2HYE: DDB1-Cul4A-Rbx1-SV5V Complex

Crystal Structure of the DDB1-Cul4A-Rbx1-SV5V Complex. Determined by X-ray diffraction at 3.1 Å resolution. Released 3 Oct 2006.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Homo sapiens, Simian virus 5
Chains: 4
Atoms: 16,943
Mol. weight: 251.51 kDa
Ligands: ZN
Released: 3 Oct 2006

Explore 2HYE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2HYE contains 58 α-helices and 147 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: 14 helices, 116 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	1
β-strand	17-21	5	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	85-93	9	3
β-strand	98-107	10	3
β-strand	115	1	4
β-strand	121-124	4	4
β-strand	130-136	7	4
β-strand	139-144	6	4
β-strand	155-158	4	4
β-strand	164-170	7	5
β-strand	177-184	8	5
β-strand	187-189	3	5
β-strand	194	1	5
β-strand	195-196	2	6
β-strand	201-202	2	6
β-strand	218-221	4	7
α-helix	222-223	2
β-strand	229-232	4	7
β-strand	237-240	4	7
β-strand	245	1	7
β-strand	248	1	7
α-helix	251-254	4
β-strand	258-263	6	8
β-strand	270-275	6	8
β-strand	279-286	8	8
β-strand	289	1	9
β-strand	295	1	9
β-strand	299-307	9	8
β-strand	311-316	6	10
β-strand	321-326	6	10
β-strand	331-336	6	10
α-helix	342-344	3
β-strand	347-353	7	10
α-helix	357	1
α-helix	359	1
β-strand	361-365	5	11
β-strand	374-379	6	11
β-strand	386-393	8	11
β-strand	394	1	12
β-strand	396-401	6	13
β-strand	410-413	4	14
β-strand	424-427	4	14
β-strand	429	1	15
β-strand	432	1	15
β-strand	435-439	5	14
β-strand	442-445	4	14
β-strand	457-463	7	16
β-strand	467-472	6	16
β-strand	476-480	5	16
β-strand	486-488	3	16
α-helix	496-498	3
β-strand	500-501	2	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	1	19
β-strand	568-570	3	18
β-strand	575-578	4	18
β-strand	581	1	19
β-strand	588-590	3	20
β-strand	593-595	3	21
β-strand	600-603	4	21
β-strand	605-606	2	20
β-strand	610-614	5	21
β-strand	617	1	22
β-strand	622	1	22
β-strand	627-630	4	21
β-strand	637	1	23
β-strand	641-642	2	24
β-strand	647-648	2	24
β-strand	652	1	23
β-strand	660-661	2	25
β-strand	666-667	2	25
β-strand	671	1	12
β-strand	678-682	5	13
β-strand	690-694	5	13
β-strand	699-704	6	13
β-strand	709-716	8	11
β-strand	723-727	5	26
β-strand	732-736	5	26
β-strand	739-741	3	27
β-strand	742-744	3	28
β-strand	748-750	3	28
α-helix	756-758	3
β-strand	762	1	26
β-strand	786-788	3	27
β-strand	790-795	6	26
β-strand	801-806	6	26
β-strand	811-819	9	29
β-strand	828-835	8	29
β-strand	846-849	4	30
β-strand	850-851	2	29
β-strand	853	1	31
β-strand	858	1	31
β-strand	863-866	4	30
β-strand	872-876	5	32
β-strand	879-883	5	32
β-strand	890-893	4	33
β-strand	899-903	5	33
β-strand	911-913	3	34
β-strand	920-925	6	34
β-strand	928	1	35
β-strand	930-934	5	34
β-strand	935-936	2	36
β-strand	941-942	2	36
β-strand	946-947	2	34
β-strand	952	1	35
β-strand	954-961	8	37
β-strand	964-969	6	37
β-strand	973-979	7	37
β-strand	992-999	8	37
β-strand	1004-1009	6	1
β-strand	1024-1032	9	1
β-strand	1037-1043	7	1
α-helix	1045-1061	17
α-helix	1063-1064	2
α-helix	1070-1073	4
β-strand	1086	1	37
β-strand	1088-1090	3	1
α-helix	1093-1095	3
α-helix	1102-1109	8
α-helix	1126-1136	11
α-helix	1137-1139	3

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	18-19	2	38
α-helix	23-32	10
β-strand	42-43	2	38
β-strand	48-49	2	39
β-strand	83	1	39
β-strand	96-97	2	40
α-helix	98-99	2
β-strand	111-114	4	39
β-strand	124	1	39
α-helix	127-137	11
β-strand	143-146	4	39
β-strand	173-178	6	39
β-strand	185-190	6	39
β-strand	202-203	2	40

Chain C: 39 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	45-46	2	14
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	168-169	2
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	41
α-helix	534-535	2
α-helix	545-559	15
β-strand	565-566	2	42
β-strand	569	1	41
α-helix	571-573	3
β-strand	575-579	5	41
β-strand	588-592	5	41
α-helix	593-601	9
β-strand	608-609	2	43
α-helix	610-616	7
α-helix	621-629	9
β-strand	639-641	3	43
β-strand	653-656	4	43
β-strand	667-668	2	41
α-helix	670-674	5
α-helix	678-706	29
β-strand	709-711	3	44
α-helix	713-722	10
α-helix	729-741	13
β-strand	746	1	44
β-strand	754-756	3	44

Chain D: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	24-33	10	41
β-strand	34-35	2	42
α-helix	65-67	3
β-strand	70-72	3	45
β-strand	78-80	3	45
α-helix	82-85	4
β-strand	95	1	46
β-strand	97	1	46
β-strand	106	1	45

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A	protein	1140	Homo sapiens	Q16531 (AlphaFold model)
Nonstructural protein V	B	protein	222	Simian virus 5	P11207 (AlphaFold model)
Cullin-4A	C	protein	759	Homo sapiens	Q13619 (AlphaFold model)
RING-box protein 1	D	protein	108	Homo sapiens	P62877 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2HYE_1 DNA damage-binding protein 1 (chains A)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TYDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKDVR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 2 (B), FASTA

>2HYE_2 Nonstructural protein V (chains B)
MDPTDLSFSPDEINKLIETGLNTVEYFTSQQVTGTSSLGKNTIPPGVTGLLTNAAEAKIQ
ESTNHQKGSVGGGAKPKKPRPKIAIVPADDKTVPGKPIPNPLLGLDSTPSTQTVLDLSGK
TLPSGSYKGVKLAKFGKENLMTRFIEEPRENPIATSSPIDFKRGRDTGGFHRREYSIGWV
GDEVKVTEWCNPSCSPITAAARRFECTCHQCPVTCSECERDT

Sequence of entity 3 (C), FASTA

>2HYE_3 Cullin-4A (chains C)
MADEAPRKGSFSALVGRTNGLTKPAALAAAPAKPGGAGGSKKLVIKNFRDRPRLPDNYTQ
DTWRKLHEAVRAVQSSTSIRYNLEELYQAVENLCSHKVSPMLYKQLRQACEDHVQAQILP
FREDSLDSVLFLKKINTCWQDHCRQMIMIRSIFLFLDRTYVLQNSTLPSIWDMGLELFRT
HIISDKMVQSKTIDGILLLIERERSGEAVDRSLLRSLLGMLSDLQVYKDSFELKFLEETN
CLYAAEGQRLMQEREVPEYLNHVSKRLEEEGDRVITYLDHSTQKPLIACVEKQLLGEHLT
AILQKGLDHLLDENRVPDLAQMYQLFSRVRGGQQALLQHWSEYIKTFGTAIVINPEKDKD
MVQDLLDFKDKVDHVIEVCFQKNERFVNLMKESFETFINKRPNKPAELIAKHVDSKLRAG
NKEATDEELERTLDKIMILFRFIHGKDVFEAFYKKDLAKRLLVGKSASVDAEKSMLSKLK
HECGAAFTSKLEGMFKDMELSKDIMVHFKQHMQNQSDSGPIDLTVNILTMGYWPTYTPME
VHLTPEMIKLQEVFKAFYLGKHSGRKLQWQTTLGHAVLKAEFKEGKKEFQVSLFQTLVLL
MFNEGDGFSFEEIKMATGIEDSELRRTLQSLACGKARVLIKSPKGKEVEDGDKFIFNGEF
KHKLFRIKINQIQMKETVEEQVSTTERVFQDRQYQIDAAIVRIMKMRKTLGHNLLVSELY
NQLKFPVKPGDLKKRIESLIDRDYMERDKDNPNQYHYVA

Sequence of entity 4 (D), FASTA

>2HYE_4 RING-box protein 1 (chains D)
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	5

Primary citation

Molecular architecture and assembly of the DDB1-CUL4A ubiquitin ligase machinery. Angers, S., Li, T., Yi, X. et al. Nature (2006) 443:590-593. DOI 10.1038/nature05175 · 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

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