8T9A: Human DDB1-DCAF12

CryoEM structure of human DDB1-DCAF12 in complex with MAGEA3. Determined by electron microscopy at 3.17 Å resolution. Released 10 Apr 2024.

Method: Electron microscopy
Resolution: 3.17 Å
Organism: Homo sapiens
Chains: 3
Atoms: 11,785
Mol. weight: 203.89 kDa
Released: 10 Apr 2024

Explore 8T9A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T9A contains 16 α-helices and 146 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: 11 helices, 117 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	1
β-strand	17-21	5	2
β-strand	30-34	5	2
β-strand	38-44	7	2
β-strand	49-56	8	2
β-strand	63-67	5	3
β-strand	76-80	5	3
β-strand	85-89	5	3
β-strand	92-94	3	4
β-strand	97-99	3	4
β-strand	102-107	6	3
β-strand	115	1	5
β-strand	122-124	3	6
β-strand	130-133	4	6
β-strand	136	1	5
β-strand	141-144	4	6
β-strand	155	1	6
β-strand	164-168	5	7
β-strand	177-184	8	7
β-strand	187-196	10	7
β-strand	201-204	4	7
β-strand	212	1	7
β-strand	219-220	2	8
β-strand	229-232	4	8
β-strand	237-240	4	8
β-strand	245-248	4	8
α-helix	253-255	3
β-strand	262-263	2	9
β-strand	270-272	3	9
β-strand	280-287	8	9
β-strand	297-306	10	9
β-strand	311	1	10
β-strand	315-318	4	11
β-strand	321-323	3	11
β-strand	326	1	10
β-strand	331-332	2	12
β-strand	335-336	2	11
β-strand	347-348	2	11
β-strand	352-353	2	12
β-strand	362	1	13
β-strand	365	1	13
β-strand	374-379	6	13
β-strand	386-391	6	13
β-strand	392	1	14
β-strand	396	1	15
β-strand	400-402	3	16
β-strand	409-413	5	17
β-strand	422	1	18
β-strand	424-429	6	17
β-strand	432-439	8	17
β-strand	442-446	5	17
β-strand	459-463	5	19
β-strand	467-471	5	19
β-strand	475-480	6	19
β-strand	486-491	6	19
α-helix	496-498	3
β-strand	500-503	4	20
β-strand	507-512	6	20
β-strand	515-522	8	20
β-strand	525-533	9	20
β-strand	538-542	5	21
β-strand	555-560	6	21
β-strand	566-570	5	21
β-strand	575-580	6	21
β-strand	588-596	9	22
β-strand	599-606	8	22
β-strand	610-617	8	22
β-strand	622-630	9	22
β-strand	637-643	7	23
β-strand	646-652	7	23
β-strand	657-662	6	23
β-strand	665-670	6	23
β-strand	676-682	7	16
β-strand	684	1	18
β-strand	690-695	6	16
β-strand	699-703	5	16
β-strand	704	1	15
β-strand	710	1	14
β-strand	715-716	2	13
β-strand	720-724	5	24
β-strand	727	1	25
β-strand	732	1	25
β-strand	733-739	7	24
α-helix	741	1
β-strand	742	1	26
α-helix	743	1
β-strand	750	1	26
β-strand	763-765	3	24
β-strand	788-794	7	24
β-strand	801-806	6	24
β-strand	811-820	10	27
β-strand	827-835	9	27
β-strand	839	1	28
β-strand	847-854	8	27
β-strand	857-864	8	27
β-strand	870-876	7	29
β-strand	879-884	6	29
β-strand	887-893	7	29
β-strand	899-905	7	29
β-strand	911-913	3	30
β-strand	916-917	2	31
β-strand	920-923	4	31
β-strand	924-925	2	30
β-strand	931-934	4	31
β-strand	935-936	2	32
β-strand	941-942	2	32
α-helix	952-953	2
β-strand	954-958	5	33
β-strand	964-969	6	33
β-strand	973-978	6	33
β-strand	979	1	34
β-strand	992	1	34
β-strand	996-999	4	33
β-strand	1006-1009	4	1
β-strand	1028-1031	4	1
β-strand	1037-1042	6	1
α-helix	1045-1058	14
α-helix	1070-1074	5
β-strand	1076-1077	2	35
β-strand	1082-1083	2	35
β-strand	1086	1	33
β-strand	1090	1	1
α-helix	1091-1095	5
α-helix	1102-1109	8
β-strand	1114	1	36
β-strand	1122	1	36
α-helix	1126-1131	6
α-helix	1134-1137	4

Chain B: 5 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	44	1	28
α-helix	46-53	8
α-helix	66-74	9
α-helix	75-77	3
β-strand	83	1	37
β-strand	92-97	6	38
β-strand	102-107	6	38
β-strand	112-116	5	38
β-strand	121-124	4	38
β-strand	146-148	3	39
β-strand	154-157	4	39
β-strand	166-169	4	39
β-strand	174-177	4	39
β-strand	189-192	4	40
β-strand	197-201	5	40
β-strand	209-211	3	40
α-helix	214-223	10
β-strand	255-257	3	41
β-strand	269-271	3	41
β-strand	275-281	7	41
β-strand	285-292	8	41
β-strand	302-304	3	42
β-strand	311-314	4	42
β-strand	318-322	5	42
β-strand	332-335	4	42
β-strand	345-349	5	43
β-strand	352-356	5	43
β-strand	362-366	5	43
β-strand	372	1	43
β-strand	393	1	43
α-helix	405-409	5
β-strand	420-425	6	37
β-strand	433-438	6	37
β-strand	449-452	4	37

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A	protein	1140	Homo sapiens	Q16531 (AlphaFold model)
DDB1- and CUL4-associated factor 12	B	protein	471	Homo sapiens	Q5T6F0 (AlphaFold model)
Melanoma-associated antigen 3	C	protein	212	Homo sapiens	P43357 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8T9A_1 DNA damage-binding protein 1 (chains A)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 2 (B), FASTA

>8T9A_2 DDB1- and CUL4-associated factor 12 (chains B)
MHHHHHHSSGRENLYFQGMARKVVSRKRKAPASPGAGSDAQGPQFGWDHSLHKRKRLPPV
KRSLVYYLKNREVRLQNETSYSRVLHGYAAQQLPSLLKEREFHLGTLNKVFASQWLNHRQ
VVCGTKCNTLFVVDVQTSQITKIPILKDQEPGGVTQQGCGIHAIELNPSRTLLATGGDNP
NSLAIYRLPTLDPVCVGDDGHKDWIFSIAWISDTMAVSGSRDGSMGLWEVTDDVLTKSDA
RHNVSRVPVYAHITHKALKDIPKEDTNPDNCKVRALAFNNKNKELGAVSLDGYFHLWKAE
NTLSKLLSTKLPYCRENVCLAYGSEWSVYAVGSQAHVSFLDPRQPSYNVKSVCSRERGSG
IRSVSFYEHIITVGTGQGSLLFYDIRAQRFLEERLSACYGSKPRLAGENLKLTTGKGWLN
HDETWRNYFSDIDFFPNAVYTHCYDSSGTKLFVAGGPLPSGLHGNYAGLWS

Sequence of entity 3 (C), FASTA

>8T9A_3 Melanoma-associated antigen 3 (chains C)
MEFQAALSRKVAELVHFLLLKYRAREPVTKAEMLGSVVGNWQYFFPVIFSKASSSLQLVF
GIELMEVDPIGHLYIFATCLGLSYDGLLGDNQIMPKAGLLIIVLAIIAREGDCAPEEKIW
EELSVLEVFEGREDSILGDPKKLLTQHFVQENYLEYRQVPGSDPACYEFLWGPRALVETS
YVKVLHHMVKISGGPHISYPPLHEWVLREGEE

Primary citation

Probing the CRL4 DCAF12 interactions with MAGEA3 and CCT5 di-Glu C-terminal degrons. Righetto, G.L., Yin, Y., Duda, D.M. et al. PNAS Nexus (2024) 3:pgae153-pgae153. DOI 10.1093/pnasnexus/pgae153 · 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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