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- PDB-9usx: Cryo-EM structure of His6-tagged D13 assembled into scaffold-like... -

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Basic information

Entry
Database: PDB / ID: 9usx
TitleCryo-EM structure of His6-tagged 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: 2.88 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: 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
G: Scaffold protein OPG125
H: Scaffold protein OPG125
I: Scaffold protein OPG125
J: Scaffold protein OPG125
K: Scaffold protein OPG125
L: Scaffold protein OPG125
M: Scaffold protein OPG125
N: Scaffold protein OPG125
O: Scaffold protein OPG125
P: Scaffold protein OPG125
Q: Scaffold protein OPG125
R: Scaffold protein OPG125


Theoretical massNumber of molelcules
Total (without water)1,170,91518
Polymers1,170,91518
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: 65050.840 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 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 scaffold-like particle assembly and ...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 scaffold-like particle assembly and vitrification, 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)aminomethane hydrochlorideTris-HCl1
32 mMBeta-mercaptoethanolBME1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Scaffold-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 ...Details: Scaffold-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.
Specimen supportDetails: X / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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 / Cs: 2.7 mm
Image recordingElectron dose: 38.6 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.5.3particle selection
4cryoSPARC4.5.3CTF correctionCTF estimation and correction with PATCH CTF
7UCSF Chimeramodel fitting
8Coot0.9.8.92model fitting
10PHENIX1.21.2_5419model refinement
11cryoSPARC4.5.3initial Euler assignmentAb initio reconstruction with no reference
12cryoSPARC4.5.3final Euler assignmentnon-uniform refinement
13cryoSPARC4.5.3classificationHeterogenous refinement
14cryoSPARC4.5.33D reconstructionLocal Refinement with Re-centering
Image processingDetails: Super-resolution mode LZW-compressed TIFF format
CTF correctionType: NONE
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 722411 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 173.77 / 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: 2.88 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00777544
ELECTRON MICROSCOPYf_angle_d0.637105480
ELECTRON MICROSCOPYf_dihedral_angle_d4.55410404
ELECTRON MICROSCOPYf_chiral_restr0.05112168
ELECTRON MICROSCOPYf_plane_restr0.00513464

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