4A0K: DDB1-DDB2-CUL4A-RBX1

Structure of DDB1-DDB2-CUL4A-RBX1 bound to a 12 bp abasic site containing DNA-duplex. Determined by X-ray diffraction at 5.93 Å resolution. Released 14 Dec 2011.

Method: X-ray diffraction
Resolution: 5.93 Å
Organisms: HOMO SAPIENS, MUS MUSCULUS, DANIO RERIO
Chains: 6
Atoms: 17,885
Mol. weight: 280.34 kDa
Released: 14 Dec 2011

Explore 4A0K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4A0K contains 58 α-helices and 153 β-strands across 4 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, 12 β-strands

Element	Residues	Length	Sheet
β-strand	46	1	1
α-helix	62-71	10
α-helix	83-93	11
α-helix	99-121	23
α-helix	130-152	23
α-helix	154-156	3
α-helix	157-161	5
α-helix	170-178	9
α-helix	179-183	5
α-helix	189-201	13
α-helix	211-223	13
α-helix	227-230	4
α-helix	232-253	22
α-helix	256-269	14
α-helix	271-274	4
α-helix	283-294	12
α-helix	300-304	5
α-helix	307-311	5
α-helix	316-328	13
α-helix	332-352	21
α-helix	355-357	3
α-helix	361-377	17
α-helix	384-398	15
α-helix	404-417	14
α-helix	421-423	3
α-helix	429-440	12
α-helix	446-462	17
α-helix	469-480	12
α-helix	489-513	25
β-strand	522-529	8	2
α-helix	534-535	2
α-helix	545-559	15
β-strand	565-566	2	3
β-strand	569	1	2
α-helix	571-573	3
β-strand	575-580	6	2
β-strand	588-592	5	2
α-helix	593-601	9
β-strand	608-609	2	4
α-helix	610-616	7
α-helix	621-629	9
β-strand	639-641	3	4
β-strand	653-656	4	4
β-strand	667-668	2	2
α-helix	670-674	5
α-helix	678-689	12
α-helix	692-706	15
α-helix	713-722	10
α-helix	729-741	13
β-strand	746	1	5
β-strand	756	1	5

Chain B: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	22-33	12	2
β-strand	34-35	2	3

Chain C: 15 helices, 108 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	6
β-strand	17-21	5	7
β-strand	30-35	6	7
β-strand	38-45	8	7
β-strand	48-56	9	7
β-strand	61-67	7	8
β-strand	76-81	6	8
β-strand	85-94	10	8
β-strand	97-107	11	8
β-strand	115	1	9
β-strand	121-124	4	10
β-strand	130-134	5	10
β-strand	136	1	9
β-strand	139-144	6	10
β-strand	155-158	4	10
β-strand	163-169	7	11
α-helix	170	1
β-strand	177-184	8	11
β-strand	187-196	10	11
β-strand	201-204	4	11
β-strand	210-211	2	11
β-strand	218-221	4	12
α-helix	222-223	2
β-strand	229-232	4	12
β-strand	237-241	5	12
β-strand	244-248	5	12
α-helix	251-254	4
β-strand	258-263	6	13
β-strand	270-275	6	13
β-strand	279-288	10	13
β-strand	296-307	12	13
α-helix	310-311	2
β-strand	313-318	6	14
β-strand	321-325	5	14
β-strand	331-336	6	14
β-strand	347-353	7	14
β-strand	359-365	7	15
β-strand	374-379	6	15
α-helix	382-384	3
β-strand	386-391	6	15
β-strand	394	1	16
β-strand	400-401	2	17
β-strand	410-413	4	1
β-strand	424-427	4	1
β-strand	429	1	18
β-strand	432	1	18
β-strand	435-439	5	1
β-strand	442-445	4	1
β-strand	457-463	7	19
β-strand	467-472	6	19
β-strand	476-480	5	19
β-strand	486-488	3	19
α-helix	496-498	3
β-strand	500-501	2	20
β-strand	507-512	6	20
β-strand	515-522	8	20
β-strand	525-533	9	20
β-strand	538-542	5	21
β-strand	555-560	6	21
β-strand	565	1	22
β-strand	568-570	3	21
β-strand	575-578	4	21
β-strand	581	1	22
β-strand	588-590	3	23
β-strand	593-595	3	24
β-strand	600-603	4	24
β-strand	605-606	2	23
β-strand	610-614	5	24
β-strand	617	1	25
β-strand	622	1	25
β-strand	627-630	4	24
β-strand	637	1	26
β-strand	641-642	2	27
β-strand	647-648	2	27
β-strand	652	1	26
β-strand	660-661	2	28
β-strand	666-667	2	28
β-strand	671	1	16
β-strand	678-682	5	17
β-strand	690-694	5	17
β-strand	699-702	4	17
β-strand	713-716	4	15
β-strand	720-727	8	29
α-helix	728-730	3
β-strand	732-743	12	29
α-helix	744	1
β-strand	749-751	3	29
β-strand	762-765	4	29
β-strand	785-795	11	29
β-strand	801-806	6	29
β-strand	811-819	9	30
β-strand	828-835	8	30
β-strand	846-853	8	30
β-strand	858-866	9	30
β-strand	870-876	7	31
β-strand	879-884	6	31
β-strand	887-893	7	31
β-strand	899-905	7	31
β-strand	911-917	7	32
β-strand	920-925	6	32
β-strand	928	1	33
β-strand	930-936	7	32
β-strand	941-947	7	32
β-strand	952	1	33
β-strand	954-959	6	34
β-strand	964-969	6	34
β-strand	973-979	7	34
α-helix	986-989	4
β-strand	991	1	32
β-strand	992-999	8	34
β-strand	1004-1009	6	6
β-strand	1025-1032	8	6
β-strand	1037-1042	6	6
α-helix	1045-1061	17
α-helix	1070-1073	4
β-strand	1076-1077	2	35
β-strand	1082-1083	2	35
β-strand	1086	1	34
β-strand	1088-1090	3	6
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1109	8
α-helix	1126-1137	12

Chain D: 4 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	105-113	9
α-helix	119-123	5
α-helix	128-134	7
β-strand	138-143	6	36
β-strand	150-155	6	37
β-strand	162-167	6	37
β-strand	172-176	5	37
β-strand	183-186	4	37
β-strand	195-200	6	38
β-strand	207-212	6	38
β-strand	216-221	6	38
β-strand	226-229	4	38
β-strand	240-246	7	39
β-strand	251-256	6	39
β-strand	260-265	6	39
β-strand	270-275	6	39
β-strand	281-287	7	40
β-strand	290-298	9	40
β-strand	302-307	6	40
β-strand	317-322	6	40
β-strand	327-332	6	41
β-strand	339-344	6	41
β-strand	348-353	6	41
β-strand	362-365	4	41
α-helix	375-377	3
β-strand	378	1	36
β-strand	380-381	2	42
β-strand	387-391	5	42
β-strand	406-410	5	42
β-strand	416-420	5	42
β-strand	422	1	43
β-strand	425	1	43
β-strand	429-434	6	36
β-strand	441-445	5	36
β-strand	448-453	6	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cullin-4A	A	protein	742	HOMO SAPIENS	Q13619 (AlphaFold model)
E3 ubiquitin-protein ligase RBX1	B	protein	117	MUS MUSCULUS	P62878 (AlphaFold model)
DNA damage-binding protein 1	C	protein	1159	HOMO SAPIENS	Q16531 (AlphaFold model)
DNA damage-binding protein 2	D	protein	382	DANIO RERIO	Q2YDS1 (AlphaFold model)
12 bp thf containing DNA	E	DNA	12	SYNTHETIC CONSTRUCT
12 bp DNA	F	DNA	12	SYNTHETIC CONSTRUCT

Sequence of entity 1 (A), FASTA

>4A0K_1 CULLIN-4A (chains A)
MHHHHHHVDEENLYFQGGGRGGSKKLVIKNFRDRPRLPDNYTQDTWRKLHEAVRAVQSST
SIRYNLEELYQAVENLCSHKVSPMLYKQLRQACEDHVQAQILPFREDSLDSVLFLKKINT
CWQDHCRQMIMIRSIFLFLDRTYVLQNSTLPSIWDMGLELFRTHIISDKMVQSKTIDGIL
LLIERERSGEAVDRSLLRSLLGMLSDLQVYKDSFELKFLEETNCLYAAEGQRLMQEREVP
EYLNHVSKRLEEEGDRVITYLDHSTQKPLIACVEKQLLGEHLTAILQKGLDHLLDENRVP
DLAQMYQLFSRVRGGQQALLQHWSEYIKTFGTAIVINPEKDKDMVQDLLDFKDKVDHVIE
VCFQKNERFVNLMKESFETFINKRPNKPAELIAKHVDSKLRAGNKEATDEELERTLDKIM
ILFRFIHGKDVFEAFYKKDLAKRLLVGKSASVDAEKSMLSKLKHECGAAFTSKLEGMFKD
MELSKDIMVHFKQHMQNQSDSGPIDLTVNILTMGYWPTYTPMEVHLTPEMIKLQEVFKAF
YLGKHSGRKLQWQTTLGHAVLKAEFKEGKKEFQVSLFQTLVLLMFNEGDGFSFEEIKMAT
GIEDSELRRTLQSLACGKARVLIKSPKGKEVEDGDKFIFNGEFKHKLFRIKINQIQMKET
VEEQVSTTERVFQDRQYQIDAAIVRIMKMRKTLGHNLLVSELYNQLKFPVKPGDLKKRIE
SLIDRDYMERDKDNPNQYHYVA

Sequence of entity 2 (B), FASTA

>4A0K_2 E3 UBIQUITIN-PROTEIN LIGASE RBX1 (chains B)
MHHHHHHVDEENLYFQGGGRGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMD
LCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Sequence of entity 3 (C), FASTA

>4A0K_3 DNA DAMAGE-BINDING PROTEIN 1 (chains C)
MHHHHHHVDENLYFQGGGRMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEI
YVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDII
TRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEE
LHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIA
VPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLF
MLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSN
EQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHAS
IDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCG
NVAHQQLIQITSASVRLVSQEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQI
HPQELRQISHTEMEHEVACLDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEM
LGGEIIPRSILMTTFESSHYLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTF
RSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTI
GTIDEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQAL
SSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKL
GKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLL
ASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGN
FEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLG
EFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKV
IKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMK
REATADDLIKVVEELTRIH

Sequence of entity 4 (D), FASTA

>4A0K_4 DNA DAMAGE-BINDING PROTEIN 2 (chains D)
MHHHHHHRRLVPRGSGGRTGGQKKVGQTSILHYIYKSSLGQSIHAQLRQCLQEPFIRSLK
SYKLHRTASPFDRRVTSLEWHPTHPTTVAVGSKGGDIILWDYDVQNKTSFIQGMGPGDAI
TGMKFNQFNTNQLFVSSIRGATTLRDFSGSVIQVFAKTDSWDYWYCCVDVSVSRQMLATG
DSTGRLLLLGLDGHEIFKEKLHKAKVTHAEFNPRCDWLMATSSVDATVKLWDLRNIKDKN
SYIAEMPHEKPVNAAYFNPTDSTKLLTTDQRNEIRVYSSYDWSKPDQIIIHPHRQFQHLT
PIKATWHPMYDLIVAGRYPDDQLLLNDKRTIDIYDANSGGLVHQLRDPNAAGIISLNKFS
PTGDVLASGMGFNILIWNREDT

Sequence of entity 5 (E), FASTA

>4A0K_5 12 BP THF CONTAINING DNA (chains E)
GCTACTNACGCA

Sequence of entity 6 (F), FASTA

>4A0K_6 12 BP DNA (chains F)
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 Q13619 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7OPC 3.0 Å, Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 4)
7OPD 3.0 Å, Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 5)
2HYE 3.1 Å, Crystal Structure of the DDB1-Cul4A-Rbx1-SV5V Complex
9LWI 3.12 Å, The head region of HBx-Smc5/6 ubiquitination complex
9V09 3.25 Å, Cryo-EM structure of lenalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub…
9V0C 3.27 Å, Cryo-EM structure of iberdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub…
9EG8 3.39 Å, Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-4A
9UUM 3.41 Å, Cryo-EM structure of mezigdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub…
9UUQ 3.41 Å, Cryo-EM structure of thalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub…
8B3I 3.5 Å, CRL4CSA-E2-Ub (state 2)
9V0E 3.51 Å, Cryo-EM structure of golcadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub…
9V0B 3.54 Å, Cryo-EM structure of avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub…

Browse structure collections

About this viewer

MolViewer shows 4A0K 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.