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9xzm

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

Method: ELECTRON MICROSCOPY Dmax: 155.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

F-box DNA helicase 1

Homo sapiens

UniProt Q8NFZ0

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Monomer Protein × 1 DNA 4 PDB declaration: pentameric（5） Consistent with all polymer counts Chain F； UniProt 75–1043 Not recorded DNA (45-MER) × 1 ;DNA (5'-D(*TP*CP*GP*CP*TP*AP*CP*CP*TP*TP*CP*GP*CP*AP*GP*TP*C)-3') ; × 1 DNA (45-MER) × 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') ; × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 10.27 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9XZM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8F5Q Crystal structure of human PCNA in complex with the PIP box of FBH1 Deposited 2022-11-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 56–64（9 aa） Fragment：PIP box (UNP residues 56-64)
Chain D 56–64（9 aa） Fragment：PIP box (UNP residues 56-64)
Chain F 56–64（9 aa） Fragment：PIP box (UNP residues 56-64)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M HEPES, pH 7.5, 0.2 M magnesium chloride, 30% PEG400
Resolution 1.90 Å R-free 0.266
9XZJ Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (consensus structure) Deposited 2025-08-27 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain F 75–1043（969 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
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) Deposited 2025-08-27 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain F 75–1043（969 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FBH1_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain F； PDBConstruct 4–972； UniProt 75–1043

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9xzm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9xzm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9xzm
Deposition date deposition_date2025-08-27
Structure title titleCryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (substrate structure)
Keywords keywordsHelicase, Translocase, Fork remodeler, Fork reversal, Replication fork, DNA binding, ISOMERASE-DNA complex; ISOMERASE/DNA
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier44.59 Å
Radius of gyration Rg (electron density) rg_electron41.68 Å
Forward intensity I(0) i0266850000.00
Molecular weight molecular_weight106750.0 kDa
Excluded volume excluded_volume122900 ų
Envelope volume envelope_volume188260 ų
Hydration-shell volume shell_volume43579 ų
Envelope diameter envelope_diameter163.2 Å
Shell Rg shell_rg39.37 Å
Envelope Rg envelope_rg43.18 Å
Shape Rg shape_rg41.47 Å
Total Rg total_rg42.08 Å
Total atoms total_atoms13586
Residues n_residues719
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax155.0 Å
Rg (real space) rg_real45.02 Å
Rg uncertainty (real space) rg_real_error1.93 Å
I(0) (real space) i0_real2.6680e+08
I(0) uncertainty (real space) i0_real_error5.1520e+06
Rg (reciprocal space) rg_reciprocal44.59 Å
I(0) (reciprocal space) i0_reciprocal266700000.0000
Solution quality estimate total_estimate0.8368
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary44.3 Å
Skewness Skewness skewness0.502
Kurtosis Kurtosis kurtosis-0.305
Angular range angular_range— – 0.1750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7379000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.766; Smooth: 0.636
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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8. Citations (1)

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9. Files and Curves (10)