[English] 日本語
Yorodumi
- EMDB-64474: Cryo-EM structure of His6-tagged D13 assembled into scaffold-like... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64474
TitleCryo-EM structure of His6-tagged D13 assembled into scaffold-like particles from vaccinia virus
Map data
Sample
  • Complex: Assembled scaffold-like particle of 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: 2.88 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

-
Structure visualization

Supplemental images

emd_64474.png

Downloads & links

-
Map

FileDownload / File: emd_64474.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 400 pix.
= 418. Å		1.05 Å/pix.
x 400 pix.
= 418. Å		1.05 Å/pix.
x 400 pix.
= 418. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.132
Minimum - Maximum-0.80275375 - 1.3767653
Average (Standard dev.)0.0003958215 (±0.04835587)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 417.99997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_64474_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_64474_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_64474_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Assembled scaffold-like particle of Vaccinia virus D13

EntireName: Assembled scaffold-like particle of Vaccinia virus D13
Components
  • Complex: Assembled scaffold-like particle of Vaccinia virus D13
    • Protein or peptide: Scaffold protein OPG125

-
Supramolecule #1: Assembled scaffold-like particle of Vaccinia virus D13

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

-
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: 65.05084 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSYYHHHHHH DYDIPTTENL YFQGAMNNTI INSLIGGDDS IKRSNVFAVD SQIPTLYMPQ YISLSGVMTN DGPDNQAIAS FEIRDQYIT ALNHLVLSLE LPEVKGMGRF GYVPYVGYKC INHVSISSCN GVIWEIEGEE LYNNCINNTI ALKHSGYSSE L NDISIGLT ...String:
MSYYHHHHHH DYDIPTTENL YFQGAMNNTI INSLIGGDDS IKRSNVFAVD SQIPTLYMPQ YISLSGVMTN DGPDNQAIAS FEIRDQYIT ALNHLVLSLE LPEVKGMGRF GYVPYVGYKC INHVSISSCN GVIWEIEGEE LYNNCINNTI ALKHSGYSSE L NDISIGLT PNDTIKEPST VYVYIKTPFD VEDTFSSLKL SDSKITVTVT FNPVSDIVIR DSSFDFETFN KEFVYVPELS FI GYMVKNV QIKPSFIEKP RRVIGQINQP TATVTEVHAA TSLSVYTKPY YGNTDNKFIS YPGYSQDEKD YIDAYVSRLL DDL VIVSDG PPTGYPESAE IVEVPEDGIV SIQDADVYVK IDNVPDNMSV YLHTNLLMFG TRKNSFIYNI SKKFSAITGT YSDA TKRTI FAHISHSINI IDTSIPVSLW TSQRNVYNGD NRSAESKAKD LFINDPFIKG IDFKNKTDII SRLEVRFGND VLYSE NGPI SRIYNELLTK SNNGTRTLTF NFTPKIFFRP TTITANVSRG KDKLSVRVVY STMDVNHPIY YVQKQLVVVC NDLYKV SYD QGVSITKIMG DNN

UniProtKB: Scaffold protein OPG125

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloride
10.0 mMTris-HClTris(hydroxymethyl)aminomethane hydrochloride
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 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.
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: X
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Wait time: 10sec Blot force: 0 Blot time: 5sec.
DetailsScaffold-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.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 38.6 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: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 42000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsSuper-resolution mode LZW-compressed TIFF format
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3)
Software - details: CTF estimation and correction with PATCH CTF
Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7vfd


Details: PDB model 7VFD was used as a template for initial model generation.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: Local Refinement with Re-centering / Number images used: 722411
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.5.3)
Software - details: Ab initio reconstruction with no reference
Details: Initial angles were assigned randomly as part of CryoSPARC's ab initio reconstruction workflow.
Final angle assignmentType: PROJECTION MATCHING
Projection matching processing - Number reference projections: 100
Projection matching processing - Merit function: 0.8
Projection matching processing - Angular sampling: 1.5 degrees
Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: non-uniform refinement
Final 3D classificationNumber classes: 5 / Avg.num./class: 10000 / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: Heterogenous refinement
Details: 3D classification was performed using CryoSPARC heterogeneous refinement. Most particles converged into a single dominant class.
FSC plot (resolution estimation)

-
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: 173.77 / Target criteria: Map-to-model correlation
Output model

PDB-9usx:
Cryo-EM structure of His6-tagged D13 assembled into scaffold-like particles from vaccinia virus

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more