8AJN: Human DDB1-DCAF12 complex

Structure of the human DDB1-DCAF12 complex. Determined by electron microscopy at 3.0 Å resolution. Released 9 Nov 2022.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 12,009
Mol. weight: 183.16 kDa
Released: 9 Nov 2022

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

Secondary structure: helices and β-sheets

8AJN contains 29 α-helices and 133 β-strands across 2 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: 18 helices, 101 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	1
β-strand	15-21	7	2
β-strand	30-35	6	2
β-strand	38-44	7	2
β-strand	49-56	8	2
β-strand	61-67	7	3
β-strand	76-81	6	3
β-strand	85-94	10	3
β-strand	97-107	11	3
α-helix	114	1
β-strand	115	1	4
α-helix	116	1
β-strand	121-124	4	4
β-strand	130-136	7	4
β-strand	139-144	6	4
β-strand	151	1	3
β-strand	155-158	4	4
β-strand	163-169	7	5
α-helix	170	1
β-strand	177-184	8	5
β-strand	187-196	10	5
β-strand	201-209	9	5
β-strand	217-221	5	6
β-strand	229-232	4	6
β-strand	237-241	5	6
β-strand	244-248	5	6
β-strand	258-263	6	7
β-strand	270-275	6	7
β-strand	279-289	11	7
β-strand	295-307	13	7
α-helix	310-311	2
β-strand	313-316	4	8
β-strand	321-325	5	8
β-strand	331-336	6	8
β-strand	347-353	7	8
β-strand	361-365	5	9
β-strand	374-379	6	9
α-helix	382-384	3
β-strand	386-392	7	9
β-strand	394	1	10
β-strand	396-402	7	11
β-strand	409-413	5	12
β-strand	422	1	13
β-strand	424-429	6	12
β-strand	432-439	8	12
β-strand	442-446	5	12
β-strand	457-463	7	14
β-strand	467-472	6	14
β-strand	476-480	5	14
β-strand	486-490	5	14
α-helix	496-498	3
β-strand	500-503	4	15
β-strand	507-512	6	15
β-strand	515-522	8	15
β-strand	525-533	9	15
β-strand	538-542	5	16
β-strand	555-560	6	16
β-strand	565-570	6	16
β-strand	576-581	6	16
β-strand	588-596	9	17
β-strand	599-606	8	17
β-strand	610-616	7	17
β-strand	623-630	8	17
β-strand	637-643	7	18
β-strand	646-652	7	18
β-strand	657-662	6	18
β-strand	665-670	6	18
β-strand	671	1	10
β-strand	678-682	5	11
β-strand	684	1	13
β-strand	690-694	5	11
β-strand	699-704	6	11
β-strand	710-716	7	9
β-strand	720-727	8	19
β-strand	732-743	12	19
β-strand	750-751	2	19
α-helix	756-759	4
β-strand	763-765	3	19
α-helix	770-772	3
β-strand	784-795	12	19
β-strand	801-806	6	19
β-strand	811-820	10	20
β-strand	827-835	9	20
β-strand	846-854	9	20
β-strand	857-866	10	20
β-strand	870-876	7	21
β-strand	879-884	6	21
β-strand	887-893	7	21
β-strand	899-905	7	21
β-strand	911-917	7	22
β-strand	920-925	6	22
β-strand	928	1	23
β-strand	930-936	7	22
β-strand	941-947	7	22
β-strand	952	1	23
β-strand	954-959	6	24
β-strand	964-969	6	24
β-strand	973-978	6	24
α-helix	986-989	4
β-strand	991	1	22
α-helix	992	1
β-strand	993-999	7	24
β-strand	1004-1009	6	1
α-helix	1014-1015	2
β-strand	1024-1032	9	1
β-strand	1037-1043	7	1
α-helix	1045-1061	17
α-helix	1063-1064	2
α-helix	1070-1074	5
β-strand	1076-1077	2	25
β-strand	1082-1083	2	25
β-strand	1086	1	24
β-strand	1090	1	1
α-helix	1091-1096	6
α-helix	1097-1099	3
α-helix	1102-1109	8
β-strand	1113-1115	3	26
β-strand	1121-1123	3	26
α-helix	1126-1137	12

Chain B: 11 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	46-55	10
α-helix	61-63	3
α-helix	64-74	11
α-helix	75-77	3
β-strand	81-83	3	27
β-strand	92-99	8	28
β-strand	102-107	6	28
β-strand	112-116	5	28
β-strand	122-125	4	28
α-helix	128-129	2
β-strand	130	1	29
β-strand	146-148	3	30
β-strand	154-158	5	30
β-strand	165-169	5	30
β-strand	174-177	4	30
β-strand	179	1	29
β-strand	187-192	6	31
β-strand	197-202	6	31
β-strand	206-211	6	31
α-helix	214-226	13
α-helix	232	1
β-strand	233	1	30
α-helix	234	1
β-strand	239-242	4	31
α-helix	243-245	3
β-strand	255-261	7	32
β-strand	266-271	6	32
β-strand	275-280	6	32
β-strand	286-292	7	32
β-strand	302-305	4	33
β-strand	310-313	4	33
β-strand	318-322	5	33
α-helix	328-330	3
β-strand	332-335	4	33
β-strand	343-349	7	34
β-strand	352-357	6	34
β-strand	361-366	6	34
β-strand	371-372	2	34
β-strand	394-395	2	34
α-helix	405-410	6
β-strand	420-426	7	27
β-strand	433-438	6	27
β-strand	448-452	5	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A	protein	1164	Homo sapiens	Q16531 (AlphaFold model)
DDB1- and CUL4-associated factor 12	B	protein	477	Homo sapiens	Q5T6F0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8AJN_1 DNA damage-binding protein 1 (chains A)
MGSSHHHHHHSAVDENLYFQGGGRMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKN
TRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGE
SIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFN
IRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEA
SMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDM
EGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKL
NVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGI
HEHASIDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQ
TFFCGNVAHQQLIQITSASVRLVSQEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRAL
YYLQIHPQELRQISHTEMEHEVACLDITPLGDSNGLSPLCAIGLWTDISARILKLPSFEL
LHKEMLGGEIIPRSILMTTFESSHYLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPT
VLRTFRSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANN
STLTIGTIDEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSA
STQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSL
VSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEF
NGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYK
PMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVG
LFHLGEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQN
RLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDD
GSGMKREATADDLIKVVEELTRIH

Sequence of entity 2 (B), FASTA

>8AJN_2 DDB1- and CUL4-associated factor 12 (chains B)
MDWSHPQFEKSAVDENLYFQGGGRMARKVVSRKRKAPASPGAGSDAQGPQFGWDHSLHKR
KRLPPVKRSLVYYLKNREVRLQNETSYSRVLHGYAAQQLPSLLKEREFHLGTLNKVFASQ
WLNHRQVVCGTKCNTLFVVDVQTSQITKIPILKDREPGGVTQQGCGIHAIELNPSRTLLA
TGGDNPNSLAIYRLPTLDPVCVGDDGHKDWIFSIAWISDTMAVSGSRDGSMGLWEVTDDV
LTKSDARHNVSRVPVYAHITHKALKDIPKEDTNPDNCKVRALAFNNKNKELGAVSLDGYF
HLWKAENTLSKLLSTKLPYCRENVCLAYGSEWSVYAVGSQAHVSFLDPRQPSYNVKSVCS
RERGSGIRSVSFYEHIITVGTGQGSLLFYDIRAQRFLEERLSACYGSKPRLAGENLKLTT
GKGWLNHDETWRNYFSDIDFFPNAVYTHCYDSSGTKLFVAGGPLPSGLHGNYAGLWS

Primary citation

Recognition of the CCT5 di-Glu degron by CRL4 DCAF12 is dependent on TRiC assembly. Pla-Prats, C., Cavadini, S., Kempf, G. et al. EMBO J (2023) 42:e112253-e112253. DOI 10.15252/embj.2022112253 · PubMed

Other PDB entries of the same protein (UniProt Q16531 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BBG 1.7 Å, Co-crystal structure of human DDB1 bound to fragment UB028671
9EJQ 1.87 Å, Crystal structure of DDB1 in complex with XS381952
9BBI 1.9 Å, Co-crystal structure of human DDB1 bound to fragment UB028669
9BZ0 1.9 Å, Structure of an STK19-containing TC-NER complex
9BBE 2.0 Å, Co-crystal structure of human DDB1 bound to fragment UB028668
9BBH 2.0 Å, Co-crystal structure of human DDB1 bound to fragment UB028670
9FJX 2.0 Å, Crystal structure of human CRBN-DDB1 in complex with Lenalidomide
9ZXN 2.07 Å, DDB1 delta with compound 26
37MF 2.1 Å, Crystal structure of DDB1 in complex with XS445479
9ZXM 2.19 Å, DDB1 delta with compound 6
8G46 2.2 Å, Cryo-EM structure of DDB1deltaB-DDA1-DCAF16-BRD4(BD2)-MMH2
8ZSW 2.25 Å, Crystal Structure of Human DDB1, a Component of the E3 Ubiquitin Ligase Complex

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