4A0L: DDB1-DDB2-CUL4B-RBX1

Structure of DDB1-DDB2-CUL4B-RBX1 bound to a 12 bp abasic site containing DNA-duplex. Determined by X-ray diffraction at 7.4 Å resolution. Released 14 Dec 2011.

Method: X-ray diffraction
Resolution: 7.4 Å
Organisms: HOMO SAPIENS, DANIO RERIO, MUS MUSCULUS
Chains: 12
Atoms: 35,553
Mol. weight: 548.74 kDa
Released: 14 Dec 2011

Explore 4A0L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4A0L contains 124 α-helices and 312 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: 16 helices, 107 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
β-strand	115	1	4
β-strand	121-124	4	5
β-strand	130-134	5	5
β-strand	136	1	4
β-strand	139-144	6	5
β-strand	155-158	4	5
β-strand	164-169	6	6
α-helix	170	1
β-strand	177-184	8	6
β-strand	187-196	10	6
β-strand	201-204	4	6
β-strand	210-212	3	6
β-strand	218-221	4	7
α-helix	222-223	2
β-strand	229-232	4	7
β-strand	237-241	5	7
β-strand	244-248	5	7
α-helix	251-254	4
β-strand	258-263	6	8
β-strand	270-275	6	8
β-strand	279-288	10	8
β-strand	296-307	12	8
α-helix	310-311	2
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	1	10
β-strand	394	1	11
β-strand	400-401	2	12
β-strand	410-413	4	13
β-strand	424-427	4	13
β-strand	429	1	14
β-strand	432	1	14
β-strand	435-439	5	13
β-strand	442-445	4	13
β-strand	457-463	7	15
β-strand	467-472	6	15
β-strand	476-480	5	15
β-strand	486-488	3	15
α-helix	496-498	3
β-strand	500-501	2	16
β-strand	507-512	6	16
β-strand	515-522	8	16
β-strand	525-533	9	16
β-strand	538-542	5	17
β-strand	555-560	6	17
β-strand	565	1	18
β-strand	568-570	3	17
β-strand	575-578	4	17
β-strand	581	1	18
β-strand	588-590	3	19
β-strand	593-595	3	20
β-strand	600-603	4	20
β-strand	605-606	2	19
β-strand	610-614	5	20
β-strand	617	1	21
β-strand	622	1	21
β-strand	627-630	4	20
β-strand	637	1	22
β-strand	641-642	2	23
β-strand	647-648	2	23
β-strand	652	1	22
β-strand	660-661	2	24
β-strand	666-667	2	24
β-strand	671	1	11
β-strand	678-682	5	12
β-strand	690-694	5	12
β-strand	699-702	4	12
β-strand	720-727	8	25
α-helix	728-730	3
β-strand	732-743	12	25
α-helix	744	1
β-strand	749-751	3	25
β-strand	762-765	4	25
β-strand	785-795	11	25
β-strand	801-806	6	25
β-strand	811-819	9	26
β-strand	828-835	8	26
β-strand	846-853	8	26
β-strand	858-866	9	26
β-strand	870-876	7	27
β-strand	879-884	6	27
β-strand	887-893	7	27
β-strand	899-905	7	27
β-strand	911-917	7	28
β-strand	920-925	6	28
β-strand	928	1	29
β-strand	930-936	7	28
β-strand	941-947	7	28
β-strand	952	1	29
β-strand	954-959	6	30
β-strand	964-969	6	30
β-strand	973-979	7	30
α-helix	986-989	4
β-strand	991	1	28
β-strand	992-999	8	30
β-strand	1004-1009	6	1
β-strand	1025-1032	8	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	31
β-strand	1082-1083	2	31
β-strand	1086	1	30
β-strand	1088-1090	3	1
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1109	8
α-helix	1126-1137	12

Chains B and D: 3 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	105-113	9
α-helix	119-134	16
β-strand	138-143	6	32
β-strand	150-155	6	33
β-strand	162-167	6	33
β-strand	172-176	5	33
β-strand	183-186	4	33
β-strand	195-200	6	34
β-strand	207-212	6	34
β-strand	216-221	6	34
β-strand	226-229	4	34
β-strand	240-246	7	35
β-strand	251-256	6	35
β-strand	260-265	6	35
β-strand	270-275	6	35
β-strand	281-287	7	36
β-strand	290-298	9	36
β-strand	302-307	6	36
β-strand	317-322	6	36
β-strand	327-332	6	37
β-strand	339-344	6	37
β-strand	348-353	6	37
β-strand	362-365	4	37
α-helix	375-377	3
β-strand	378	1	32
β-strand	380-381	2	38
β-strand	387-391	5	38
β-strand	406-410	5	38
β-strand	416-420	5	38
β-strand	422	1	39
β-strand	425	1	39
β-strand	429-434	6	32
β-strand	441-445	5	32
β-strand	448-453	6	32

Chain C: 16 helices, 108 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	40
β-strand	17-21	5	41
β-strand	30-35	6	41
β-strand	38-45	8	41
β-strand	48-56	9	41
β-strand	61-67	7	42
β-strand	76-81	6	42
β-strand	85-94	10	42
β-strand	97-107	11	42
β-strand	115	1	43
β-strand	121-124	4	44
β-strand	130-134	5	44
β-strand	136	1	43
β-strand	139-144	6	44
β-strand	155-158	4	44
β-strand	164-169	6	45
α-helix	170	1
β-strand	177-184	8	45
β-strand	187-196	10	45
β-strand	201-204	4	45
β-strand	210-212	3	45
β-strand	218-221	4	46
α-helix	222-223	2
β-strand	229-232	4	46
β-strand	237-241	5	46
β-strand	244-248	5	46
α-helix	251-254	4
β-strand	258-263	6	47
β-strand	270-275	6	47
β-strand	279-288	10	47
β-strand	296-307	12	47
α-helix	310-311	2
β-strand	313-318	6	48
β-strand	321-325	5	48
β-strand	331-336	6	48
β-strand	347-353	7	48
β-strand	359-365	7	49
β-strand	374-379	6	49
α-helix	382-384	3
β-strand	386-393	8	49
β-strand	394	1	50
β-strand	396-401	6	51
β-strand	410-413	4	52
β-strand	424-427	4	52
β-strand	429	1	53
β-strand	432	1	53
β-strand	435-439	5	52
β-strand	442-445	4	52
β-strand	457-463	7	54
β-strand	467-472	6	54
β-strand	476-480	5	54
β-strand	486-488	3	54
α-helix	496-498	3
β-strand	500-501	2	55
β-strand	507-512	6	55
β-strand	515-522	8	55
β-strand	525-533	9	55
β-strand	538-542	5	56
β-strand	555-560	6	56
β-strand	565	1	57
β-strand	568-570	3	56
β-strand	575-578	4	56
β-strand	581	1	57
β-strand	588-590	3	58
β-strand	593-595	3	59
β-strand	600-603	4	59
β-strand	605-606	2	58
β-strand	610-614	5	59
β-strand	617	1	60
β-strand	622	1	60
β-strand	627-630	4	59
β-strand	637	1	61
β-strand	641-642	2	62
β-strand	647-648	2	62
β-strand	652	1	61
β-strand	660-661	2	63
β-strand	666-667	2	63
β-strand	671	1	50
β-strand	678-682	5	51
β-strand	690-694	5	51
β-strand	699-704	6	51
β-strand	709-716	8	49
β-strand	720-727	8	64
α-helix	728-730	3
β-strand	732-743	12	64
α-helix	744	1
β-strand	749-751	3	64
β-strand	762-765	4	64
β-strand	785-795	11	64
β-strand	801-806	6	64
β-strand	811-819	9	65
β-strand	828-835	8	65
β-strand	846-853	8	65
β-strand	858-866	9	65
β-strand	870-876	7	66
β-strand	879-884	6	66
β-strand	887-893	7	66
β-strand	899-905	7	66
β-strand	911-917	7	67
β-strand	920-925	6	67
β-strand	928	1	68
β-strand	930-936	7	67
β-strand	941-947	7	67
β-strand	952	1	68
β-strand	954-959	6	69
β-strand	964-969	6	69
β-strand	973-979	7	69
α-helix	986-989	4
β-strand	991	1	67
β-strand	992-999	8	69
β-strand	1004-1009	6	40
β-strand	1025-1032	8	40
β-strand	1037-1042	6	40
α-helix	1045-1061	17
α-helix	1063-1064	2
α-helix	1070-1073	4
β-strand	1076-1077	2	70
β-strand	1082-1083	2	70
β-strand	1086	1	69
β-strand	1088-1090	3	40
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1109	8
α-helix	1126-1137	12

Chain E: 44 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	197	1	12
β-strand	201	1	13
α-helix	216-218	3
α-helix	224-227	4
α-helix	240-244	5
α-helix	254-268	15
α-helix	272-275	4
α-helix	282-306	25
α-helix	308-310	3
α-helix	311-315	5
α-helix	316-317	2
α-helix	322-323	2
α-helix	324-331	8
α-helix	332-336	5
α-helix	341-357	17
α-helix	367-377	11
α-helix	381-385	5
α-helix	386-403	18
α-helix	410-427	18
α-helix	428-430	3
α-helix	438-444	7
α-helix	445-449	5
α-helix	453-459	7
α-helix	461-466	6
α-helix	470-480	11
α-helix	486-505	20
α-helix	509-511	3
α-helix	516-532	17
α-helix	538-552	15
α-helix	558-569	12
α-helix	584-594	11
α-helix	600-616	17
α-helix	625-631	7
α-helix	640-643	4
α-helix	647-669	23
β-strand	676-677	2	79
β-strand	680-683	4	80
α-helix	690-692	3
α-helix	701-704	4
α-helix	706-712	7
β-strand	714	1	81
β-strand	717	1	81
β-strand	721-734	14	80
β-strand	742-746	5	80
α-helix	747-754	8
α-helix	755-757	3
β-strand	762-763	2	82
α-helix	764-771	8
α-helix	775-781	7
β-strand	793-795	3	82
β-strand	807-810	4	82
β-strand	821-822	2	80
α-helix	826-828	3
α-helix	832-860	29
β-strand	863-865	3	83
α-helix	870-876	7
α-helix	883-894	12
β-strand	900-901	2	83
β-strand	908-910	3	83

Chain F: 0 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	22-24	3	80
β-strand	26-27	2	79
β-strand	28-33	6	80

Chain H: 42 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	201	1	52
α-helix	216-218	3
α-helix	224-228	5
α-helix	240-244	5
α-helix	254-268	15
α-helix	272-275	4
α-helix	282-306	25
α-helix	308-310	3
α-helix	311-315	5
α-helix	316-317	2
α-helix	322-323	2
α-helix	324-335	12
α-helix	341-357	17
α-helix	366-376	11
α-helix	381-385	5
α-helix	386-403	18
α-helix	410-427	18
α-helix	437-444	8
α-helix	445-449	5
α-helix	453-459	7
α-helix	461-467	7
α-helix	470-480	11
α-helix	486-505	20
α-helix	509-511	3
α-helix	516-532	17
α-helix	538-552	15
α-helix	558-569	12
α-helix	584-594	11
α-helix	601-616	16
α-helix	625-631	7
α-helix	640-643	4
α-helix	647-669	23
β-strand	676-677	2	84
β-strand	680-683	4	85
α-helix	690-692	3
α-helix	701-704	4
α-helix	706-712	7
β-strand	714	1	86
β-strand	717	1	86
β-strand	719-734	16	85
β-strand	742-746	5	85
α-helix	747-754	8
α-helix	755-757	3
β-strand	762-763	2	87
α-helix	764-771	8
α-helix	775-781	7
β-strand	793-795	3	87
β-strand	807-810	4	87
β-strand	821-822	2	85
α-helix	826-828	3
α-helix	832-860	29
β-strand	863-865	3	88
α-helix	870-876	7
α-helix	883-894	12
β-strand	900-901	2	88
β-strand	908-910	3	88

Chain I: 0 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	22-24	3	85
β-strand	26-27	2	84
β-strand	28-35	8	85

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A, C	protein	1144	HOMO SAPIENS	Q16531 (AlphaFold model)
DNA damage-binding protein 2	B, D	protein	382	DANIO RERIO	Q2YDS1 (AlphaFold model)
Cullin-4B	E, H	protein	726	HOMO SAPIENS	Q13620 (AlphaFold model)
E3 ubiquitin-protein ligase RBX1	F, I	protein	98	MUS MUSCULUS	P62878 (AlphaFold model)
12 bp thf containing DNA duplex	R, T	DNA	12	SYNTHETIC CONSTRUCT
12 bp DNA duplex	S, U	DNA	12	SYNTHETIC CONSTRUCT

Sequence of entity 1 (A, C), FASTA

>4A0L_1 DNA DAMAGE-BINDING PROTEIN 1 (chains A, C)
GGGRMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVG
MYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPS
ETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAP
TICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQES
ITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVT
LKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNL
GPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSD
PNRETDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASV
RLVSQEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEH
EVACLDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTF
ESSHYLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRP
TVIYSSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVP
LYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTA
PHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMV
YPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTE
KELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSA
VEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQN
LGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSF
HTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEEL
TRIH

Sequence of entity 2 (B, D), FASTA

>4A0L_2 DNA DAMAGE-BINDING PROTEIN 2 (chains B, D)
MHHHHHHRRLVPRGSGGRTGGQKKVGQTSILHYIYKSSLGQSIHAQLRQCLQEPFIRSLK
SYKLHRTASPFDRRVTSLEWHPTHPTTVAVGSKGGDIILWDYDVQNKTSFIQGMGPGDAI
TGMKFNQFNTNQLFVSSIRGATTLRDFSGSVIQVFAKTDSWDYWYCCVDVSVSRQMLATG
DSTGRLLLLGLDGHEIFKEKLHKAKVTHAEFNPRCDWLMATSSVDATVKLWDLRNIKDKN
SYIAEMPHEKPVNAAYFNPTDSTKLLTTDQRNEIRVYSSYDWSKPDQIIIHPHRQFQHLT
PIKATWHPMYDLIVAGRYPDDQLLLNDKRTIDIYDANSGGLVHQLRDPNAAGIISLNKFS
PTGDVLASGMGFNILIWNREDT

Sequence of entity 3 (E, H), FASTA

>4A0L_3 CULLIN-4B (chains E, H)
GGGRGSAKKLVIKNFKDKPKLPENYTDETWQKLKEAVEAIQNSTSIKYNLEELYQAVENL
CSYKISANLYKQLRQICEDHIKAQIHQFREDSLDSVLFLKKIDRCWQNHCRQMIMIRSIF
LFLDRTYVLQNSMLPSIWDMGLELFRAHIISDQKVQNKTIDGILLLIERERNGEAIDRSL
LRSLLSMLSDLQIYQDSFEQRFLEETNRLYAAEGQKLMQEREVPEYLHHVNKRLEEEADR
LITYLDQTTQKSLIATVEKQLLGEHLTAILQKGLNNLLDENRIQDLSLLYQLFSRVRGGV
QVLLQQWIEYIKAFGSTIVINPEKDKTMVQELLDFKDKVDHIIDICFLKNEKFINAMKEA
FETFINKRPNKPAELIAKYVDSKLRAGNKEATDEELEKMLDKIMIIFRFIYGKDVFEAFY
KKDLAKRLLVGKSASVDAEKSMLSKLKHECGAAFTSKLEGMFKDMELSKDIMIQFKQYMQ
NQNVPGNIELTVNILTMGYWPTYVPMEVHLPPEMVKLQEIFKTFYLGKHSGRKLQWQSTL
GHCVLKAEFKEGKKELQVSLFQTLVLLMFNEGEEFSLEEIKQATGIEDGELRRTLQSLAC
GKARVLAKNPKGKDIEDGDKFICNDDFKHKLFRIKINQIQMKETVEEQASTTERVFQDRQ
YQIDAAIVRIMKMRKTLSHNLLVSEVYNQLKFPVKPADLKKRIESLIDRDYMERDKENPN
QYNYIA

Sequence of entity 4 (F, I), FASTA

>4A0L_4 E3 UBIQUITIN-PROTEIN LIGASE RBX1 (chains F, I)
MGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTV
AWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Sequence of entity 5 (R, T), FASTA

>4A0L_5 12 BP THF CONTAINING DNA DUPLEX (chains R, T)
GCTACTNACGCA

Sequence of entity 6 (S, U), FASTA

>4A0L_6 12 BP DNA DUPLEX (chains S, U)
TGCGTAAGTAGC

Primary citation

The Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase Architecture, Targeting, and Activation. Fischer, E.S., Scrima, A., Bohm, K. et al. Cell (2011) 147:1024. DOI 10.1016/J.CELL.2011.10.035 · 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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