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- PDB-9xzm: Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiq... -

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Basic information

Entry
Database: PDB / ID: 9xzm
TitleCryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (substrate structure)
Components
  • (DNA (45-MER)) x 2
  • DNA (5'-D(*CP*TP*GP*AP*CP*GP*CP*TP*TP*CP*CP*AP*TP*CP*GP*CP*TP*GP*TP*CP*TP*AP*G)-3')
  • DNA (5'-D(*TP*CP*GP*CP*TP*AP*CP*CP*TP*TP*CP*GP*CP*AP*GP*TP*C)-3')
  • F-box DNA helicase 1
KeywordsISOMERASE/DNA / Helicase / Translocase / Fork remodeler / Fork reversal / Replication fork / DNA binding / ISOMERASE-DNA complex
Function / homology
Function and homology information


response to intra-S DNA damage checkpoint signaling / DNA translocase activity / DNA catabolic process / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / SCF ubiquitin ligase complex / DNA 3'-5' helicase / 3'-5' DNA helicase activity / replication fork processing / negative regulation of double-strand break repair via homologous recombination / DNA helicase activity ...response to intra-S DNA damage checkpoint signaling / DNA translocase activity / DNA catabolic process / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / SCF ubiquitin ligase complex / DNA 3'-5' helicase / 3'-5' DNA helicase activity / replication fork processing / negative regulation of double-strand break repair via homologous recombination / DNA helicase activity / double-strand break repair via homologous recombination / positive regulation of protein phosphorylation / single-stranded DNA binding / double-stranded DNA binding / protein ubiquitination / DNA repair / DNA damage response / chromatin / ATP hydrolysis activity / ATP binding / nucleus
Similarity search - Function
UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / F-box domain profile. / F-box-like / F-box-like domain superfamily / F-box domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / F-box DNA helicase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.27 Å
AuthorsMullins, E.A. / Schiltz, C.J. / Eichman, B.F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM136401 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA092584 United States
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for fork reversal and RAD51 regulation by the SCF ubiquitin ligase complex of F-box helicase 1.
Authors: Briana H Greer / Javier Mendia-Garcia / Elwood A Mullins / Emma M Peacock / Sander K Haigh / Carl J Schiltz / Clara Aicart-Ramos / Miaw-Sheue Tsai / David Cortez / Fernando Moreno-Herrero / Brandt F Eichman /
Abstract: Replication fork reversal helps maintain genomic stability during replication stress. F-box helicase 1 (FBH1) catalyzes fork reversal and is an SCF (SKP-CUL1-F-box) E3 ubiquitin ligase that limits ...Replication fork reversal helps maintain genomic stability during replication stress. F-box helicase 1 (FBH1) catalyzes fork reversal and is an SCF (SKP-CUL1-F-box) E3 ubiquitin ligase that limits RAD51 association with chromatin. Here, we show that preferential binding of SCF to the lagging strand template at DNA fork structures stimulates helicase activity and is required for fork reversal. A cryo-EM structure of SCF bound to DNA representing a stalled fork reveals an intimate interaction between FBH1 and the fork junction. Disruption of this interface severely curtails fork reversal in vitro and replication progression in cells, providing a model for how ssDNA translocation by FBH1 facilitates annealing of parental DNA by a fundamentally different mechanism than the fork remodelers SMARCAL, HLTF, and ZRANB3. The structure provides a model for SCF disassembly of RAD51 filaments through translocation and ubiquitination, and implies that RAD51 is associated with the lagging strand at stalled forks.
History
DepositionAug 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.1Mar 11, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: DNA (45-MER)
B: DNA (5'-D(*TP*CP*GP*CP*TP*AP*CP*CP*TP*TP*CP*GP*CP*AP*GP*TP*C)-3')
Y: DNA (45-MER)
A: DNA (5'-D(*CP*TP*GP*AP*CP*GP*CP*TP*TP*CP*CP*AP*TP*CP*GP*CP*TP*GP*TP*CP*TP*AP*G)-3')
F: F-box DNA helicase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,0248
Polymers149,4115
Non-polymers6133
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA chain , 4 types, 4 molecules XBYA

#1: DNA chain DNA (45-MER)


Mass: 13921.935 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*TP*CP*GP*CP*TP*AP*CP*CP*TP*TP*CP*GP*CP*AP*GP*TP*C)-3')


Mass: 5114.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (45-MER)


Mass: 13872.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*CP*TP*GP*AP*CP*GP*CP*TP*TP*CP*CP*AP*TP*CP*GP*CP*TP*GP*TP*CP*TP*AP*G)-3')


Mass: 6983.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 1 molecules F

#5: Protein F-box DNA helicase 1 / hFBH1 / DNA 3'-5' helicase 1 / F-box only protein 18


Mass: 109518.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBH1, FBX18, FBXO18 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8NFZ0, DNA 3'-5' helicase

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Non-polymers , 3 types, 3 molecules

#6: 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.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
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

Component
IDNameTypeEntity IDParent-IDSource
1Heterotetrameric SCF-FBH1 protein complex bound to a 3-way DNA forkCOMPLEX#1-#50MULTIPLE SOURCES
2Heterotetrameric SCF-FBH1 protein complexCOMPLEX#51RECOMBINANT
33-way DNA forkCOMPLEX#1-#41NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Homo sapiens (human)9606
43synthetic construct (others)32630
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1151.8GATAN K3 BIOQUANTUM (6k x 4k)
2154.5GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2cryoSPARCparticle selection
3PHENIX1.21.2_5419:model refinement
6cryoSPARCCTF correction
11cryoSPARCinitial Euler assignment
12RELIONfinal Euler assignment
13RELIONclassification
14RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 10.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7718 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model building
ID 3D fitting-IDAccession codeDetailsInitial refinement model-IDSource nameType
11D_1000299443Partial model from focused refinement1Otherexperimental model
21Ideal B-form DNA generated by CootOtherin silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047747
ELECTRON MICROSCOPYf_angle_d0.57111012
ELECTRON MICROSCOPYf_dihedral_angle_d26.3513168
ELECTRON MICROSCOPYf_chiral_restr0.0421240
ELECTRON MICROSCOPYf_plane_restr0.004959

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