[English] 日本語
Yorodumi
- EMDB-71786: Cryo-EM structure of ATPgammaS-bound Vientovirus FB Rep hexamer w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71786
TitleCryo-EM structure of ATPgammaS-bound Vientovirus FB Rep hexamer with endonuclease domain density
Map datasharpened map of 3D auto-refined map from Relion (primary map)
Sample
  • Complex: ATPgammaS-bound Vientovirus FB Rep with endonuclease domain density
    • Protein or peptide: Replication-associated protein
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsSF3 helicase / DNA binding protein / Replication / Viral protein
Function / homology
Function and homology information


nucleotidyltransferase activity / endonuclease activity / DNA replication / RNA helicase activity / hydrolase activity / host cell nucleus / DNA binding / RNA binding / ATP binding / metal ion binding
Similarity search - Function
: / CRESS-DNA virus replication initiator protein (Rep) endonuclease domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Replication-associated protein
Similarity search - Component
Biological speciesVientovirus FB / Human lung-associated vientovirus FB
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsMontermoso S / Gupta K / Pumroy RA / Moiseenkova-Bell V / Bushman FD / Van Duyne GD
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P30AI045008 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM108751 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI007632 United States
Department of Health & Human Services (HHS)S10OD018483 United States
National Science Foundation (NSF, United States)DMR2342336 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1P30GM124166 United States
CitationJournal: To Be Published
Title: Structures of nucleotide-bound Redondovirus Rep protein link conformation and function
Authors: Montermoso S / Gupta K / Pumroy RA / Moiseenkova-Bell V / Bushman FD / Van Duyne GD
History
DepositionJul 22, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_71786.png

Downloads & links

-
Map

FileDownload / File: emd_71786.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map of 3D auto-refined map from Relion (primary map)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 288 pix.
= 241.92 Å		0.84 Å/pix.
x 288 pix.
= 241.92 Å		0.84 Å/pix.
x 288 pix.
= 241.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.4
Minimum - Maximum-17.450168999999999 - 33.184109999999997
Average (Standard dev.)-0.000000000000773 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 241.92 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: 3D auto-refined map from Relion

Fileemd_71786_additional_1.map
Annotation3D auto-refined map from Relion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 2 from 3D auto-refinement in Relion

Fileemd_71786_half_map_1.map
Annotationhalf map 2 from 3D auto-refinement in Relion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 1 from 3D auto-refinement in Relion

Fileemd_71786_half_map_2.map
Annotationhalf map 1 from 3D auto-refinement in Relion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ATPgammaS-bound Vientovirus FB Rep with endonuclease domain density

EntireName: ATPgammaS-bound Vientovirus FB Rep with endonuclease domain density
Components
  • Complex: ATPgammaS-bound Vientovirus FB Rep with endonuclease domain density
    • Protein or peptide: Replication-associated protein
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: ATPgammaS-bound Vientovirus FB Rep with endonuclease domain density

SupramoleculeName: ATPgammaS-bound Vientovirus FB Rep with endonuclease domain density
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Vientovirus FB
Molecular weightTheoretical: 243 KDa

-
Macromolecule #1: Replication-associated protein

MacromoleculeName: Replication-associated protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human lung-associated vientovirus FB
Molecular weightTheoretical: 24.360986 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: EKREKAELMI NGNLRELFME GVLGAIDIIR AEKLRNIFQV QAPADKYQKK LILWFKGETG EGKTKTAVDI AERFFNGEYW MSNETLKWF DGYRGQPVAI IDDFRKSMLT EWSFLLRLLD GYNLIVQVKG GFVKWQPKVI IVTSPASPSE AFQWVNKEGE I IEWDKQVQ ...String:
EKREKAELMI NGNLRELFME GVLGAIDIIR AEKLRNIFQV QAPADKYQKK LILWFKGETG EGKTKTAVDI AERFFNGEYW MSNETLKWF DGYRGQPVAI IDDFRKSMLT EWSFLLRLLD GYNLIVQVKG GFVKWQPKVI IVTSPASPSE AFQWVNKEGE I IEWDKQVQ LTRRLTYEDE EQIYNFPLWN QDQLKLENTI RKYLGLAPM

UniProtKB: Replication-associated protein

-
Macromolecule #2: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 6 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

-
Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid
300.0 mMNaClsodium chloride
0.1 mMTCEPtris(2-carboxyethyl)phosphine
2.5 %C3H8O3glycerol
5.0 mMMgCl2magnesium chloride
5.0 mMC10H16N5O12P3SAdenosine 5'-O-(3-thiotriphosphate

Details: 20 mM HEPES-NaOH pH 7.5, 300 mM NaCl, 0.1 mM TCEP, 2.5% glycerol added with 5 mM MgCl2 and 5mM ATPgammaS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.03 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5605 / Average exposure time: 1.42 sec. / Average electron dose: 41.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 5286720
CTF correctionSoftware:
Namedetails
cryoSPARC (ver. 4.5.3)Patch CTF estimation
RELION (ver. 5.0-beta)CTFFind-4.1.14

Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0-beta) / Number images used: 75338
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: nonuniform refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0-beta) / Software - details: 3D auto-refinement
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 5.0-beta)

-
Atomic model buiding 1

Initial modelPDB ID:

9pqj


Chain - Residue range: 121-327 / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsInitial rigid body fitting was done in ChimeraX followed by flexible fitting in coot
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 80.79
Output model

PDB-9pqm:
Cryo-EM structure of ATPgammaS-bound Vientovirus FB Rep hexamer with endonuclease domain density

+
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