8TNQ: DDB1dB:CRBN:PT-179:SD40, conformation 1

Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 1. Determined by electron microscopy at 2.41 Å resolution. Released 13 Mar 2024.

Method: Electron microscopy
Resolution: 2.41 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 3
Atoms: 9,641
Mol. weight: 202.12 kDa
Ligands: MIQ, ZN
Released: 13 Mar 2024

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

Secondary structure: helices and β-sheets

8TNQ contains 35 α-helices and 91 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: 16 helices, 68 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	1
β-strand	17-21	5	2
β-strand	30-35	6	2
β-strand	38-45	8	2
β-strand	48-56	9	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	5
β-strand	130-134	5	5
β-strand	136	1	4
β-strand	139-144	6	5
β-strand	155-158	4	5
β-strand	163-169	7	6
α-helix	170	1
β-strand	177-183	7	6
β-strand	188-196	9	6
β-strand	201-204	4	6
β-strand	210-211	2	6
β-strand	218-221	4	7
β-strand	229-232	4	7
β-strand	237-241	5	7
β-strand	244-248	5	7
α-helix	251-255	5
β-strand	258-263	6	8
β-strand	270-275	6	8
β-strand	279-289	11	8
β-strand	295-307	13	8
β-strand	313-318	6	9
β-strand	321-325	5	9
β-strand	331-336	6	9
β-strand	347-353	7	9
β-strand	359-365	7	10
β-strand	374-379	6	10
α-helix	382-384	3
β-strand	386-391	6	10
β-strand	711-716	6	10
β-strand	720-727	8	11
β-strand	732-743	12	11
β-strand	749-751	3	11
β-strand	762-765	4	11
β-strand	785-795	11	11
β-strand	801-806	6	11
α-helix	807-808	2
β-strand	811-819	9	12
β-strand	828-835	8	12
β-strand	845-854	10	12
β-strand	857-866	10	12
β-strand	870-876	7	13
β-strand	879-884	6	13
β-strand	887-893	7	13
β-strand	899-906	8	13
β-strand	913-917	5	14
β-strand	920-924	5	14
β-strand	930-936	7	14
β-strand	941-948	8	14
β-strand	954-959	6	15
β-strand	964-969	6	15
β-strand	973-979	7	15
α-helix	986-989	4
β-strand	991	1	14
β-strand	992-999	8	15
β-strand	1004-1009	6	1
β-strand	1024-1032	9	1
β-strand	1037-1043	7	1
α-helix	1045-1059	15
α-helix	1063-1064	2
α-helix	1070-1074	5
β-strand	1076-1078	3	16
β-strand	1081-1083	3	16
β-strand	1086	1	15
β-strand	1088-1090	3	1
α-helix	1091-1095	5
α-helix	1096-1098	3
α-helix	1102-1109	8
β-strand	1113	1	17
α-helix	1122	1
β-strand	1123	1	17
α-helix	1124	1
α-helix	1126-1137	12

Chain B: 16 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	53-56	4
β-strand	65-66	2	18
α-helix	73-74	2
β-strand	78-83	6	18
β-strand	96-101	6	18
α-helix	104-116	13
β-strand	119-127	9	18
β-strand	132-147	16	18
α-helix	149-151	3
β-strand	154-172	19	18
β-strand	178-184	7	18
β-strand	188	1	19
α-helix	193-196	4
α-helix	201-203	3
α-helix	221-231	11
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-264	15
α-helix	270-272	3
α-helix	277-285	9
α-helix	292-300	9
β-strand	303	1	19
α-helix	304-317	14
β-strand	320-323	4	20
β-strand	330-333	4	20
α-helix	334-336	3
β-strand	337	1	21
β-strand	341	1	22
β-strand	344	1	22
β-strand	346-350	5	21
β-strand	356-362	7	21
β-strand	368-375	8	21
β-strand	384-391	8	21
β-strand	397-404	8	21
β-strand	413-418	6	21
α-helix	419-421	3
β-strand	422-425	4	20

Chain C: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	17-18	2	23
α-helix	19	1
β-strand	25-26	2	23
α-helix	30-36	7
α-helix	45-48	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A	protein	860	Homo sapiens	Q16531 (AlphaFold model)
Protein cereblon	B	protein	485	Homo sapiens	Q96SW2 (AlphaFold model)
Maltose/maltodextrin-binding periplasmic protein,SD40	C	protein	455	Escherichia coli, Homo sapiens	P0AEX9 (AlphaFold model), Q13422 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8TNQ_1 DNA damage-binding protein 1 (chains A)
MGSSHHHHHHSAVDENLYFQGGGRMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKN
TRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGE
SIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFN
IRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEA
SMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDM
EGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKL
NVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGG
NGNSGEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQA
LSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCK
LGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKL
LASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEG
NFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHL
GEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNK
VIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGM
KREATADDLIKVVEELTRIH

Sequence of entity 2 (B), FASTA

>8TNQ_2 Protein cereblon (chains B)
MDYKDDDDKSAVDENLYFQGGGRGGSAHIVMVDAYKPTKGGSGMAGEGDQQDAAHNMGNH
LPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDS
CQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGT
TAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAV
QLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRI
KKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNK
CTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTE
HSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDK
VILCL

Sequence of entity 3 (C), FASTA

>8TNQ_3 Maltose/maltodextrin-binding periplasmic protein,SD40 (chains C)
MGLNDIFEAQKIEWHEGSSHHHHHHGSSKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTG
IKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPF
TWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQ
EPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSI
AEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPN
KELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPN
IPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITKLEVLFQGPDYKDDDDKSGGGGL
LLFCPICGFTCRQKGNLLRHINLHTGEKLFKYHLY

Ligands and cofactors

ID	Name	Formula	Copies
MIQ	2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-1,3(2H)-dione	C17 H17 N3 O5	1
ZN	Zinc ion	Zn	2

Primary citation

Continuous evolution of compact protein degradation tags regulated by selective molecular glues. Mercer, J.A.M., DeCarlo, S.J., Roy Burman, S.S. et al. Science (2024) 383:eadk4422-eadk4422. DOI 10.1126/science.adk4422 · 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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