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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: To Be Published
Title: F-box helicase 1 reverses replication forks through assembly on the lagging strand template at the fork junction
Authors: Greer, B.H. / Mendia Garcia, J. / Mullins, E.A. / Peacock, E.M. / Haigh, S. / Schiltz, C.J. / Tsai, M.-S. / Cortez, D. / Moreno-Herrero, F. / Eichman, B.F.
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
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 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
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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