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

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Entry
Database: PDB / ID: 9xzj
TitleCryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (consensus structure)
Components
  • (DNA (45-MER)) x 2
  • Cullin-1
  • 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')
  • E3 ubiquitin-protein ligase RBX1
  • F-box DNA helicase 1
  • S-phase kinase-associated protein 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 / regulation of xenophagy / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / synaptic assembly at neuromuscular junction / regulation of cell cycle process / neural crest cell differentiation / DNA translocase activity / regulation of BMP signaling pathway / PcG protein complex ...response to intra-S DNA damage checkpoint signaling / regulation of xenophagy / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / synaptic assembly at neuromuscular junction / regulation of cell cycle process / neural crest cell differentiation / DNA translocase activity / regulation of BMP signaling pathway / PcG protein complex / negative regulation of beige fat cell differentiation / regulation of mitophagy / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / regulation of centrosome duplication / cullin-RING ubiquitin ligase complex / maintenance of protein location in nucleus / Cul7-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / cellular response to chemical stress / regulation of TOR signaling / positive regulation of protein autoubiquitination / RNA polymerase II transcription initiation surveillance / protein neddylation / DNA catabolic process / ubiquitin ligase activator activity / regulation of DNA damage checkpoint / NEDD8 ligase activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of response to oxidative stress / protein K27-linked ubiquitination / VCB complex / Cul5-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / negative regulation of mitophagy / Prolactin receptor signaling / limb development / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / DNA 3'-5' helicase / centrosome duplication / replication fork processing / cilium assembly / protein monoubiquitination / 3'-5' DNA helicase activity / cullin family protein binding / negative regulation of double-strand break repair via homologous recombination / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / ubiquitin-like ligase-substrate adaptor activity / signal transduction in response to DNA damage / Nuclear events stimulated by ALK signaling in cancer / protein K48-linked ubiquitination / negative regulation of insulin receptor signaling pathway / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / animal organ morphogenesis / intrinsic apoptotic signaling pathway / transcription-coupled nucleotide-excision repair / post-translational protein modification / regulation of mitotic cell cycle / DNA helicase activity / molecular function activator activity / negative regulation of canonical NF-kappaB signal transduction / cellular response to amino acid stimulus / site of DNA damage / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / T cell activation / G1/S transition of mitotic cell cycle / negative regulation of canonical Wnt signaling pathway / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of DVL / cell population proliferation / Degradation of CRY and PER proteins / Activation of NF-kappaB in B cells / Iron uptake and transport / Degradation of GLI1 by the proteasome / Recognition of DNA damage by PCNA-containing replication complex / double-strand break repair via homologous recombination / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / RING-type E3 ubiquitin transferase / positive regulation of protein phosphorylation / regulation of circadian rhythm / Hedgehog 'on' state / beta-catenin binding / Vif-mediated degradation of APOBEC3G / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome
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 / SKP1 component, dimerisation / S-phase kinase-associated protein 1 ...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 / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / : / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin, N-terminal / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin alpha solenoid domain / Cullin / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / E3 ubiquitin-protein ligase RBX1 / S-phase kinase-associated protein 1 / Cullin-1 / F-box DNA helicase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 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
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Cullin-1
R: E3 ubiquitin-protein ligase RBX1
F: F-box DNA helicase 1
S: S-phase kinase-associated protein 1
X: 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')
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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,79511
Polymers270,1828
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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Protein , 4 types, 4 molecules CRFS

#1: Protein Cullin-1 / CUL-1


Mass: 89800.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13616
#2: Protein E3 ubiquitin-protein ligase RBX1 / E3 ubiquitin-protein transferase RBX1 / Protein ZYP / RING finger protein 75 / RING-box protein 1 / ...E3 ubiquitin-protein transferase RBX1 / Protein ZYP / RING finger protein 75 / RING-box protein 1 / Rbx1 / Regulator of cullins 1 / ROC1


Mass: 12289.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBX1, RNF75, ROC1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P62877, RING-type E3 ubiquitin transferase, cullin-RING-type E3 NEDD8 transferase
#3: 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
#4: Protein S-phase kinase-associated protein 1 / SKP1 / Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of ...SKP1 / Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti protein II / OCP-II / RNA polymerase II elongation factor-like protein / SIII / Transcription elongation factor B polypeptide 1-like / p19skp1


Mass: 18679.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63208

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DNA chain , 4 types, 4 molecules XABY

#5: DNA chain DNA (45-MER)


Mass: 13921.935 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: 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)
#7: 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)
#8: DNA chain DNA (45-MER)


Mass: 13872.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 3 molecules

#9: 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#10: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

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

Component
IDNameTypeEntity IDParent-IDSource
1Heterotetrameric SCF-FBH1 protein complex bound to a 3-way DNA forkCOMPLEX#1-#80MULTIPLE SOURCES
2Heterotetrameric SCF-FBH1 protein complexCOMPLEX#1-#41RECOMBINANT
33-way DNA forkCOMPLEX#5-#81NATURAL
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
IDNameCategory
1Topazparticle selection
2cryoSPARCparticle selection
3EPUimage acquisition
5cryoSPARCCTF correction
8UCSF ChimeraXmodel fitting
10cryoSPARCinitial Euler assignment
11RELIONfinal Euler assignment
13RELION3D reconstruction
14Cootmodel refinement
15PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 829277 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingAccession code: D_1000299442 / Details: Partial model from focused refinement / Source name: Other / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00417100
ELECTRON MICROSCOPYf_angle_d0.48123655
ELECTRON MICROSCOPYf_dihedral_angle_d19.2196707
ELECTRON MICROSCOPYf_chiral_restr0.0372660
ELECTRON MICROSCOPYf_plane_restr0.0032577

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