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- EMDB-72361: Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiq... -

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Basic information

Entry
Database: EMDB / ID: EMD-72361
TitleCryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (body structure)
Map dataFull map
Sample
  • Complex: Heterotetrameric SCF-FBH1 protein complex bound to a 3-way DNA fork
    • Complex: Heterotetrameric SCF-FBH1 protein complex
      • Protein or peptide: Cullin-1
      • Protein or peptide: F-box DNA helicase 1
      • Protein or peptide: S-phase kinase-associated protein 1
    • Complex: 3-way DNA fork
      • DNA: DNA (45-MER)
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsHelicase / 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 / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / PcG protein complex / DNA translocase activity / positive regulation of ubiquitin protein ligase activity / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling ...response to intra-S DNA damage checkpoint signaling / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / PcG protein complex / DNA translocase activity / positive regulation of ubiquitin protein ligase activity / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / DNA catabolic process / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / SCF ubiquitin ligase complex / DNA 3'-5' helicase / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / 3'-5' DNA helicase activity / Prolactin receptor signaling / ubiquitin ligase complex scaffold activity / replication fork processing / cullin family protein binding / protein monoubiquitination / negative regulation of double-strand break repair via homologous recombination / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / intrinsic apoptotic signaling pathway / DNA helicase activity / molecular function activator activity / animal organ morphogenesis / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / G1/S transition of mitotic cell cycle / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / double-strand break repair via homologous recombination / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / beta-catenin binding / Degradation of beta-catenin by the destruction complex / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Interleukin-1 signaling / protein polyubiquitination / Orc1 removal from chromatin / positive regulation of protein phosphorylation / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / : / Regulation of PLK1 Activity at G2/M Transition / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / single-stranded DNA binding / Neddylation / double-stranded DNA binding / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / cell population proliferation / protein ubiquitination / chromatin remodeling / protein domain specific binding / DNA repair / DNA damage response / ubiquitin protein ligase binding / centrosome / chromatin / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
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 / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin alpha solenoid domain / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
S-phase kinase-associated protein 1 / Cullin-1 / F-box DNA helicase 1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsMullins EA / Schiltz CJ / Eichman BF
Funding support United States, 2 items
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 BH / Mendia Garcia J / Mullins EA / Peacock EM / Haigh S / Schiltz CJ / Tsai M-S / Cortez D / Moreno-Herrero F / Eichman BF
History
DepositionAug 27, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72361.png

Downloads & links

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Map

FileDownload / File: emd_72361.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 540 pix.
= 441.72 Å		0.82 Å/pix.
x 540 pix.
= 441.72 Å		0.82 Å/pix.
x 540 pix.
= 441.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.818 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00408
Minimum - Maximum-0.008483055 - 0.024979625
Average (Standard dev.)0.0000031816949 (±0.0003296796)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 441.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72361_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_72361_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_72361_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_72361_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Heterotetrameric SCF-FBH1 protein complex bound to a 3-way DNA fork

EntireName: Heterotetrameric SCF-FBH1 protein complex bound to a 3-way DNA fork
Components
  • Complex: Heterotetrameric SCF-FBH1 protein complex bound to a 3-way DNA fork
    • Complex: Heterotetrameric SCF-FBH1 protein complex
      • Protein or peptide: Cullin-1
      • Protein or peptide: F-box DNA helicase 1
      • Protein or peptide: S-phase kinase-associated protein 1
    • Complex: 3-way DNA fork
      • DNA: DNA (45-MER)
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Heterotetrameric SCF-FBH1 protein complex bound to a 3-way DNA fork

SupramoleculeName: Heterotetrameric SCF-FBH1 protein complex bound to a 3-way DNA fork
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: Heterotetrameric SCF-FBH1 protein complex

SupramoleculeName: Heterotetrameric SCF-FBH1 protein complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: 3-way DNA fork

SupramoleculeName: 3-way DNA fork / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Cullin-1

MacromoleculeName: Cullin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.800305 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSSTRSQNPH GLKQIGLDQI WDDLRAGIQQ VYTRQSMAKS RYMELYTHVY NYCTSVHQSN QARGAGVPPS KSKKGQTPGG AQFVGLELY KRLKEFLKNY LTNLLKDGED LMDESVLKFY TQQWEDYRFS SKVLNGICAY LNRHWVRREC DEGRKGIYEI Y SLALVTWR ...String:
MSSTRSQNPH GLKQIGLDQI WDDLRAGIQQ VYTRQSMAKS RYMELYTHVY NYCTSVHQSN QARGAGVPPS KSKKGQTPGG AQFVGLELY KRLKEFLKNY LTNLLKDGED LMDESVLKFY TQQWEDYRFS SKVLNGICAY LNRHWVRREC DEGRKGIYEI Y SLALVTWR DCLFRPLNKQ VTNAVLKLIE KERNGETINT RLISGVVQSY VELGLNEDDA FAKGPTLTVY KESFESQFLA DT ERFYTRE STEFLQQNPV TEYMKKAEAR LLEEQRRVQV YLHESTQDEL ARKCEQVLIE KHLEIFHTEF QNLLDADKNE DLG RMYNLV SRIQDGLGEL KKLLETHIHN QGLAAIEKCG EAALNDPKMY VQTVLDVHKK YNALVMSAFN NDAGFVAALD KACG RFINN NAVTKMAQSS SKSPELLARY CDSLLKKSSK NPEEAELEDT LNQVMVVFKY IEDKDVFQKF YAKMLAKRLV HQNSA SDDA EASMISKLKQ ACGFEYTSKL QRMFQDIGVS KDLNEQFKKH LTNSEPLDLD FSIQVLSSGS WPFQQSCTFA LPSELE RSY QRFTAFYASR HSGRKLTWLY QLSKGELVTN CFKNRYTLQA STFQMAILLQ YNTEDAYTVQ QLTDSTQIKM DILAQVL QI LLKSKLLVLE DENANVDEVE LKPDTLIKLY LGYKNKKLRV NINVPMETEQ KQEQETTHKN IEEDRKLLIQ AAIVRIMK M RKVLKHQQLL GEVLTQLSSR FKPRVPVIKK CIDILIEKEY LERVDGEKDT YSYLA

UniProtKB: Cullin-1

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Macromolecule #2: F-box DNA helicase 1

MacromoleculeName: F-box DNA helicase 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA 3'-5' helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 109.518734 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SNAMAKSNSV GQDSCQDSEG DMIFPAESSC ALPQEGSAGP GSPGSAPPSR KRSWSSEEES NQATGTSRWD GVSKKAPRHH LSVPCTRPR EARQEAEDST SRLSAESGET DQDAGDVGPD PIPDSYYGLL GTLPCQEALS HICSLPSEVL RHVFAFLPVE D LYWNLSLV ...String:
SNAMAKSNSV GQDSCQDSEG DMIFPAESSC ALPQEGSAGP GSPGSAPPSR KRSWSSEEES NQATGTSRWD GVSKKAPRHH LSVPCTRPR EARQEAEDST SRLSAESGET DQDAGDVGPD PIPDSYYGLL GTLPCQEALS HICSLPSEVL RHVFAFLPVE D LYWNLSLV CHLWREIISD PLFIPWKKLY HRYLMNEEQA VSKVDGILSN CGIEKESDLC VLNLIRYTAT TKCSPSVDPE RV LWSLRDH PLLPEAEACV RQHLPDLYAA AGGVNIWALV AAVVLLSSSV NDIQRLLFCL RRPSSTVTMP DVTETLYCIA VLL YAMREK GINISNRIHY NIFYCLYLQE NSCTQATKVK EEPSVWPGKK TIQLTHEQQL ILNHKMEPLQ VVKIMAFAGT GKTS TLVKY AEKWSQSRFL YVTFNKSIAK QAERVFPSNV ICKTFHSMAY GHIGRKYQSK KKLNLFKLTP FMVNSVLAEG KGGFI RAKL VCKTLENFFA SADEELTIDH VPIWCKNSQG QRVMVEQSEK LNGVLEASRL WDNMRKLGEC TEEAHQMTHD GYLKLW QLS KPSLASFDAI FVDEAQDCTP AIMNIVLSQP CGKIFVGDPH QQIYTFRGAV NALFTVPHTH VFYLTQSFRF GVEIAYV GA TILDVCKRVR KKTLVGGNHQ SGIRGDAKGQ VALLSRTNAN VFDEAVRVTE GEFPSRIHLI GGIKSFGLDR IIDIWILL Q PEEERRKQNL VIKDKFIRRW VHKEGFSGFK RYVTAAEDKE LEAKIAVVEK YNIRIPELVQ RIEKCHIEDL DFAEYILGT VHKAKGLEFD TVHVLDDFVK VPCARHNLPQ LPHFRVESFS EDEWNLLYVA VTRAKKRLIM TKSLENILTL AGEYFLQAEL TSNVLKTGV VRCCVGQCNN AIPVDTVLTM KKLPITYSNR KENKGGYLCH SCAEQRIGPL AFLTASPEQV RAMERTVENI V LPRHEALL FLVF

UniProtKB: F-box DNA helicase 1

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Macromolecule #3: S-phase kinase-associated protein 1

MacromoleculeName: S-phase kinase-associated protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.679965 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MPSIKLQSSD GEIFEVDVEI AKQSVTIKTM LEDLGMDDEG DDDPVPLPNV NAAILKKVIQ WCTHHKDDPP PPEDDENKEK RTDDIPVWD QEFLKVDQGT LFELILAANY LDIKGLLDVT CKTVANMIKG KTPEEIRKTF NIKNDFTEEE EAQVRKENQW C EEK

UniProtKB: S-phase kinase-associated protein 1

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Macromolecule #4: DNA (45-MER)

MacromoleculeName: DNA (45-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.921935 KDa
SequenceString:
(DG)(DA)(DC)(DT)(DG)(DC)(DG)(DA)(DA)(DG) (DG)(DT)(DA)(DG)(DC)(DG)(DA)(DC)(DA)(DG) (DA)(DT)(DC)(DC)(DC)(DC)(DT)(DG)(DA) (DC)(DG)(DA)(DA)(DC)(DT)(DG)(DA)(DG)(DT) (DC) (DC)(DT)(DG)(DA)(DG)

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Macromolecule #5: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 1 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #0 - Average electron dose: 51.8 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #1 - Average electron dose: 54.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab initio reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 181442
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1ldk


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9xzl:
Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (body structure)

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