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- EMDB-64471: Two interacting D13 trimers at mode I interface in Twister assembly -

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Basic information

Entry
Database: EMDB / ID: EMD-64471
TitleTwo interacting D13 trimers at mode I interface in Twister assembly
Map data
Sample
  • Complex: Two neighboring trimers within mode I interface in Twister assembly
    • Protein or peptide: Scaffold protein OPG125
KeywordsVaccinia virus / Immature virion / D13 scaffold protein assembly / Cryo-EM / VIRAL PROTEIN
Function / homologyPoxvirus rifampicin-resistance / Poxvirus rifampicin resistance protein / response to antibiotic / membrane / Scaffold protein OPG125
Function and homology information
Biological speciesVaccinia virus / Orthopoxvirus vaccinia
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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_64471.png

Downloads & links

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Map

FileDownload / File: emd_64471.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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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: 0.0768
Minimum - Maximum-0.4105846 - 0.63521105
Average (Standard dev.)0.00013737023 (±0.015361783)
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_64471_msk_1.map
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Half map: #2

Fileemd_64471_half_map_1.map
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Half map: #1

Fileemd_64471_half_map_2.map
Projections & Slices
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Sample components

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Entire : Two neighboring trimers within mode I interface in Twister assembly

EntireName: Two neighboring trimers within mode I interface in Twister assembly
Components
  • Complex: Two neighboring trimers within mode I interface in Twister assembly
    • Protein or peptide: Scaffold protein OPG125

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Supramolecule #1: Two neighboring trimers within mode I interface in Twister assembly

SupramoleculeName: Two neighboring trimers within mode I interface in Twister assembly
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vaccinia virus

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Macromolecule #1: Scaffold protein OPG125

MacromoleculeName: Scaffold protein OPG125 / type: protein_or_peptide / ID: 1 / Details: VACV scaffold protein D13 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Orthopoxvirus vaccinia
Molecular weightTheoretical: 62.019609 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AMNNTIINSL IGGDDSIKRS NVFAVDSQIP TLYMPQYISL SGVMTNDGPD NQAIASFEIR DQYITALNHL VLSLELPEVK GMGRFGYVP YVGYKCINHV SISSCNGVIW EIEGEELYNN CINNTIALKH SGYSSELNDI SIGLTPNDTI KEPSTVYVYI K TPFDVEDT ...String:
AMNNTIINSL IGGDDSIKRS NVFAVDSQIP TLYMPQYISL SGVMTNDGPD NQAIASFEIR DQYITALNHL VLSLELPEVK GMGRFGYVP YVGYKCINHV SISSCNGVIW EIEGEELYNN CINNTIALKH SGYSSELNDI SIGLTPNDTI KEPSTVYVYI K TPFDVEDT FSSLKLSDSK ITVTVTFNPV SDIVIRDSSF DFETFNKEFV YVPELSFIGY MVKNVQIKPS FIEKPRRVIG QI NQPTATV TEVHAATSLS VYTKPYYGNT DNKFISYPGY SQDEKDYIDA YVSRLLDDLV IVSDGPPTGY PESAEIVEVP EDG IVSIQD ADVYVKIDNV PDNMSVYLHT NLLMFGTRKN SFIYNISKKF SAITGTYSDA TKRTIFAHIS HSINIIDTSI PVSL WTSQR NVYNGDNRSA ESKAKDLFIN DPFIKGIDFK NKTDIISRLE VRFGNDVLYS ENGPISRIYN ELLTKSNNGT RTLTF NFTP KIFFRPTTIT ANVSRGKDKL SVRVVYSTMD VNHPIYYVQK QLVVVCNDLY KVSYDQGVSI TKIMGDNN

UniProtKB: Scaffold protein OPG125

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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: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 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
Output model

PDB-9usu:
Two interacting D13 trimers at mode I interface in Twister assembly

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