8S7D: SKP1-FBXO22

Name: PDB 8S7D: Cryo-EM structure of SKP1-FBXO22 in complex with a BACH1 BTB dimer at 3.2A resolution
Published: 2024-12-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Cryo-EM structure of SKP1-FBXO22 in complex with a BACH1 BTB dimer at 3.2A resolution. Determined by electron microscopy at 3.2 Å resolution. Released 11 Dec 2024.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,488
Mol. weight: 90.65 kDa
Released: 11 Dec 2024

Explore 8S7D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8S7D contains 33 α-helices and 36 β-strands across 4 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 A: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	1
α-helix	12-25	14
β-strand	32-36	5	2
β-strand	39-43	5	2
α-helix	45-50	6
α-helix	54-59	6
β-strand	70	1	2
α-helix	77-89	13
β-strand	91-94	4	3
α-helix	99-109	11
α-helix	117-120	4

Chain B: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	3
α-helix	12-26	15
β-strand	32-36	5	4
β-strand	39-43	5	4
α-helix	45-51	7
β-strand	52	1	5
α-helix	53-59	7
β-strand	69-70	2	4
α-helix	77-89	13
β-strand	91-92	2	1
α-helix	99-109	11
β-strand	111	1	5
α-helix	116-122	7

Chain C: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	19-22	4
α-helix	27-31	5
α-helix	54-63	10
α-helix	87-92	6
α-helix	97-110	14
α-helix	113-127	15
α-helix	132-139	8
α-helix	141-143	3
α-helix	147-156	10

Chain D: 12 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	19-25	7
α-helix	27-35	9
α-helix	39-45	7
α-helix	50-61	12
β-strand	67	1	6
β-strand	71	1	6
α-helix	84-91	8
β-strand	99-107	9	6
α-helix	108-111	4
α-helix	129-137	9
β-strand	144-150	7	6
β-strand	153	1	7
β-strand	154-155	2	8
α-helix	164-165	2
β-strand	166-167	2	8
β-strand	174-180	7	6
β-strand	191-193	3	9
α-helix	203-208	6
β-strand	219-225	7	9
α-helix	236-243	8
β-strand	249-255	7	9
β-strand	257-261	5	6
β-strand	274-280	7	9
β-strand	285	1	10
β-strand	287-288	2	3
β-strand	291	1	7
α-helix	299-310	12
β-strand	319-326	8	7
α-helix	341-348	8
β-strand	354-359	6	7
β-strand	362-363	2	9
β-strand	368-369	2	3
β-strand	373-378	6	3
β-strand	387-388	2	9
β-strand	393-398	6	7
β-strand	399	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription regulator protein BACH1	A, B	protein	125	Homo sapiens	O14867 (AlphaFold model)
S-phase kinase-associated protein 1	C	protein	163	Homo sapiens	P63208 (AlphaFold model)
F-box only protein 22	D	protein	395	Homo sapiens	Q8NEZ5 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8S7D_1 Transcription regulator protein BACH1 (chains A, B)
QSMSVFAYESSVHSTNVLLSLNDQRKKDVLCDVTIFVEGQRFRAHRSVLAACSSYFHSRI
VGQADGELNITLPEEVTVKGFEPLIQFAYTAKLILSKENVDEVCKCVEFLSVHNIEESCF
QFLKF

Sequence of entity 2 (C), FASTA

>8S7D_2 S-phase kinase-associated protein 1 (chains C)
MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQ
WCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTC
KTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK

Sequence of entity 3 (D), FASTA

>8S7D_3 F-box only protein 22 (chains D)
GGSGSSVDPRSTFVLSNLAEVVERVLTFLPAKALLRVACVCRLWRECVRRVLRTHRSVTW
ISAGLAEAGHLEGHCLVRVVAEELENVRILPHTVLYMADSETFISLEECRGHKRARKRTS
METALALEKLFPKQCQVLGIVTPGIVVTPMGSGSNRPQEIEIGESGFALLFPQIEGIKIQ
PFHFIKDPKNLTLERHQLTEVGLLDNPELRVVLVFGYNCCKVGASNYLQQVVSTFSDMNI
ILAGGQVDNLSSLTSEKNPLDIDASGVVGLSFSGHRIQSATVLLNEDVSDEKTAEAAMQR
LKAANIPEHNTIGFMFACVGRGFQYYRAKGNVEADAFRKFFPSVPLFGFFGNGEIGCDRI
VTGNFILRKCNEVKDDDLFHSYTTIMALIHLGSSK

Primary citation

Dual BACH1 regulation by complementary SCF-type E3 ligases. Goretzki, B., Khoshouei, M., Schroder, M. et al. Cell (2024) 187:7585-7602.e25. DOI 10.1016/j.cell.2024.11.006 · PubMed

Other PDB entries of the same protein (UniProt O14867 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GRA 1.47 Å, Homodimer of BACH1 BTB domain in complex with 2-Methyl-2,4-pentanediol
9GP5 1.9 Å, Homodimer of BACH1 F9A mutant BTB domain
9GR9 2.25 Å, Homodimer of BACH1 BTB domain
2IHC 2.44 Å, Crystal structure of the bric-a-brac (BTB) domain of human BACH1
8UBT 3.1 Å, Structure of SCF-FBXL17-BACH1BTB E3 ligase complex
8UAH 3.3 Å, Structure of BACH1 BTB domain-bound FBXL17 ubiquitin ligase
8UA3 3.8 Å, Cryo-EM Structure of FBOX22-BACH1BTB
8UA6 3.9 Å, Cryo-EM Structure of SCF-FBOX22-BACH1BTB
8UBV 4.1 Å, Cryo-EM structure of dimeric FBXL17-BACH1BTB E3 ubiquitin ligase complex
29HH 4.2 Å, Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with…
8UBU 4.6 Å, Cryo-EM structure of dimeric SCF-FBXL17-BACH1BTB E3 ligase complex close conformation

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