8UBT: SCF-FBXL17-BACH1BTB E3 ligase complex

Name: PDB 8UBT: Structure of SCF-FBXL17-BACH1BTB E3 ligase complex
Published: 2024-11-06
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure of SCF-FBXL17-BACH1BTB E3 ligase complex. Determined by electron microscopy at 3.1 Å resolution. Released 6 Nov 2024.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,642
Mol. weight: 165.53 kDa
Released: 6 Nov 2024

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

Secondary structure: helices and β-sheets

8UBT contains 63 α-helices and 25 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: 29 helices, 0 β-strands

Element	Residues	Length
α-helix	24-26	3
α-helix	28-31	4
α-helix	39-53	15
α-helix	87-103	17
α-helix	116-119	4
α-helix	121-127	7
α-helix	129-132	4
α-helix	139-142	4
α-helix	159-166	8
α-helix	175-177	3
α-helix	180-187	8
α-helix	198-210	13
α-helix	228	1
α-helix	229-233	5
α-helix	234-251	18
α-helix	257-273	17
α-helix	284-287	4
α-helix	289-291	3
α-helix	304-312	9
α-helix	317-327	11
α-helix	335-337	3
α-helix	338-355	18
α-helix	358-360	3
α-helix	363-383	21
α-helix	389-399	11
α-helix	417-429	13
α-helix	441-453	13
α-helix	460-475	16
α-helix	482-494	13

Chain B: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	13-16	4	1
α-helix	18-21	4
α-helix	25-32	8
β-strand	45-46	2	1
α-helix	52-64	13
α-helix	68-70	3
α-helix	87-92	6
α-helix	97-110	14
α-helix	113-127	15
α-helix	132-139	8
α-helix	147-156	10

Chain C: 19 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	321-323	3
α-helix	326-333	8
α-helix	338-342	5
α-helix	345-347	3
α-helix	350-356	7
α-helix	378-384	7
β-strand	390	1	2
α-helix	401-403	3
α-helix	407-410	4
β-strand	416	1	2
β-strand	417-418	2	3
α-helix	427-436	10
β-strand	442-444	3	3
α-helix	453-462	10
β-strand	468-470	3	3
α-helix	479-487	9
β-strand	494-497	4	3
α-helix	505-511	7
β-strand	520-523	4	3
β-strand	529	1	4
α-helix	530-533	4
β-strand	544-546	3	3
β-strand	548	1	5
β-strand	552	1	4
α-helix	556-562	7
β-strand	570-571	2	3
β-strand	574	1	5
α-helix	581-590	10
β-strand	596-597	2	3
β-strand	600	1	6
α-helix	608-615	8
β-strand	621-622	2	3
β-strand	625	1	6
α-helix	635-641	7
β-strand	647-648	2	3
α-helix	660-667	8
β-strand	672	1	3
α-helix	682-687	6

Chain D: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	21-29	9
β-strand	36-40	5	7
β-strand	43-47	5	7
α-helix	50-55	6
α-helix	57-64	8
β-strand	71-74	4	7
α-helix	81-84	4
α-helix	89-92	4
α-helix	104-113	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cullin-1	A	protein	764	Homo sapiens	Q13616 (AlphaFold model)
S-phase kinase-associated protein 1	B	protein	163	Homo sapiens	P63208 (AlphaFold model)
F-box/LRR-repeat protein 17	C	protein	392	Homo sapiens	Q9UF56 (AlphaFold model)
Transcription regulator protein BACH1	D	protein	122	Homo sapiens	O14867 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8UBT_1 Cullin-1 (chains A)
KQIGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSNQARGAGVPPSKS
KKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYTQQWEDYRFSSKV
LNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVTNAVLKLIEKERN
GETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADTERFYTRESTEFL
QQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHLEIFHTEFQNLLD
ADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAALNDPKMYVQTVLD
VHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPELLARYCDSLLKK
SSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSASDDAEASMISKL
KQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVLSSGSWPFQQSCT
FALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYTLQASTFQMAILL
QYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDEVELKPDTLIKLY
LGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLG
EVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA

Sequence of entity 2 (B), FASTA

>8UBT_2 S-phase kinase-associated protein 1 (chains B)
MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQ
WCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTC
KTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK

Sequence of entity 3 (C), FASTA

>8UBT_3 F-box/LRR-repeat protein 17 (chains C)
CHREPPPETPDINQLPPSILLKIFSNLSLDERCLSASLVCKYWRDLCLDFQFWKQLDLSS
RQQVTDELLEKIASRSQNIIEINISDCRSMSDNGVCVLAFKCPGLLRYTAYRCKQLSDTS
IIAVASHCPLLQKVHVGNQDKLTDEGLKQLGSKCRELKDIHFGQCYKISDEGMIVIAKGC
LKLQRIYMQENKLVTDQSVKAFAEHCPELQYVGFMGCSVTSKGVIHLTKLRNLSSLDLRH
ITELDNETVMEIVKRCKNLSSLNLCLNWIINDRCVEVIAKEGQNLKELYLVSCKITDYAL
IAIGRYSMTIETVDVGWCKEITDQGATLIAQSSKSLRYLGLMRCDKVNEVTVEQLVQQYP
HITFSTVLQDCKRTLERAYQMGWTPNMSAASS

Sequence of entity 4 (D), FASTA

>8UBT_4 Transcription regulator protein BACH1 (chains D)
SVFAYESSVHSTNVLLSLNDQRKKDVLCDVTIFVEGQRFRAHRSVLAACSSYFHSRIVGQ
ADGELNITLPEEVTVKGFEPLIQFAYTAKLILSKENVDEVCKCVEFLSVHNIEESCFQFL
KF

Primary citation

Recognition of BACH1 quaternary structure degrons by two F-box proteins under oxidative stress. Cao, S., Garcia, S.F., Shi, H. et al. Cell (2024) 187:7568-7584.e22. DOI 10.1016/j.cell.2024.10.012 · 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
9XZL 3.0 Å, Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex…

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