8TNR: DDB1dB:CRBN:PT-179:SD40, conformation 2

Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 2. Determined by electron microscopy at 2.5 Å resolution. Released 13 Mar 2024.

Method: Electron microscopy
Resolution: 2.5 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 3
Atoms: 9,707
Mol. weight: 202.12 kDa
Ligands: MIQ, ZN
Released: 13 Mar 2024

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

Secondary structure: helices and β-sheets

8TNR contains 33 α-helices and 90 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: 13 helices, 69 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	57	1	3
β-strand	61-67	7	4
β-strand	76-81	6	4
β-strand	85-94	10	4
β-strand	97-107	11	4
α-helix	114	1
β-strand	115	1	5
α-helix	116	1
β-strand	121-124	4	6
β-strand	130-134	5	6
β-strand	136	1	5
β-strand	139-144	6	6
β-strand	155-158	4	6
β-strand	163-169	7	7
α-helix	170	1
β-strand	177-184	8	7
β-strand	187-196	10	7
β-strand	201-204	4	7
β-strand	210-211	2	7
β-strand	218-221	4	8
β-strand	229-232	4	8
β-strand	237-241	5	8
β-strand	244-248	5	8
α-helix	252-255	4
β-strand	258-263	6	9
β-strand	270-275	6	9
β-strand	279-289	11	9
β-strand	295-307	13	9
β-strand	313-318	6	10
β-strand	321-325	5	10
β-strand	331-336	6	10
β-strand	347-353	7	10
β-strand	359-365	7	11
β-strand	374-379	6	11
α-helix	382-384	3
β-strand	386-392	7	11
β-strand	710-716	7	11
β-strand	720-727	8	12
β-strand	732-742	11	12
β-strand	750-751	2	12
β-strand	762-765	4	12
β-strand	785-795	11	12
β-strand	801-806	6	12
α-helix	807-808	2
β-strand	811-819	9	13
β-strand	828-835	8	13
β-strand	846-854	9	13
β-strand	857-866	10	13
β-strand	870-876	7	14
β-strand	879-884	6	14
β-strand	887-893	7	14
β-strand	899-906	8	14
β-strand	913-917	5	15
β-strand	920-924	5	15
β-strand	930-936	7	15
β-strand	941-948	8	15
β-strand	954-959	6	16
β-strand	964-969	6	16
β-strand	973-978	6	16
α-helix	986-989	4
β-strand	993-999	7	16
β-strand	1004-1009	6	1
β-strand	1024-1032	9	1
β-strand	1037-1043	7	1
α-helix	1045-1059	15
β-strand	1065	1	3
α-helix	1070-1074	5
β-strand	1076	1	17
β-strand	1083	1	17
β-strand	1086	1	16
β-strand	1088-1090	3	1
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1108	7
β-strand	1113-1114	2	18
β-strand	1122-1123	2	18
α-helix	1126-1137	12

Chain B: 17 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	52-55	4
α-helix	58-60	3
β-strand	65-66	2	19
β-strand	78-83	6	19
α-helix	91-92	2
β-strand	96-101	6	19
α-helix	104-114	11
β-strand	119-123	5	19
α-helix	129-131	3
β-strand	135-147	13	19
α-helix	149-151	3
β-strand	154-171	18	19
β-strand	179-184	6	19
β-strand	188	1	20
α-helix	200-203	4
α-helix	219-231	13
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-262	13
α-helix	270-272	3
α-helix	277-287	11
α-helix	292-300	9
β-strand	303	1	20
α-helix	304-317	14
β-strand	320-323	4	21
β-strand	330-333	4	21
α-helix	334-336	3
β-strand	337	1	22
β-strand	346-350	5	22
β-strand	356-362	7	22
β-strand	368-375	8	22
β-strand	384-391	8	22
β-strand	397-404	8	22
β-strand	413-418	6	22
α-helix	419-421	3
β-strand	422-425	4	21

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	30-38	9
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

>8TNR_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

>8TNR_2 Protein cereblon (chains B)
MDYKDDDDKSAVDENLYFQGGGRGGSAHIVMVDAYKPTKGGSGMAGEGDQQDAAHNMGNH
LPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDS
CQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGT
TAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAV
QLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRI
KKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNK
CTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTE
HSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDK
VILCL

Sequence of entity 3 (C), FASTA

>8TNR_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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