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- EMDB-71788: Cryo-EM structure of ATPgammaS-bound Vientovirus FB Rep double he... -

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Basic information

Entry
Database: EMDB / ID: EMD-71788
TitleCryo-EM structure of ATPgammaS-bound Vientovirus FB Rep double hexamer with C1 symmetry
Map datasharpened map of 3D auto-refined map from Relion (primary map)
Sample
  • Complex: ATPgammaS-bound Vientovirus FB Rep double hexamer with C1 symmetry
    • Protein or peptide: Replication-associated protein
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
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: 3.32 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 23, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71788.png

Downloads & links

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Map

FileDownload / File: emd_71788.map.gz / Format: CCP4 / Size: 325 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 440 pix.
= 369.6 Å		0.84 Å/pix.
x 440 pix.
= 369.6 Å		0.84 Å/pix.
x 440 pix.
= 369.6 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: 5.4
Minimum - Maximum-16.866641999999999 - 35.349170000000001
Average (Standard dev.)0.000000000002556 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 369.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: 3D auto-refined map from Relion (raw map)

Fileemd_71788_additional_1.map
Annotation3D auto-refined map from Relion (raw map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_71788_half_map_1.map
Annotationhalf map 1 from 3D auto-refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_71788_half_map_2.map
Annotationhalf map 2 from 3D auto-refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ATPgammaS-bound Vientovirus FB Rep double hexamer with C1 symmetry

EntireName: ATPgammaS-bound Vientovirus FB Rep double hexamer with C1 symmetry
Components
  • Complex: ATPgammaS-bound Vientovirus FB Rep double hexamer with C1 symmetry
    • Protein or peptide: Replication-associated protein
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Supramolecule #1: ATPgammaS-bound Vientovirus FB Rep double hexamer with C1 symmetry

SupramoleculeName: ATPgammaS-bound Vientovirus FB Rep double hexamer with C1 symmetry
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Vientovirus FB

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Macromolecule #1: Replication-associated protein

MacromoleculeName: Replication-associated protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
EC number: Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
Source (natural)Organism: Human lung-associated vientovirus FB
Molecular weightTheoretical: 37.991738 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SLRLQNKNLY LTYLDTEERI FSELILITEL AERLDKYGVK YAIACKEVAP STGTVHYHCL ICCENVISTR NGKELLTIEN IMPHVGRIQ NNLVNIVNYI KKDGSFAEVN KENAPKKKEM EKREKAELMI NGNLRELFME GVLGAIDIIR AEKLRNIFQV Q APADKYQK ...String:
SLRLQNKNLY LTYLDTEERI FSELILITEL AERLDKYGVK YAIACKEVAP STGTVHYHCL ICCENVISTR NGKELLTIEN IMPHVGRIQ NNLVNIVNYI KKDGSFAEVN KENAPKKKEM EKREKAELMI NGNLRELFME GVLGAIDIIR AEKLRNIFQV Q APADKYQK KLILWFKGET GEGKTKTAVD IAERFFNGEY WMSNETLKWF DGYRGQPVAI IDDFRKSMLT EWSFLLRLLD GY NLIVQVK GGFVKWQPKV IIVTSPASPS EAFQWVNKEG EIIEWDKQVQ LTRRLTYEDE EQIYNFPLWN QDQLKLENTI RKY LGLAPM

UniProtKB: Replication-associated protein

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 18 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 12 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

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

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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

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

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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

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Image processing

Particle selectionNumber selected: 138554
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: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0-beta) / Number images used: 28346
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

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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 manual building and flexible fitting in coot
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 49.35
Output model

PDB-9pqq:
Cryo-EM structure of ATPgammaS-bound Vientovirus FB Rep double hexamer with C1 symmetry

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