6WCQ: Substrate-bound DQC ubiquitin ligase

Name: PDB 6WCQ: Structure of a substrate-bound DQC ubiquitin ligase
Published: 2020-08-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure of a substrate-bound DQC ubiquitin ligase. Determined by electron microscopy at 8.5 Å resolution. Released 19 Aug 2020.

Method: Electron microscopy
Resolution: 8.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,140
Mol. weight: 183.75 kDa
Released: 19 Aug 2020

Explore 6WCQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6WCQ contains 56 α-helices and 23 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: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	13-16	4	1
α-helix	18-22	5
α-helix	25-34	10
β-strand	45-46	2	1
α-helix	52-64	13
α-helix	68-70	3
α-helix	87-92	6
α-helix	97-109	13
α-helix	113-127	15
α-helix	132-139	8
α-helix	147-156	10

Chain B: 20 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	321-323	3
α-helix	326-334	9
α-helix	338-343	6
α-helix	345-347	3
α-helix	350-357	8
β-strand	365-366	2	2
α-helix	370-372	3
α-helix	376-384	9
β-strand	390-392	3	2
α-helix	401-410	10
β-strand	416-419	4	2
α-helix	427-436	10
β-strand	442-445	4	2
α-helix	453-462	10
β-strand	468-472	5	2
α-helix	479-487	9
β-strand	494-498	5	2
α-helix	505-512	8
β-strand	520-524	5	2
α-helix	530-533	4
α-helix	534-538	5
β-strand	544-546	3	2
α-helix	555-564	10
β-strand	570-572	3	2
α-helix	581-590	10
β-strand	596-598	3	2
β-strand	605	1	3
α-helix	606-615	10
β-strand	621-623	3	2
β-strand	629	1	3
α-helix	632-641	10
β-strand	647-649	3	2
α-helix	658-667	10
β-strand	672-673	2	2
α-helix	676-688	13

Chain C: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	51-55	5	4
α-helix	63-73	11
β-strand	79-83	5	5
β-strand	91-95	5	5
α-helix	97-103	7
α-helix	105-111	7
β-strand	121-125	5	5
α-helix	130-142	13
β-strand	144-148	5	4
α-helix	152-162	11
α-helix	165-177	13

Chain D: 21 helices, 0 β-strands

Element	Residues	Length
α-helix	21-31	11
α-helix	39-52	14
α-helix	86-101	16
α-helix	114-136	23
α-helix	138-142	5
α-helix	160-167	8
α-helix	171-175	5
α-helix	176-188	13
α-helix	198-210	13
α-helix	227	1
α-helix	228-233	6
α-helix	234-254	21
α-helix	257-278	22
α-helix	281-283	3
α-helix	285-292	8
α-helix	293-297	5
α-helix	300-312	13
α-helix	316-326	11
α-helix	334-355	22
α-helix	363-383	21
α-helix	389-399	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
S-phase kinase-associated protein 1	A	protein	163	Homo sapiens	P63208 (AlphaFold model)
F-box/LRR-repeat protein 17	B	protein	396	Homo sapiens	Q9UF56 (AlphaFold model)
Kelch-like ECH-associated protein 1	C	protein	631	Homo sapiens	Q14145 (AlphaFold model)
Cullin-1	D	protein	434	Homo sapiens	Q13616 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6WCQ_1 S-phase kinase-associated protein 1 (chains A)
MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQ
WCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTC
KTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK

Sequence of entity 2 (B), FASTA

>6WCQ_2 F-box/LRR-repeat protein 17 (chains B)
GEFMCHREPPPETPDINQLPPSILLKIFSNLSLDERCLSASLVCKYWRDLCLDFQFWKQL
DLSSRQQVTDELLEKIASRSQNIIEINISDCRSMSDNGVCVLAFKCPGLLRYTAYRCKQL
SDTSIIAVASHCPLLQKVHVGNQDKLTDEGLKQLGSKCRELKDIHFGQCYKISDEGMIVI
AKGCLKLQRIYMQENKLVTDQSVKAFAEHCPELQYVGFMGCSVTSKGVIHLTKLRNLSSL
DLRHITELDNETVMEIVKRCKNLSSLNLCLNWIINDRCVEVIAKEGQNLKELYLVSCKIT
DYALIAIGRYSMTIETVDVGWCKEITDQGATLIAQSSKSLRYLGLMRCDKVNEVTVEQLV
QQYPHITFSTVLQDCKRTLERAYQMGWTPNMSAASS

Sequence of entity 3 (C), FASTA

>6WCQ_3 Kelch-like ECH-associated protein 1 (chains C)
GGGSGGSMQPDPRPSGAGACCRFLPLQSQCPEGAGDAVMYASTECKAEVTPSQHGNRTFS
YTLEDHTKQAFGIMNELRLSQQLCDVTLQVKYQDAPAAQFMAHKVALASSSPVFKAMFTN
GLREQGMEVVSIEGIHPKVMERLIEFAYTASISMGEKCVLHVMNGAVMYQIDSVVRACSD
FLVQQLDPSNAIGIANFAEQIGCVELHQRAREYIYMHFGEVAKQEEFFNLSHCQLVTLIS
RDDLNVRCESEVFHACINWVKYDCEQRRFYVQALLRAVRCHSLTPNFLQMQLQKCEILQS
DSRCKDYLVKIFEELTLHKPTQVMPCRAPKVGRLIYTAGGYFRQSLSYLEAYNPSDGTWL
RLADLQVPRSGLAGCVVGGLLYAVGGRNNSPDGNTDSSALDCYNPMTNQWSPCAPMSVPR
NRIGVGVIDGHIYAVGGSHGCIHHNSVERYEPERDEWHLVAPMLTRRIGVGVAVLNRLLY
AVGGFDGTNRLNSAECYYPERNEWRMITAMNTIRSGAGVCVLHNCIYAAGGYDGQDQLNS
VERYDVETETWTFVAPMKHRRSALGITVHQGRIYVLGGYDGHTFLDSVECYDPDTDTWSE
VTRMTSGRSGVGVAVTMEPCRKQIDQQNCTC

Sequence of entity 4 (D), FASTA

>6WCQ_4 Cullin-1 (chains D)
MSSTRSQNPHGLKQIGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSN
QARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYT
QQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVT
NAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADT
ERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHL
EIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAAL
NDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPE
LLARYCDSLLKKSS

Primary citation

Structural basis for dimerization quality control. Mena, E.L., Jevtic, P., Greber, B.J. et al. Nature (2020) 586:452-456. DOI 10.1038/s41586-020-2636-7 · PubMed

Other PDB entries of the same protein (UniProt P63208 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1FS1 1.8 Å, Insights into scf ubiquitin ligases from the structure of the SKP1-SKP2 complex
6M90 2.05 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2776 ternary complex
2AST 2.3 Å, Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide
6M92 2.35 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2663 ternary complex
2E31 2.4 Å, Structural basis for selection of glycosylated substrate by SCFFbs1 ubiquitin ligase
6M91 2.4 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-103094 ternary complex
2OVR 2.5 Å, Structure of the Skp1-Fbw7-CyclinEdegN complex
6M93 2.5 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-1933 ternary complex
6WNX 2.5 Å, FBXW11-SKP1 in complex with a pSer33/pSer37 Beta-Catenin peptide
5IBK 2.5 Å, Skp1-F-box in complex with a ubiquitin variant
6O60 2.5 Å, Crystal structure of GGTase3-FBXL2-SKP1 complex
5JH5 2.55 Å, Structural Basis for the Hierarchical Assembly of the Core of PRC1.1

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