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- EMDB-80609: Cryo-EM structure of the A17(1-16) peptide-bound N-terminal 17 re... -

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Basic information

Entry
Database: EMDB / ID: EMD-80609
TitleCryo-EM structure of the A17(1-16) peptide-bound N-terminal 17 residue truncated D13 trimer from vaccinia virus
Map dataSharpen
Sample
  • Complex: A17(1-16) peptide-bound N-terminal 17 residue truncated D13 trimer from vaccinia virus
    • 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: 3.04 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)RS-2022-NR069270 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
DepositionApr 28, 2026-
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_80609.png

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Map

FileDownload / File: emd_80609.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpen
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 360 pix.
= 234. Å		0.65 Å/pix.
x 360 pix.
= 234. Å		0.65 Å/pix.
x 360 pix.
= 234. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0397
Minimum - Maximum-0.24541801 - 0.40102425
Average (Standard dev.)0.000259051 (±0.011330051)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 233.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_80609_msk_1.map
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Additional map: Unsharpen

Fileemd_80609_additional_1.map
AnnotationUnsharpen
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Half map: Half A

Fileemd_80609_half_map_1.map
AnnotationHalf_A
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Half map: Half B

Fileemd_80609_half_map_2.map
AnnotationHalf_B
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Sample components

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Entire : A17(1-16) peptide-bound N-terminal 17 residue truncated D13 trime...

EntireName: A17(1-16) peptide-bound N-terminal 17 residue truncated D13 trimer from vaccinia virus
Components
  • Complex: A17(1-16) peptide-bound N-terminal 17 residue truncated D13 trimer from vaccinia virus
    • Protein or peptide: Scaffold protein OPG125

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Supramolecule #1: A17(1-16) peptide-bound N-terminal 17 residue truncated D13 trime...

SupramoleculeName: A17(1-16) peptide-bound N-terminal 17 residue truncated D13 trimer from vaccinia virus
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 / Details: VACV D13 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Orthopoxvirus vaccinia
Molecular weightTheoretical: 60.160508 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: RSNVFAVDSQ IPTLYMPQYI SLSGVMTNDG PDNQAIASFE IRDQYITALN HLVLSLELPE VKGMGRFGYV PYVGYKCINH VSISSCNGV IWEIEGEELY NNCINNTIAL KHSGYSSELN DISIGLTPND TIKEPSTVYV YIKTPFDVED TFSSLKLSDS K ITVTVTFN ...String:
RSNVFAVDSQ IPTLYMPQYI SLSGVMTNDG PDNQAIASFE IRDQYITALN HLVLSLELPE VKGMGRFGYV PYVGYKCINH VSISSCNGV IWEIEGEELY NNCINNTIAL KHSGYSSELN DISIGLTPND TIKEPSTVYV YIKTPFDVED TFSSLKLSDS K ITVTVTFN PVSDIVIRDS SFDFETFNKE FVYVPELSFI GYMVKNVQIK PSFIEKPRRV IGQINQPTAT VTEVHAATSL SV YTKPYYG NTDNKFISYP GYSQDEKDYI DAYVSRLLDD LVIVSDGPPT GYPESAEIVE VPEDGIVSIQ DADVYVKIDN VPD NMSVYL HTNLLMFGTR KNSFIYNISK KFSAITGTYS DATKRTIFAH ISHSINIIDT SIPVSLWTSQ RNVYNGDNRS AESK AKDLF INDPFIKGID FKNKTDIISR LEVRFGNDVL YSENGPISRI YNELLTKSNN GTRTLTFNFT PKIFFRPTTI TANVS RGKD KLSVRVVYST MDVNHPIYYV QKQLVVVCND LYKVSYDQGV SITKIMGDNN

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

Concentration5 mg/mL
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.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Wait time: 0sec Blot force: 0 Blot time: 5sec.
DetailsThe specimen concentration is reported based on the trimeric unit, as the exact concentration of fully A17 peptide-bound particles could not be precisely determined.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 53.12 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: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsFractionated into 50 frames in LZW-compressed TIFF format.
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7vfd

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 123726
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationNumber classes: 2 / Avg.num./class: 300000 / Software - Name: cryoSPARC (ver. 4.5.3)
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 / Target criteria: Map-to-model correlation
Output model

PDB-26fe:
Cryo-EM structure of the A17(1-16) peptide-bound N-terminal 17 residue truncated D13 trimer from vaccinia virus

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