia virus D13 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Orthopoxvirus vaccinia
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSYYHHHHHH DYDIPTTENL YFQGAMNNTI INSLIGGDDS IKRSNVFAVD SQIPTLYMPQ YISLSGVMTN DGPDNQAIAS FEIRDQYITA LNHLVLSLEL PEVKGMGRFG YVPYVGYKCI NHVSISSCNG VIWEIEGEEL YNNCINNTIA LKHSGYSSEL NDISIGLTPN ...String:
MSYYHHHHHH DYDIPTTENL YFQGAMNNTI INSLIGGDDS IKRSNVFAVD SQIPTLYMPQ YISLSGVMTN DGPDNQAIAS FEIRDQYITA LNHLVLSLEL PEVKGMGRFG YVPYVGYKCI NHVSISSCNG VIWEIEGEEL YNNCINNTIA LKHSGYSSEL NDISIGLTPN DTIKEPSTVY VYIKTPFDVE DTFSSLKLSD SKITVTVTFN PVSDIVIRDS SFDFETFNKE FVYVPELSFI GYMVKNVQIK PSFIEKPRRV IGQINQPTAT VTEVHAATSL SVYTKPYYGN TDNKFISYPG YSQDEKDYID AYVSRLLDDL VIVSDGPPTG YPESAEIVEV PEDGIVSIQD ADVYVKIDNV PDNMSVYLHT NLLMFGTRKN SFIYNISKKF SAITGTYSDA TKRTIFAHIS HSINIIDTSI PVSLWTSQRN VYNGDNRSAE SKAKDLFIND PFIKGIDFKN KTDIISRLEV RFGNDVLYSE NGPISRIYNE LLTKSNNGTR TLTFNFTPKI FFRPTTITAN VSRGKDKLSV RVVYSTMDVN HPIYYVQKQL VVVCNDLYKV SYDQGVSITK IMGDNN

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 8
Details: The protein was initially purified in a buffer containing 500mM NaCl, 150mM Tris-HCl (pH 7.5), 25mM L-arginine, 25mM L-glutamic acid, and 2mM BME. For particle assembly, the buffer was ...Details: The protein was initially purified in a buffer containing 500mM NaCl, 150mM Tris-HCl (pH 7.5), 25mM L-arginine, 25mM L-glutamic acid, and 2mM BME. For particle assembly, the buffer was exchanged to 10mM Tris-HCl (pH 8.0), 150mM NaCl, and 2mM BME.
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Details: 15mA 50sec
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K
DetailsScaffold-like particles composed of His6-tagged D13 trimers. The specimen concentration is reported based on the trimeric unit, as the exact concentration of fully assembled particles could not be precisely determined.
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Gold fiducials (AURION) / Diameter: 10 nm

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.24 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: RELION (ver. 5.0-beta-0) / Software - details: Postprocess / Number images used: 37
CTF correctionSoftware - Name: RELION (ver. 5.0-beta-0) / Software - details: CTFFIND4.1.14
Details: CTF parameters were estimated using CTFFIND 4.1.14. Phase flipping correction was applied in RELION 5.0-beta during subtomogram averaging.
Type: PHASE FLIPPING ONLY

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