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- PDB-9ut0: Cryo-EM structure of A17(1-16) peptide-bound D13 assembled into s... -

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Basic information

Entry
Database: PDB / ID: 9ut0
TitleCryo-EM structure of A17(1-16) peptide-bound D13 assembled into scaffold-like particles from vaccinia virus
ComponentsScaffold protein OPG125
KeywordsVIRAL PROTEIN / Vaccinia virus / Immature virion / D13 Scaffold protein assembly / Cryo-EM
Function / homologyPoxvirus rifampicin-resistance / Poxvirus rifampicin resistance protein / response to antibiotic / membrane / identical protein binding / Scaffold protein OPG125
Function and homology information
Biological speciesOrthopoxvirus vaccinia
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsJang, Y.T. / Kim, S.M. / Lee, S.N. / Ryu, B.H. / Jeong, H.S. / Kang, E.S. / Sul, J.H. / Kim, Y.H. / Jo, D.G. / Hyun, J.K.
Funding support Korea, Republic Of, 1items
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, Y.T. / Kim, S.M. / Lee, S.N. / Ryu, B.H. / Jeong, H.S. / Kang, E.S. / Sul, J.H. / Kim, Y.H. / Jo, D.G. / Hyun, J.K.
History
DepositionMay 2, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Scaffold protein OPG125
B: Scaffold protein OPG125
C: Scaffold protein OPG125
D: Scaffold protein OPG125
E: Scaffold protein OPG125
F: Scaffold protein OPG125
H: Scaffold protein OPG125
G: Scaffold protein OPG125
I: Scaffold protein OPG125
K: Scaffold protein OPG125
L: Scaffold protein OPG125
J: Scaffold protein OPG125
N: Scaffold protein OPG125
M: Scaffold protein OPG125
O: Scaffold protein OPG125
R: Scaffold protein OPG125
Q: Scaffold protein OPG125
P: Scaffold protein OPG125


Theoretical massNumber of molelcules
Total (without water)1,115,07418
Polymers1,115,07418
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Scaffold protein OPG125 / 62 kDa protein / Rifampicin resistance protein


Mass: 61948.531 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG125, VACWR118, D13L / Plasmid: pPROEX / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P68440
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Assembled scaffold-like particle of A17(1-16) peptide-bound Vaccinia virus D13
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.195 MDa / Experimental value: YES
Source (natural)Organism: Vaccinia virus
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3) / Plasmid: pPROEX
Buffer solutionpH: 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.
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium chlorideNaCl1
210 mMTris(hydroxymethyl)aminomethaneTris-HCI1
32 mMBeta-mercaptoethanolBME1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The specimen concentration is reported based on the trimeric unit, as the exact concentration of fully assembled particles could not be precisely determined.
Specimen supportDetails: 15mA 60sec / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K / Details: Wait time: 10sec Blot force: 0 Blot time: 5sec

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 42000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 45.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.7.1particle selection
2EPU3image acquisition
4cryoSPARC4.7.1CTF correctionCTF estimation and correction with PATCH CTF
7UCSF Chimeramodel fitting
8Coot0.9.8.92model fitting
10cryoSPARC4.7.1initial Euler assignmentAb initio reconstruction with no reference
11cryoSPARC4.7.1final Euler assignmentnon-uniform refinement
12cryoSPARC4.5.3classification3D classification
13cryoSPARC4.7.13D reconstructionNon-uniform refinement
20PHENIX1.21.2_5419model refinement
Image processingDetails: Super-resolution mode LZW-compressed TIFF format
CTF correctionType: NONE
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 643673 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 161 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Map-to-model correlation
Details: Model 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. ...Details: Model 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.
RefinementHighest resolution: 3.63 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00377437
ELECTRON MICROSCOPYf_angle_d0.5105338
ELECTRON MICROSCOPYf_dihedral_angle_d4.30210387
ELECTRON MICROSCOPYf_chiral_restr0.04612150
ELECTRON MICROSCOPYf_plane_restr0.00413446

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