8AJO: DNA damage-binding protein 1

Negative-stain electron microscopy structure of DDB1-DCAF12-CCT5. Determined by electron microscopy at 30.6 Å resolution. Released 9 Nov 2022.

Method: Electron microscopy
Resolution: 30.6 Å
Organism: Homo sapiens
Chains: 3
Atoms: 10,269
Mol. weight: 245.59 kDa
Released: 9 Nov 2022

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

Secondary structure: helices and β-sheets

8AJO contains 51 α-helices and 158 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 A: 17 helices, 106 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	1
β-strand	17-21	5	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	164-169	6	5
α-helix	170	1
β-strand	171	1	6
β-strand	177-184	8	5
β-strand	187-196	10	5
β-strand	201-204	4	5
β-strand	210-211	2	5
β-strand	218-221	4	7
β-strand	228	1	6
β-strand	229-232	4	7
β-strand	237-241	5	7
β-strand	244-248	5	7
α-helix	251-253	3
β-strand	258-263	6	8
β-strand	270-275	6	8
β-strand	279-289	11	8
β-strand	295-307	13	8
α-helix	310-311	2
β-strand	313-316	4	9
β-strand	321-325	5	9
β-strand	331-336	6	9
β-strand	347-353	7	9
α-helix	357	1
β-strand	359-365	7	10
β-strand	374-379	6	10
α-helix	382-384	3
β-strand	386-393	8	10
β-strand	394	1	11
β-strand	396-402	7	12
β-strand	410-413	4	13
β-strand	422	1	14
β-strand	424-429	6	13
β-strand	432-439	8	13
β-strand	442-446	5	13
β-strand	457-463	7	15
β-strand	467-472	6	15
β-strand	476-480	5	15
β-strand	486-490	5	15
β-strand	500-503	4	16
β-strand	507-512	6	16
β-strand	515-522	8	16
β-strand	525-533	9	16
β-strand	538-542	5	17
β-strand	555-560	6	17
β-strand	565-570	6	17
β-strand	575-581	7	17
β-strand	588-596	9	18
β-strand	599-606	8	18
β-strand	610-617	8	18
β-strand	622-630	9	18
β-strand	637-643	7	19
β-strand	646-652	7	19
β-strand	657-662	6	19
β-strand	665-670	6	19
β-strand	671	1	11
β-strand	678-682	5	12
β-strand	684	1	14
β-strand	690-694	5	12
β-strand	699-704	6	12
β-strand	710-716	7	10
β-strand	720-727	8	20
β-strand	732-743	12	20
β-strand	749-751	3	20
α-helix	756-759	4
β-strand	762-765	4	20
β-strand	785-795	11	20
β-strand	801-806	6	20
β-strand	811-821	11	21
β-strand	824-835	12	21
β-strand	846-854	9	21
β-strand	857-866	10	21
β-strand	870-876	7	22
β-strand	879-884	6	22
β-strand	887-893	7	22
β-strand	899-905	7	22
β-strand	911-917	7	23
β-strand	920-925	6	23
β-strand	928	1	24
β-strand	930-936	7	23
β-strand	941-947	7	23
β-strand	952	1	24
β-strand	958-959	2	25
β-strand	964-968	5	25
β-strand	973-978	6	25
α-helix	986-989	4
β-strand	991	1	23
α-helix	992	1
β-strand	993-994	2	25
β-strand	997	1	26
β-strand	998-999	2	25
β-strand	1004-1009	6	1
β-strand	1025-1032	8	1
β-strand	1037-1043	7	1
α-helix	1045-1058	14
α-helix	1065-1067	3
α-helix	1070-1073	4
β-strand	1076-1077	2	27
β-strand	1082-1083	2	27
β-strand	1086	1	26
β-strand	1088-1090	3	1
α-helix	1091-1095	5
α-helix	1096-1098	3
α-helix	1102-1109	8
β-strand	1113-1115	3	28
β-strand	1121-1123	3	28
α-helix	1126-1136	11

Chain B: 13 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	46-53	8
α-helix	64-74	11
α-helix	75-77	3
β-strand	81-84	4	29
β-strand	92-97	6	30
β-strand	102-107	6	30
β-strand	112-116	5	30
β-strand	121-125	5	30
α-helix	126-129	4
β-strand	130	1	31
β-strand	147-148	2	32
β-strand	154-158	5	32
β-strand	165-169	5	32
β-strand	175-177	3	32
α-helix	178	1
β-strand	179	1	31
α-helix	180	1
β-strand	190-192	3	33
β-strand	197-201	5	33
β-strand	206-211	6	33
α-helix	214-226	13
α-helix	232	1
β-strand	233	1	32
α-helix	234	1
β-strand	239-242	4	33
α-helix	243-244	2
β-strand	255-261	7	34
β-strand	266-271	6	34
β-strand	275-280	6	34
β-strand	286-292	7	34
β-strand	302-305	4	35
β-strand	310-313	4	35
β-strand	318-322	5	35
β-strand	332-335	4	35
β-strand	343-349	7	36
β-strand	352-357	6	36
β-strand	361-366	6	36
β-strand	371-372	2	36
α-helix	373	1
β-strand	374	1	37
α-helix	375	1
β-strand	391	1	37
β-strand	393-395	3	36
β-strand	400-402	3	38
α-helix	405-410	6
β-strand	419-426	8	29
β-strand	433-439	7	29
β-strand	441	1	39
β-strand	445-447	3	38
β-strand	448-452	5	29

Chain C: 21 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	31-48	18
α-helix	56-58	3
β-strand	59-62	4	40
β-strand	68-71	4	40
α-helix	74-80	7
α-helix	82-83	2
α-helix	86-101	16
α-helix	106-125	20
α-helix	130-147	18
α-helix	158-174	17
α-helix	183-197	15
α-helix	198-200	3
β-strand	209-215	7	41
β-strand	222-225	4	41
β-strand	228-230	3	42
β-strand	249-251	3	43
α-helix	271-293	23
β-strand	300-302	3	43
α-helix	308-316	9
β-strand	321-322	2	43
α-helix	327-337	11
β-strand	342	1	43
α-helix	350-352	3
β-strand	358-364	7	42
β-strand	369-375	7	42
β-strand	383-389	7	41
α-helix	392-414	23
β-strand	418-419	2	44
α-helix	424-439	16
α-helix	445-454	10
α-helix	457-464	8
α-helix	470-483	14
β-strand	508-509	2	44
α-helix	510-527	18
α-helix	535-536	2
β-strand	539	1	39

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)
T-complex protein 1 subunit epsilon	C	protein	565	Homo sapiens	P48643 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8AJO_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

>8AJO_2 DDB1- and CUL4-associated factor 12 (chains B)
MDWSHPQFEKSAVDENLYFQGGGRMARKVVSRKRKAPASPGAGSDAQGPQFGWDHSLHKR
KRLPPVKRSLVYYLKNREVRLQNETSYSRVLHGYAAQQLPSLLKEREFHLGTLNKVFASQ
WLNHRQVVCGTKCNTLFVVDVQTSQITKIPILKDREPGGVTQQGCGIHAIELNPSRTLLA
TGGDNPNSLAIYRLPTLDPVCVGDDGHKDWIFSIAWISDTMAVSGSRDGSMGLWEVTDDV
LTKSDARHNVSRVPVYAHITHKALKDIPKEDTNPDNCKVRALAFNNKNKELGAVSLDGYF
HLWKAENTLSKLLSTKLPYCRENVCLAYGSEWSVYAVGSQAHVSFLDPRQPSYNVKSVCS
RERGSGIRSVSFYEHIITVGTGQGSLLFYDIRAQRFLEERLSACYGSKPRLAGENLKLTT
GKGWLNHDETWRNYFSDIDFFPNAVYTHCYDSSGTKLFVAGGPLPSGLHGNYAGLWS

Sequence of entity 3 (C), FASTA

>8AJO_3 T-complex protein 1 subunit epsilon (chains C)
MGSSHHHHHHSAVDENLYFQGGGRMASMGTLAFDEYGRPFLIIKDQDRKSRLMGLEALKS
HIMAAKAVANTMRTSLGPNGLDKMMVDKDGDVTVTNDGATILSMMDVDHQIAKLMVELSK
SQDDEIGDGTTGVVVLAGALLEEAEQLLDRGIHPIRIADGYEQAARVAIEHLDKISDSVL
VDIKDTEPLIQTAKTTLGSKVVNSCHRQMAEIAVNAVLTVADMERRDVDFELIKVEGKVG
GRLEDTKLIKGVIVDKDFSHPQMPKKVEDAKIAILTCPFEPPKPKTKHKLDVTSVEDYKA
LQKYEKEKFEEMIQQIKETGANLAICQWGFDDEANHLLLQNNLPAVRWVGGPEIELIAIA
TGGRIVPRFSELTAEKLGFAGLVQEISFGTTKDKMLVIEQCKNSRAVTIFIRGGNKMIIE
EAKRSLHDALCVIRNLIRDNRVVYGGGAAEISCALAVSQEADKCPTLEQYAMRAFADALE
VIPMALSENSGMNPIQTMTEVRARQVKEMNPALGIDCLHKGTNDMKQQHVIETLIGKKQQ
ISLATQMVRMILKIDDIRKPGESEE

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

Browse structure collections

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