9V09: DNA damage-binding protein 1

Cryo-EM structure of lenalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly. Determined by electron microscopy at 3.25 Å resolution. Released 19 Aug 2026.

Method: Electron microscopy
Resolution: 3.25 Å
Organism: Homo sapiens
Chains: 8
Atoms: 20,550
Mol. weight: 318.64 kDa
Ligands: LVY, ZN
Released: 19 Aug 2026

Explore 9V09 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9V09 contains 80 α-helices and 166 β-strands across 8 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: 39 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	58-74	17
α-helix	83-94	12
α-helix	99-116	18
α-helix	119-122	4
α-helix	128-152	25
α-helix	154-159	6
α-helix	168-169	2
α-helix	170-178	9
α-helix	179-183	5
α-helix	186-204	19
α-helix	211-223	13
α-helix	227-232	6
α-helix	233-244	12
α-helix	246-251	6
α-helix	256-276	21
α-helix	280-282	3
α-helix	283-294	12
α-helix	296-298	3
α-helix	299-313	15
α-helix	316-328	13
α-helix	332-353	22
α-helix	355-358	4
α-helix	361-378	18
α-helix	384-397	14
α-helix	398-400	3
α-helix	405-416	12
α-helix	426-440	15
α-helix	446-463	18
α-helix	469-483	15
α-helix	489-514	26
β-strand	526-529	4	28
α-helix	534-535	2
α-helix	545-561	17
β-strand	566-570	5	28
β-strand	575-578	4	29
β-strand	589-592	4	29
α-helix	593-602	10
α-helix	610-616	7
α-helix	621-633	13
β-strand	640-642	3	30
β-strand	653-655	3	30
α-helix	656-657	2
α-helix	695-707	13
α-helix	712-720	9
α-helix	729-741	13
β-strand	745-747	3	31
β-strand	755-757	3	31

Chain B: 13 helices, 104 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	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	63-67	5	3
β-strand	76-80	5	3
β-strand	85-94	10	3
β-strand	97-107	11	3
β-strand	115	1	4
β-strand	121-124	4	5
β-strand	130-134	5	5
β-strand	136	1	4
β-strand	139	1	6
β-strand	141-144	4	5
β-strand	155	1	5
β-strand	158	1	6
β-strand	164-169	6	7
β-strand	177-182	6	7
β-strand	189-196	8	7
β-strand	201-204	4	7
β-strand	210-211	2	7
β-strand	219-221	3	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	258-263	6	9
β-strand	270-275	6	9
β-strand	280-284	5	9
β-strand	287	1	10
β-strand	297	1	10
β-strand	301-304	4	9
α-helix	310-311	2
β-strand	313-316	4	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
β-strand	386-391	6	12
β-strand	394	1	13
β-strand	396-403	8	14
β-strand	410-413	4	15
β-strand	424-428	5	15
β-strand	433-439	7	15
β-strand	442-445	4	15
β-strand	457-463	7	16
β-strand	467-472	6	16
β-strand	476-480	5	16
β-strand	485-490	6	16
β-strand	500-503	4	17
β-strand	507-512	6	17
β-strand	515-522	8	17
β-strand	525-533	9	17
β-strand	538-542	5	18
β-strand	555-560	6	18
β-strand	565-570	6	18
β-strand	578-581	4	18
α-helix	587	1
β-strand	588-595	8	19
β-strand	600-606	7	19
β-strand	610-615	6	19
β-strand	624-630	7	19
β-strand	637-642	6	20
β-strand	647-652	6	20
β-strand	657-661	5	20
β-strand	666-670	5	20
β-strand	671	1	13
β-strand	678	1	14
β-strand	681-682	2	14
β-strand	690-694	5	14
β-strand	698-704	7	14
β-strand	711-712	2	12
β-strand	715-716	2	12
β-strand	720-727	8	21
β-strand	732-741	10	21
β-strand	751	1	21
β-strand	764-765	2	21
β-strand	786-795	10	21
β-strand	801-806	6	21
α-helix	807-808	2
β-strand	811-819	9	22
β-strand	828-835	8	22
β-strand	846-854	9	22
β-strand	857-866	10	22
β-strand	874-875	2	23
β-strand	880-881	2	23
β-strand	890	1	23
β-strand	893	1	24
β-strand	899	1	24
β-strand	903	1	23
β-strand	913-917	5	25
β-strand	920-924	5	25
β-strand	930-936	7	25
β-strand	941-948	8	25
β-strand	957-961	5	26
β-strand	964-968	5	26
β-strand	974-978	5	26
α-helix	988-990	3
β-strand	991	1	25
α-helix	992	1
β-strand	993-998	6	26
β-strand	1007-1009	3	1
β-strand	1025-1030	6	1
β-strand	1037-1042	6	1
α-helix	1045-1061	17
α-helix	1063-1064	2
α-helix	1070-1073	4
β-strand	1076-1077	2	27
β-strand	1082-1083	2	27
β-strand	1086	1	26
β-strand	1088-1090	3	1
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1108	7
α-helix	1126-1137	12

Chain C: 12 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	78-83	6	32
α-helix	91-92	2
β-strand	93	1	32
β-strand	97-99	3	32
α-helix	104-114	11
β-strand	119-123	5	32
β-strand	135-141	7	32
β-strand	157-167	11	32
β-strand	171	1	32
β-strand	179-184	6	32
β-strand	188	1	33
α-helix	201-203	3
α-helix	208-210	3
α-helix	221-231	11
α-helix	233-237	5
α-helix	242-246	5
α-helix	251-264	14
α-helix	277-285	9
α-helix	292-300	9
β-strand	303	1	33
α-helix	304-315	12
β-strand	321-322	2	34
α-helix	334-336	3
β-strand	346	1	35
β-strand	349-350	2	36
β-strand	356-357	2	36
β-strand	359-362	4	35
β-strand	368-370	3	37
β-strand	375	1	35
β-strand	384-388	5	35
β-strand	389-391	3	37
β-strand	400-404	5	35
β-strand	414-418	5	35
β-strand	423-424	2	34

Chain D: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	4-15	12
β-strand	22-25	4	38
β-strand	32-38	7	38
α-helix	39-40	2
β-strand	49-55	7	38
β-strand	66-69	4	38
β-strand	78	1	39
β-strand	83	1	38
β-strand	84	1	39
α-helix	87-90	4
α-helix	99-110	12
α-helix	121-129	9
α-helix	132-141	10
α-helix	142-146	5

Chain I: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	146-147	2	40
β-strand	154-155	2	40
α-helix	158-166	9
β-strand	175	1	41
β-strand	182	1	41
α-helix	187-196	10

Chain N: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	42
β-strand	12-16	5	42
β-strand	22	1	43
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	42
β-strand	48-49	2	42
α-helix	50-51	2
β-strand	55	1	43
α-helix	56-59	4
β-strand	66-71	6	42

Chain R: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	26-27	2	29
β-strand	30-34	5	28
β-strand	42	1	44
β-strand	47	1	44
α-helix	69-70	2
β-strand	71-72	2	45
β-strand	73	1	46
β-strand	78-79	2	45
α-helix	81-90	10
β-strand	103	1	46

Chain U: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	47
β-strand	12-16	5	47
β-strand	22	1	48
α-helix	23-33	11
β-strand	41-44	4	47
β-strand	55	1	48
β-strand	65-71	7	47

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	B	protein	1140	Homo sapiens	Q16531 (AlphaFold model)
Cullin-4A	A	protein	775	Homo sapiens	Q13619 (AlphaFold model)
Protein cereblon	C	protein	427	Homo sapiens	Q96SW2 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 D1	D	protein	146	Homo sapiens	P51668 (AlphaFold model)
Zinc finger protein Aiolos	I	protein	58	Homo sapiens	Q9UKT9
NEDD8	N	protein	76	Homo sapiens	Q15843
E3 ubiquitin-protein ligase RBX1, N-terminally processed	R	protein	111	Homo sapiens	P62877
Ubiquitin	U	protein	76	Homo sapiens	P62979

Sequence of entity 1 (B), FASTA

>9V09_1 DNA damage-binding protein 1 (chains B)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 2 (A), FASTA

>9V09_2 Cullin-4A (chains A)
GPGSGWSHPQFEKGSGSADEAPRKGSFSALVGRTNGLTKPAALAAAPAKPGGAGGSKKLV
IKNFRDRPRLPDNYTQDTWRKLHEAVRAVQSSTSIRYNLEELYQAVENLCSHKVSPMLYK
QLRQACEDHVQAQILPFREDSLDSVLFLKKINTCWQDHCRQMIMIRSIFLFLDRTYVLQN
STLPSIWDMGLELFRTHIISDKMVQSKTIDGILLLIERERSGEAVDRSLLRSLLGMLSDL
QVYKDSFELKFLEETNCLYAAEGQRLMQEREVPEYLNHVSKRLEEEGDRVITYLDHSTQK
PLIACVEKQLLGEHLTAILQKGLDHLLDENRVPDLAQMYQLFSRVRGGQQALLQHWSEYI
KTFGTAIVINPEKDKDMVQDLLDFKDKVDHVIEVCFQKNERFVNLMKESFETFINKRPNK
PAELIAKHVDSKLRAGNKEATDEELERTLDKIMILFRFIHGKDVFEAFYKKDLAKRLLVG
KSASVDAEKSMLSKLKHECGAAFTSKLEGMFKDMELSKDIMVHFKQHMQNQSDSGPIDLT
VNILTMGYWPTYTPMEVHLTPEMIKLQEVFKAFYLGKHSGRKLQWQTTLGHAVLKAEFKE
GKKEFQVSLFQTLVLLMFNEGDGFSFEEIKMATGIEDSELRRTLQSLACGKARVLIKSPK
GKEVEDGDKFIFNGEFKHKLFRIKINQIQMKETVEEQVSTTERVFQDRQYQIDAAIVRIM
KMRKTLGHNLLVSELYNQLKFPVKPGDLKKRIESLIDRDYMERDKDNPNQYHYVA

Sequence of entity 3 (C), FASTA

>9V09_3 Protein cereblon (chains C)
GSSHHHHHHHHSSGLEVLFQGPGSSAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDD
DSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQF
GTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMS
AVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMD
RIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIM
NKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPS
TEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISP
DKVILCL

Sequence of entity 4 (D), FASTA

>9V09_4 Ubiquitin-conjugating enzyme E2 D1 (chains D)
ALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPTDYP
FKPPKIAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPNPDDPLVP
DIAQIYKSDKEKYNRHAREWTQKYAM

Sequence of entity 5 (I), FASTA

>9V09_5 Zinc finger protein Aiolos (chains I)
GPGERPFQCNQCGASFTQKGNLLRHICLHTGEKPFKCHLCNYATQRRDALTGHLRTHS

Sequence of entity 6 (N), FASTA

>9V09_6 NEDD8 (chains N)
MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK
ILGGSVLHLVLALRGG

Sequence of entity 7 (R), FASTA

>9V09_7 E3 ubiquitin-protein ligase RBX1, N-terminally processed (chains R)
GPGSAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQ
ANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Sequence of entity 8 (U), FASTA

>9V09_8 Ubiquitin (chains U)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
LVY	S-Lenalidomide	C13 H13 N3 O3	1
ZN	Zinc ion	Zn	6

Primary citation

Cryo-EM structure of lenalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly. Deng, Z.H., Ai, H.S., Liu, L. To be published.

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 9V09 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.