8TNP: DDB1dB:CRBN:Pomalidomide:SD40

Cryo-EM structure of DDB1dB:CRBN:Pomalidomide:SD40. Determined by electron microscopy at 3.3 Å resolution. Released 13 Mar 2024.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 3
Atoms: 9,241
Mol. weight: 202.05 kDa
Ligands: ZN, Y70
Released: 13 Mar 2024

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

Secondary structure: helices and β-sheets

8TNP contains 25 α-helices and 84 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: 9 helices, 65 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	4
β-strand	15-21	7	5
β-strand	30-35	6	5
β-strand	38-43	6	5
β-strand	50-56	7	5
β-strand	63-67	5	6
β-strand	76-80	5	6
β-strand	86-94	9	6
β-strand	97-106	10	6
β-strand	115	1	7
β-strand	121-124	4	7
β-strand	130-136	7	7
β-strand	139-144	6	7
β-strand	155-158	4	7
β-strand	164-169	6	8
β-strand	177-184	8	8
β-strand	187-196	10	8
β-strand	201-204	4	8
β-strand	210-211	2	8
β-strand	218-221	4	9
β-strand	229-232	4	9
β-strand	237-241	5	9
β-strand	244-248	5	9
α-helix	251-253	3
β-strand	258-263	6	10
β-strand	270-275	6	10
β-strand	279-289	11	10
β-strand	295-307	13	10
α-helix	310-311	2
β-strand	313-317	5	11
β-strand	321-325	5	11
β-strand	331-336	6	11
β-strand	347-353	7	11
β-strand	359-365	7	12
β-strand	374-379	6	12
α-helix	382-384	3
β-strand	386-391	6	12
β-strand	711-716	6	12
β-strand	720-721	2	13
β-strand	725-727	3	13
β-strand	732-742	11	13
β-strand	750-751	2	13
β-strand	763-765	3	13
β-strand	785-795	11	13
β-strand	801-806	6	13
β-strand	811-819	9	14
β-strand	828-835	8	14
β-strand	846-854	9	14
β-strand	857-866	10	14
β-strand	870-875	6	15
β-strand	880-884	5	15
β-strand	888-893	6	15
β-strand	899-905	7	15
β-strand	913-917	5	16
β-strand	920-924	5	16
β-strand	927	1	17
β-strand	930-936	7	16
β-strand	941-948	8	16
β-strand	953	1	17
β-strand	957-959	3	18
β-strand	964-969	6	18
β-strand	973-978	6	18
α-helix	988-990	3
β-strand	993-998	6	18
β-strand	1007-1009	3	4
β-strand	1025-1030	6	4
β-strand	1037-1042	6	4
α-helix	1045-1058	14
α-helix	1070-1073	4
β-strand	1086	1	18
β-strand	1089-1090	2	4
α-helix	1091-1095	5
α-helix	1102-1109	8
α-helix	1126-1138	13

Chain B: 14 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	78-83	6	1
α-helix	91-92	2
β-strand	93	1	1
β-strand	96-101	6	1
α-helix	104-115	12
β-strand	121-125	5	1
β-strand	133-147	15	1
α-helix	149-151	3
β-strand	154-172	19	1
β-strand	178-184	7	1
α-helix	190-192	3
α-helix	193-195	3
α-helix	202-206	5
α-helix	221-231	11
α-helix	233-237	5
α-helix	242-245	4
α-helix	250-265	16
α-helix	277-285	9
α-helix	293-299	7
α-helix	304-317	14
β-strand	320-323	4	2
β-strand	330-333	4	2
α-helix	334-336	3
β-strand	337	1	3
β-strand	346-350	5	3
β-strand	356-362	7	3
β-strand	368-375	8	3
β-strand	384-391	8	3
β-strand	397-404	8	3
β-strand	413-418	6	3
β-strand	422-425	4	2

Chain C: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	19
β-strand	25	1	19
α-helix	30-38	9
α-helix	45-47	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein cereblon	B	protein	485	Homo sapiens	Q96SW2 (AlphaFold model)
DNA damage-binding protein 1	A	protein	860	Homo sapiens	Q16531 (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 (B), FASTA

>8TNP_1 Protein cereblon (chains B)
MDYKDDDDKSAVDENLYFQGGGRGGSAHIVMVDAYKPTKGGSGMAGEGDQQDAAHNMGNH
LPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDS
CQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGT
TAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAV
QLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRI
KKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNK
CTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTE
HSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDK
VILCL

Sequence of entity 2 (A), FASTA

>8TNP_2 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 3 (C), FASTA

>8TNP_3 Maltose/maltodextrin-binding periplasmic protein,SD40 (chains C)
MGLNDIFEAQKIEWHEGSSHHHHHHGSSKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTG
IKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPF
TWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQ
EPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSI
AEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPN
KELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPN
IPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITKLEVLFQGPDYKDDDDKSGGGGL
LLFCPICGFTCRQKGNLLRHINLHTGEKLFKYHLY

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
Y70	S-Pomalidomide	C13 H11 N3 O4	1

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 Q96SW2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4M91 1.1 Å, crystal structure of hN33/Tusc3-peptide 1
9CUO 1.6 Å, Crystal structure of CRBN with compound 3
9OHQ 1.6 Å, Structure of CRBN:IKZF2:Compound 15
9DOM 1.69 Å, PVTX-405: A Potent, Highly Selective, and Orally Efficacious Molecular Glue Degrader of…
7BQV 1.8 Å, Cereblon in complex with SALL4 and (S)-5-hydroxythalidomide
9O91 1.86 Å, Structure of IKZF2:CRBN:Compound 5 ternary structure
7BQU 1.9 Å, Cereblon in complex with SALL4 and (S)-thalidomide
9GAO 1.95 Å, Crystal structure of CRBNmidi in complex with 2-(4-(2,6-dioxopiperidin-3-yl)phenoxy)-N-me…
9FJX 2.0 Å, Crystal structure of human CRBN-DDB1 in complex with Lenalidomide
8RQC 2.15 Å, Crystal structure of CRBN-midi in complex with mezigdomide and IKZF1 ZF2
8RQ8 2.19 Å, Crystal structure of CRBN-midi in complex with mezigdomide
9OHR 2.34 Å, Structure of CRBN:IKZF2:Compound 35

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