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- PDB-9pqf: Xray crystal structure of Vientovirus FB Rep endonuclease domain ... -

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Basic information

Entry
Database: PDB / ID: 9pqf
TitleXray crystal structure of Vientovirus FB Rep endonuclease domain 2-114 with Mg2+ ion
ComponentsReplication-associated protein
KeywordsREPLICATION / Endonuclease / 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
MALONATE ION / Replication-associated protein
Similarity search - Component
Biological speciesHuman lung-associated vientovirus FB
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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: PLoS Pathog / Year: 2026
Title: Structures of nucleotide-bound Redondovirus Rep protein link conformation and function.
Authors: Saira Montermoso / Kushol Gupta / Ruth Anne Pumroy / Vera Moiseenkova-Bell / Frederic D Bushman / Gregory D Van Duyne /
Abstract: Circular Rep-encoding single-stranded DNA (CRESS-DNA) virus Rep proteins are multidomain enzymes that mediate viral DNA rolling-circle replication. Reps nick viral DNA to expose a 3' end for ...Circular Rep-encoding single-stranded DNA (CRESS-DNA) virus Rep proteins are multidomain enzymes that mediate viral DNA rolling-circle replication. Reps nick viral DNA to expose a 3' end for polymerase extension, provide an NTP-dependent helicase activity for DNA unwinding, and join nicked ends to form circular viral genomes. Here, we present the first structures of a Rep protein from the Redondoviridae family, a newly discovered family of human-associated CRESS-DNA viruses that replicates within the oral protozoan Entamoeba gingivalis. Using cryo-EM, we characterized the hexameric structures of a Redondovirus Rep helicase bound with ATPγS, representing the initial ATP-bound state, and with ADP, reflecting the protein state after hydrolysis. The ADP state, but not the ATP state of Rep shows a staircase arrangement of DNA-binding loops that plays a central role in current models for SF3 helicase function. Additionally, we determined a head-to-tail dodecameric structure of ATPγS-bound Rep, in which both the helicase and endonuclease domains are ordered. Conservation of residues involved in stabilizing the dodecamer suggest that this assembly may be functionally relevant for many CRESS-DNA viruses. The positioning of endonuclease domains in the Rep hexamer, combined with our biophysical analyses of Rep oligomerization, provide new insights into Rep function during viral replication.
History
DepositionJul 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2026Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replication-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0303
Polymers12,9041
Non-polymers1262
Water88349
1
A: Replication-associated protein
hetero molecules

A: Replication-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0606
Polymers25,8082
Non-polymers2534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area2390 Å2
ΔGint-25 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.944, 62.974, 64.705
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21A-332-

HOH

31A-347-

HOH

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Components

#1: Protein Replication-associated protein / ATP-dependent helicase Rep / RepP


Mass: 12903.830 Da / Num. of mol.: 1 / 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 100 mM ammonium malonate pH 5.8, 200 mM potassium fluoride, 15% w/v PEG 4000, 15% v/v ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 27, 2024 / Details: KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.8→45.13 Å / Num. obs: 9971 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 23.34 Å2 / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.076 / Rrim(I) all: 0.209 / Net I/σ(I): 5.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 1 / Num. unique obs: 475 / CC1/2: 0.816 / Rpim(I) all: 0.171 / Rrim(I) all: 0.466

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Processing

Software
NameVersionClassification
PHENIX1.21-5207refinement
DIALSdev20231129data scaling
DIALSdev20231129data reduction
PHASER2.8.3phasing
PDB_EXTRACT4.3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.13 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 982 9.85 %Random selection
Rwork0.1799 ---
obs0.1836 9970 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.91 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms904 0 8 49 961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007922
X-RAY DIFFRACTIONf_angle_d0.91246
X-RAY DIFFRACTIONf_dihedral_angle_d13.949348
X-RAY DIFFRACTIONf_chiral_restr0.061147
X-RAY DIFFRACTIONf_plane_restr0.006160
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork
1.8-1.890.29215911.40.2461237
1.89-2.010.2786153110.19971239
2.01-2.170.25271369.60.19011275
2.17-2.390.24381309.20.17971281
2.39-2.730.21231067.50.1871311
2.73-3.440.20981409.70.18491296
3.44-45.130.186215810.50.16051349

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