9W2F: DDB1-CRBN

Cryo-EM structure of DDB1-CRBN in complex with dHuR-2 and HuR. Determined by electron microscopy at 3.4 Å resolution. Released 22 Apr 2026.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 3
Atoms: 9,924
Mol. weight: 180.84 kDa
Ligands: A1EUN, ZN
Released: 22 Apr 2026

Explore 9W2F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9W2F contains 32 α-helices and 98 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: 15 helices, 76 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	18-21	4	2
β-strand	30-34	5	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	85-89	5	3
β-strand	92-94	3	4
β-strand	97-99	3	4
β-strand	102-107	6	3
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
β-strand	177-184	8	7
β-strand	187-194	8	7
β-strand	196	1	8
β-strand	201	1	8
α-helix	212-213	2
β-strand	216-221	6	9
β-strand	229-233	5	9
β-strand	237-240	4	9
β-strand	245-248	4	9
α-helix	251-253	3
β-strand	258-263	6	10
β-strand	270-275	6	10
β-strand	279-284	6	10
β-strand	287-288	2	11
β-strand	296-297	2	11
β-strand	301-307	7	10
α-helix	310-311	2
β-strand	313-316	4	12
β-strand	321-325	5	12
β-strand	331-336	6	12
α-helix	340-341	2
β-strand	347-348	2	12
β-strand	352-353	2	12
β-strand	362-365	4	13
β-strand	374-379	6	13
α-helix	382-384	3
β-strand	386-391	6	13
β-strand	711-716	6	13
β-strand	720-723	4	14
β-strand	726-727	2	14
β-strand	732-743	12	14
α-helix	744	1
β-strand	749-751	3	14
β-strand	762-765	4	14
β-strand	785-795	11	14
β-strand	801-806	6	14
β-strand	811-819	9	15
β-strand	828-835	8	15
β-strand	846-851	6	15
β-strand	853-854	2	16
β-strand	857-858	2	16
β-strand	862-866	5	15
β-strand	870-876	7	17
β-strand	879-884	6	17
β-strand	887-893	7	17
β-strand	899-903	5	17
β-strand	906	1	17
β-strand	913-917	5	18
β-strand	920-925	6	18
β-strand	929-934	6	18
β-strand	943-949	7	18
β-strand	954-961	8	19
β-strand	964-969	6	19
β-strand	973-978	6	19
α-helix	986-989	4
β-strand	991	1	18
β-strand	993-998	6	19
β-strand	1004-1009	6	20
β-strand	1025	1	21
β-strand	1028-1032	5	20
β-strand	1037-1040	4	1
β-strand	1042	1	21
α-helix	1045-1058	14
α-helix	1070-1073	4
β-strand	1076	1	22
β-strand	1083	1	22
β-strand	1090	1	1
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1108	7
α-helix	1127-1137	11

Chain B: 14 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	54-56	3
α-helix	58-60	3
β-strand	65	1	23
β-strand	78-83	6	23
β-strand	97-100	4	23
α-helix	104-112	9
β-strand	120-123	4	23
β-strand	135-147	13	23
β-strand	154-169	16	23
β-strand	174	1	24
β-strand	177	1	24
β-strand	178-184	7	23
α-helix	185-187	3
α-helix	193-195	3
α-helix	201-203	3
α-helix	219-231	13
α-helix	234-237	4
α-helix	242-246	5
α-helix	250-264	15
α-helix	277-285	9
α-helix	292-300	9
α-helix	304-315	12
β-strand	360	1	25
β-strand	382	1	26
β-strand	384	1	26
β-strand	404	1	26
β-strand	417	1	25
α-helix	419-421	3

Chain C: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	21-23	3	27
β-strand	25	1	28
α-helix	33-41	9
β-strand	46	1	29
β-strand	65-67	3	27
β-strand	68	1	29
α-helix	74-75	2
α-helix	76-80	5
β-strand	83	1	30
β-strand	91	1	30
β-strand	92	1	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A	protein	1140	Homo sapiens	Q16531 (AlphaFold model)
Protein cereblon	B	protein	381	Homo sapiens	Q96SW2 (AlphaFold model)
ELAV-like protein 1	C	protein	85	Homo sapiens	Q15717 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9W2F_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

>9W2F_2 Protein cereblon (chains B)
NIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHP
QEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQR
FKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWW
QKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRV
AACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCG
PMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTA
TKKDMSPQKFWGLTRSALLPT

Sequence of entity 3 (C), FASTA

>9W2F_3 ELAV-like protein 1 (chains C)
GDIGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDA
ERAINTLNGLRLQSKTIKVSYARPS

Ligands and cofactors

ID	Name	Formula	Copies
A1EUN	(3S)-3-[6-[1-[(4-methoxyphenyl)methyl]pyrazol-4-yl]-1-benzofuran-3-yl]piperidin…	C24 H21 N3 O4	1
ZN	Zinc ion	Zn	1

Primary citation

Molecular glue degraders of HuR suppress BRAF-mutant colorectal cancer. Lu, X., Wang, X., Yang, Z. et al. Nature (2026) 655:780-789. DOI 10.1038/s41586-026-10613-5 · 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

About this viewer

MolViewer shows 9W2F directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.