9XZJ | pdb_00009xzj

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

PDB DOI: https://doi.org/10.2210/pdb9XZJ/pdb
EM Map EMD-72358: EMDB EMDataResource

Classification: ISOMERASE/DNA
Organism(s): Homo sapiens, synthetic construct
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2025-08-27 Released: 2026-01-28
Deposition Author(s): Mullins, E.A., Schiltz, C.J., Eichman, B.F.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.13 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

F-box helicase 1 reverses replication forks through assembly on the lagging strand template at the fork junction

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.

To be published.

Macromolecule Content

Total Structure Weight: 270.79 kDa
Atom Count: 16,522
Modeled Residue Count: 1,849
Deposited Residue Count: 2,149
Unique protein chains: 4
Unique nucleic acid chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cullin-1	A [auth C]	776	Homo sapiens	Mutation(s): 0 Gene Names: CUL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13616 (Homo sapiens) Explore Q13616 Go to UniProtKB: Q13616
PHAROS: Q13616 GTEx: ENSG00000055130
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13616
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RBX1	B [auth R]	108	Homo sapiens	Mutation(s): 0 Gene Names: RBX1, RNF75, ROC1 EC: 2.3.2.27 (PDB Primary Data), 2.3.2.32 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P62877 (Homo sapiens) Explore P62877 Go to UniProtKB: P62877
PHAROS: P62877 GTEx: ENSG00000100387
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62877
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
F-box DNA helicase 1	C [auth F]	972	Homo sapiens	Mutation(s): 0 Gene Names: FBH1, FBX18, FBXO18 EC: 5.6.2.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFZ0 (Homo sapiens) Explore Q8NFZ0 Go to UniProtKB: Q8NFZ0
PHAROS: Q8NFZ0 GTEx: ENSG00000134452
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8NFZ0
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
S-phase kinase-associated protein 1	D [auth S]	163	Homo sapiens	Mutation(s): 0 Gene Names: SKP1, EMC19, OCP2, SKP1A, TCEB1L
UniProt & NIH Common Fund Data Resources
Find proteins for P63208 (Homo sapiens) Explore P63208 Go to UniProtKB: P63208
PHAROS: P63208 GTEx: ENSG00000113558
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63208
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (45-MER)	E [auth X]	45	synthetic construct
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (5'-D(CPTPGPAPCPGPCPTPTPCPCPAPTPCPGPCPTPGPTPCPTPAP*G)-3')	F [auth A]	23	synthetic construct
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (5'-D(TPCPGPCPTPAPCPCPTPTPCPGPCPAPGPTP*C)-3')	G [auth B]	17	synthetic construct
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Length	Organism	Image
DNA (45-MER)	H [auth Y]	45	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS (Subject of Investigation/LOI) Query on AGS Download Ideal Coordinates CCD File SDF format, chain I [auth F] MOL2 format, chain I [auth F] mmCIF format, chain I [auth F]	I [auth F]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain I [auth F] Interactions & Density Focus chain I [auth F]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain K [auth F] MOL2 format, chain K [auth F] mmCIF format, chain K [auth F]	K [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth F] Interactions & Density Focus chain K [auth F]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth F] MOL2 format, chain J [auth F] mmCIF format, chain J [auth F]	J [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth F] Interactions & Density Focus chain J [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.13 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	Coot
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-01-28

Deposition Author(s):

Mullins, E.A.

Schiltz, C.J.

Eichman, B.F.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM136401
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P01 CA092584