9XZL: F-box helicase 1

Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (body structure). Determined by electron microscopy at 3.0 Å resolution. Released 28 Jan 2026.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 10,111
Mol. weight: 232.53 kDa
Ligands: ZN, MG, AGS
Released: 28 Jan 2026

Explore 9XZL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9XZL contains 86 α-helices and 29 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain C: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	17-32	16
α-helix	39-53	15
α-helix	78-107	30
α-helix	112-136	25
α-helix	138-140	3
α-helix	141-145	5
α-helix	146-151	6
α-helix	159-167	9
α-helix	168-172	5
α-helix	173-192	20
α-helix	198-211	14
α-helix	226-228	3
α-helix	229-233	5
α-helix	234-254	21
α-helix	257-278	22
α-helix	283-295	13
α-helix	297-299	3

Chain F: 59 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	138-140	3
α-helix	143-150	8
α-helix	155-160	6
α-helix	162-164	3
α-helix	167-174	8
α-helix	180-189	10
α-helix	193-205	13
α-helix	215-226	12
α-helix	234-241	8
α-helix	247-257	11
α-helix	259-262	4
α-helix	270-280	11
α-helix	284-294	11
α-helix	297-299	3
α-helix	303-323	21
α-helix	329-343	15
α-helix	369-376	8
β-strand	384-388	5	1
α-helix	395-405	11
β-strand	411-415	5	1
α-helix	418-427	10
β-strand	432-436	5	1
α-helix	437-441	5
α-helix	442-446	5
α-helix	447-451	5
β-strand	455	1	2
α-helix	462-468	7
α-helix	470	1
α-helix	476-491	16
α-helix	499-501	3
β-strand	505-507	3	3
β-strand	513-515	3	3
α-helix	516-517	2
α-helix	518-536	19
α-helix	544-546	3
β-strand	548	1	2
α-helix	550-559	10
β-strand	569-573	5	1
α-helix	575-577	3
α-helix	580-587	8
β-strand	592-597	6	1
α-helix	599-601	3
α-helix	605-607	3
α-helix	612-615	4
β-strand	620-623	4	1
β-strand	626	1	4
α-helix	632-646	15
β-strand	654	1	4
β-strand	661	1	5
β-strand	670-674	5	5
α-helix	677-688	12
α-helix	693-695	3
β-strand	696-698	3	5
α-helix	707-717	11
α-helix	720-726	7
α-helix	733-737	5
α-helix	744-754	11
α-helix	757-769	13
α-helix	770-772	3
α-helix	773-783	11
β-strand	784	1	5
α-helix	788-790	3
β-strand	793-797	5	5
α-helix	798-801	4
β-strand	806-811	6	5
α-helix	816-818	3
α-helix	822-827	6
α-helix	833-835	3
α-helix	838-849	12
β-strand	851-856	6	5
α-helix	859-867	9
β-strand	873-877	5	6
α-helix	878-881	4
β-strand	888	1	7
α-helix	896	1
β-strand	897	1	7
α-helix	898-899	2
β-strand	904-908	5	6
α-helix	909-910	2
β-strand	911-912	2	8
β-strand	918-919	2	8
β-strand	922-924	3	6
α-helix	926-933	8
α-helix	934-939	6
α-helix	943-947	5

Chain S: 10 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	13-17	5	9
α-helix	18-21	4
α-helix	25-33	9
β-strand	45-46	2	9
α-helix	52-64	13
α-helix	68-74	7
α-helix	87-92	6
α-helix	97-110	14
α-helix	113-127	15
α-helix	132-139	8
α-helix	147-157	11
α-helix	158-160	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cullin-1	C	protein	776	Homo sapiens	Q13616 (AlphaFold model)
F-box DNA helicase 1	F	protein	972	Homo sapiens	Q8NFZ0 (AlphaFold model)
S-phase kinase-associated protein 1	S	protein	163	Homo sapiens	P63208 (AlphaFold model)
DNA (45-mer)	X	DNA	45	synthetic construct

Sequence of entity 1 (C), FASTA

>9XZL_1 Cullin-1 (chains C)
MSSTRSQNPHGLKQIGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSN
QARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYT
QQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVT
NAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADT
ERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHL
EIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAAL
NDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPE
LLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSA
SDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVL
SSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYT
LQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDE
VELKPDTLIKLYLGYKNKKLRVNINVPMETEQKQEQETTHKNIEEDRKLLIQAAIVRIMK
MRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA

Sequence of entity 2 (F), FASTA

>9XZL_2 F-box DNA helicase 1 (chains F)
SNAMAKSNSVGQDSCQDSEGDMIFPAESSCALPQEGSAGPGSPGSAPPSRKRSWSSEEES
NQATGTSRWDGVSKKAPRHHLSVPCTRPREARQEAEDSTSRLSAESGETDQDAGDVGPDP
IPDSYYGLLGTLPCQEALSHICSLPSEVLRHVFAFLPVEDLYWNLSLVCHLWREIISDPL
FIPWKKLYHRYLMNEEQAVSKVDGILSNCGIEKESDLCVLNLIRYTATTKCSPSVDPERV
LWSLRDHPLLPEAEACVRQHLPDLYAAAGGVNIWALVAAVVLLSSSVNDIQRLLFCLRRP
SSTVTMPDVTETLYCIAVLLYAMREKGINISNRIHYNIFYCLYLQENSCTQATKVKEEPS
VWPGKKTIQLTHEQQLILNHKMEPLQVVKIMAFAGTGKTSTLVKYAEKWSQSRFLYVTFN
KSIAKQAERVFPSNVICKTFHSMAYGHIGRKYQSKKKLNLFKLTPFMVNSVLAEGKGGFI
RAKLVCKTLENFFASADEELTIDHVPIWCKNSQGQRVMVEQSEKLNGVLEASRLWDNMRK
LGECTEEAHQMTHDGYLKLWQLSKPSLASFDAIFVDEAQDCTPAIMNIVLSQPCGKIFVG
DPHQQIYTFRGAVNALFTVPHTHVFYLTQSFRFGVEIAYVGATILDVCKRVRKKTLVGGN
HQSGIRGDAKGQVALLSRTNANVFDEAVRVTEGEFPSRIHLIGGIKSFGLDRIIDIWILL
QPEEERRKQNLVIKDKFIRRWVHKEGFSGFKRYVTAAEDKELEAKIAVVEKYNIRIPELV
QRIEKCHIEDLDFAEYILGTVHKAKGLEFDTVHVLDDFVKVPCARHNLPQLPHFRVESFS
EDEWNLLYVAVTRAKKRLIMTKSLENILTLAGEYFLQAELTSNVLKTGVVRCCVGQCNNA
IPVDTVLTMKKLPITYSNRKENKGGYLCHSCAEQRIGPLAFLTASPEQVRAMERTVENIV
LPRHEALLFLVF

Sequence of entity 3 (S), FASTA

>9XZL_3 S-phase kinase-associated protein 1 (chains S)
MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQ
WCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTC
KTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK

Sequence of entity 4 (X), FASTA

>9XZL_4 DNA (45-MER) (chains X)
GACTGCGAAGGTAGCGACAGATCCCCTGACGAACTGAGTCCTGAG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
MG	Magnesium ion	Mg	1
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	1

Primary citation

Structural basis for fork reversal and RAD51 regulation by the SCF ubiquitin ligase complex of F-box helicase 1. Greer, B.H., Mendia-Garcia, J., Mullins, E.A. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-68752-2 · PubMed

Other PDB entries of the same protein (UniProt Q13616 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3TDU 1.5 Å, N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein…
5V89 1.55 Å, Structure of DCN4 PONY domain bound to CUL1 WHB
3TDZ 2.0 Å, N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein…
8CAF 2.66 Å, N8C_Fab3b in complex with NEDD8-CUL1(WHB)
7Z8R 2.7 Å, CAND1-CUL1-RBX1
7Z8V 2.7 Å, CAND1-SCF-SKP2 (SKP1deldel) CAND1 engaged SCF rocked
8OR3 2.9 Å, CAND1-CUL1-RBX1-SKP1-SKP2-DCNL1
9QO4 2.95 Å, Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex
1LDJ 3.0 Å, Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex
4F52 3.0 Å, Structure of a Glomulin-RBX1-CUL1 complex
7Z8T 3.0 Å, CAND1-SCF-SKP2 CAND1 engaged SCF rocked
9EFV 3.03 Å, Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3

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