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- EMDB-64477: Cryo-EM structure of A17(1-16) peptide-bound D13 assembled into s... -

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Basic information

Entry
Database: EMDB / ID: EMD-64477
TitleCryo-EM structure of A17(1-16) peptide-bound D13 assembled into scaffold-like particles from vaccinia virus
Map dataUnsharpen
Sample
  • Complex: Assembled scaffold-like particle of A17(1-16) peptide-bound Vaccinia virus D13
    • 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 / identical protein binding / Scaffold protein OPG125
Function and homology information
Biological speciesVaccinia virus / Orthopoxvirus vaccinia
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
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
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_64477.png

Downloads & links

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Map

FileDownload / File: emd_64477.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpen
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 384 pix.
= 396.288 Å		1.03 Å/pix.
x 384 pix.
= 396.288 Å		1.03 Å/pix.
x 384 pix.
= 396.288 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.032 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0265
Minimum - Maximum-0.13837077 - 0.2804543
Average (Standard dev.)0.00028432868 (±0.009993364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 396.28796 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64477_msk_1.map
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Additional map: Unsharpen

Fileemd_64477_additional_1.map
AnnotationUnsharpen
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Half map: Unsharpen

Fileemd_64477_half_map_1.map
AnnotationUnsharpen
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Histogram

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Half map: Unsharpen

Fileemd_64477_half_map_2.map
AnnotationUnsharpen
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Sample components

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Entire : Assembled scaffold-like particle of A17(1-16) peptide-bound Vacci...

EntireName: Assembled scaffold-like particle of A17(1-16) peptide-bound Vaccinia virus D13
Components
  • Complex: Assembled scaffold-like particle of A17(1-16) peptide-bound Vaccinia virus D13
    • Protein or peptide: Scaffold protein OPG125

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Supramolecule #1: Assembled scaffold-like particle of A17(1-16) peptide-bound Vacci...

SupramoleculeName: Assembled scaffold-like particle of A17(1-16) peptide-bound Vaccinia virus D13
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vaccinia virus
Molecular weightTheoretical: 195 KDa

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Macromolecule #1: Scaffold protein OPG125

MacromoleculeName: Scaffold protein OPG125 / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Orthopoxvirus vaccinia
Molecular weightTheoretical: 61.948531 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNNTIINSLI GGDDSIKRSN VFAVDSQIPT LYMPQYISLS GVMTNDGPDN QAIASFEIRD QYITALNHLV LSLELPEVKG MGRFGYVPY VGYKCINHVS ISSCNGVIWE IEGEELYNNC INNTIALKHS GYSSELNDIS IGLTPNDTIK EPSTVYVYIK T PFDVEDTF ...String:
MNNTIINSLI GGDDSIKRSN VFAVDSQIPT LYMPQYISLS GVMTNDGPDN QAIASFEIRD QYITALNHLV LSLELPEVKG MGRFGYVPY VGYKCINHVS ISSCNGVIWE IEGEELYNNC INNTIALKHS GYSSELNDIS IGLTPNDTIK EPSTVYVYIK T PFDVEDTF SSLKLSDSKI TVTVTFNPVS DIVIRDSSFD FETFNKEFVY VPELSFIGYM VKNVQIKPSF IEKPRRVIGQ IN QPTATVT EVHAATSLSV YTKPYYGNTD NKFISYPGYS QDEKDYIDAY VSRLLDDLVI VSDGPPTGYP ESAEIVEVPE DGI VSIQDA DVYVKIDNVP DNMSVYLHTN LLMFGTRKNS FIYNISKKFS AITGTYSDAT KRTIFAHISH SINIIDTSIP VSLW TSQRN VYNGDNRSAE SKAKDLFIND PFIKGIDFKN KTDIISRLEV RFGNDVLYSE NGPISRIYNE LLTKSNNGTR TLTFN FTPK IFFRPTTITA NVSRGKDKLS VRVVYSTMDV NHPIYYVQKQ LVVVCNDLYK VSYDQGVSIT KIMGDNN

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
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloride
10.0 mMTris-HCITris(hydroxymethyl)aminomethane
2.0 mMBMEBeta-mercaptoethanol

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 R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0002 kPa / Details: 15mA 60sec
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Details: Wait time: 10sec Blot force: 0 Blot time: 5sec.
DetailsThe specimen concentration is reported based on the trimeric unit, as the exact concentration of fully assembled particles could not be precisely determined.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.5 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 / Nominal magnification: 42000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsSuper-resolution mode LZW-compressed TIFF format
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1)
Software - details: CTF estimation and correction with PATCH CTF
Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7vfd

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Software - details: Non-uniform refinement / Number images used: 643673
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.7.1)
Software - details: Ab initio reconstruction with no reference
Final angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.7.1) / Software - details: non-uniform refinement
Final 3D classificationNumber classes: 5 / Avg.num./class: 500 / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: 3D classification
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsModel building was proceeded by manually fitting the cryo-EM structure of D13 (PDB ID 7VFD) into our cryo-EM map using UCSF Chimera. The model was subsequently inspected and adjusted in Coot. Coordinate refinements were performed using the real-space refinement routine in the Phenix software suite.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 161 / Target criteria: Map-to-model correlation
Output model

PDB-9ut0:
Cryo-EM structure of A17(1-16) peptide-bound D13 assembled into scaffold-like particles from vaccinia virus

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