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- PDB-9pqm: Cryo-EM structure of ATPgammaS-bound Vientovirus FB Rep hexamer w... -

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Basic information

Entry
Database: PDB / ID: 9pqm
TitleCryo-EM structure of ATPgammaS-bound Vientovirus FB Rep hexamer with endonuclease domain density
ComponentsReplication-associated protein
KeywordsREPLICATION / SF3 helicase / DNA binding protein / 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Replication-associated protein
Similarity search - Component
Biological speciesHuman lung-associated vientovirus FB
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsMontermoso, S. / Gupta, K. / Pumroy, R.A. / Moiseenkova-Bell, V. / Bushman, F.D. / Van Duyne, G.D.
Funding support United States, 6items
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, R.A. / Moiseenkova-Bell, V. / Bushman, F.D. / Van Duyne, G.D.
History
DepositionJul 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 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: Replication-associated protein
B: Replication-associated protein
C: Replication-associated protein
D: Replication-associated protein
E: Replication-associated protein
F: Replication-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,45118
Polymers146,1666
Non-polymers3,28512
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
Replication-associated protein / ATP-dependent helicase Rep / RepP


Mass: 24360.986 Da / Num. of mol.: 6 / Mutation: T2S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human lung-associated vientovirus FB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4D6K5Y8
#2: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: ATPgammaS-bound Vientovirus FB Rep with endonuclease domain density
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.243 MDa / Experimental value: YES
Source (natural)Organism: Vientovirus FB
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
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
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acidHEPES1
2300 mMsodium chlorideNaCl1
30.1 mMtris(2-carboxyethyl)phosphineTCEP1
42.5 %glycerolC3H8O31
55 mMmagnesium chlorideMgCl21
65 mMAdenosine 5'-O-(3-thiotriphosphateC10H16N5O12P3S1
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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 defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingAverage exposure time: 1.42 sec. / Electron dose: 41.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5605

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.5.3particle selectionBlob picking for initial particle picking, then template-based picking for whole dataset.
4cryoSPARC4.5.3CTF correctionPatch CTF estimation
5RELION5.0-betaCTF correctionCTFFind-4.1.14
8UCSF ChimeraX1.9model fitting
9Coot0.9.8.96model fitting
11cryoSPARC4.5.3initial Euler assignmentnonuniform refinement
12RELION5.0-betafinal Euler assignment3D auto-refinement
13RELION5.0-betaclassification
14RELION5.0-beta3D reconstruction
15PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5286720
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75338 / Symmetry type: POINT
Atomic model buildingB value: 80.79 / Protocol: RIGID BODY FIT / Space: REAL
Details: Initial rigid body fitting was done in ChimeraX followed by flexible fitting in coot
Atomic model buildingPDB-ID: 9PQJ

9pqj


Accession code: 9PQJ / Chain residue range: 121-327 / Pdb chain residue range: 121-327 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00610758
ELECTRON MICROSCOPYf_angle_d0.60514562
ELECTRON MICROSCOPYf_dihedral_angle_d12.2131464
ELECTRON MICROSCOPYf_chiral_restr0.0451536
ELECTRON MICROSCOPYf_plane_restr0.0051818

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