6DSZ: DDB1

Name: PDB 6DSZ: Crystal structure of DDB1 in complex with DET1- and DDB1-associated protein 1 (DDA1)
Published: 2018-12-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of DDB1 in complex with DET1- and DDB1-associated protein 1 (DDA1). Determined by X-ray diffraction at 3.09 Å resolution. Released 12 Dec 2018.

Method: X-ray diffraction
Resolution: 3.09 Å
Organism: Homo sapiens
Chains: 4
Atoms: 17,408
Mol. weight: 258.67 kDa
Released: 12 Dec 2018

Explore 6DSZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6DSZ contains 24 α-helices and 204 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: 12 helices, 100 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	1
β-strand	17-22	6	2
β-strand	29-34	6	2
β-strand	38-45	8	2
β-strand	48-56	9	2
β-strand	61-67	7	3
α-helix	75	1
β-strand	76-81	6	3
β-strand	85-92	8	3
β-strand	99-107	9	3
β-strand	115	1	4
α-helix	116	1
β-strand	122-124	3	4
β-strand	130-136	7	4
β-strand	139-144	6	4
β-strand	151	1	3
β-strand	155-156	2	4
β-strand	163-169	7	5
α-helix	170	1
β-strand	177-183	7	5
β-strand	188-196	9	5
β-strand	201-204	4	5
α-helix	208-209	2
β-strand	210-211	2	5
β-strand	218-221	4	6
β-strand	229-232	4	6
β-strand	237-241	5	6
β-strand	244-248	5	6
β-strand	258-263	6	7
β-strand	270-275	6	7
β-strand	279-287	9	7
β-strand	297-307	11	7
β-strand	313-316	4	8
β-strand	321-325	5	8
β-strand	331-336	6	8
β-strand	347-353	7	8
β-strand	362-365	4	9
β-strand	374-379	6	9
α-helix	382-384	3
β-strand	386-392	7	9
β-strand	394	1	10
β-strand	398-400	3	11
β-strand	410-413	4	12
β-strand	422	1	13
β-strand	424-428	5	12
β-strand	432	1	14
β-strand	433-437	5	12
β-strand	445	1	12
β-strand	454	1	14
β-strand	459-460	2	15
β-strand	467-471	5	15
β-strand	476-480	5	15
β-strand	486-490	5	15
β-strand	500-503	4	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	566-570	5	17
β-strand	576-578	3	17
α-helix	587	1
β-strand	588-594	7	18
β-strand	601-606	6	18
β-strand	610-615	6	18
β-strand	629-630	2	18
β-strand	637-640	4	19
β-strand	649-652	4	19
β-strand	657-661	5	19
β-strand	666-670	5	19
β-strand	671	1	10
β-strand	678-682	5	11
β-strand	684	1	13
β-strand	690-694	5	11
β-strand	699-702	4	11
β-strand	710-716	7	9
β-strand	720-727	8	20
β-strand	732-742	11	20
β-strand	785-795	11	20
β-strand	801-806	6	20
β-strand	811-819	9	21
β-strand	828-835	8	21
β-strand	846-853	8	21
β-strand	858-866	9	21
β-strand	870-875	6	22
β-strand	880-884	5	22
β-strand	887-890	4	22
β-strand	892	1	23
β-strand	900	1	23
β-strand	914-918	5	24
β-strand	921-924	4	24
β-strand	931-935	5	24
β-strand	942-944	3	24
β-strand	947	1	25
β-strand	954-961	8	26
β-strand	964-969	6	26
β-strand	973-979	7	26
β-strand	991	1	25
β-strand	992-999	8	26
β-strand	1004-1009	6	1
β-strand	1025-1032	8	1
β-strand	1037-1042	6	1
α-helix	1045-1055	11
α-helix	1070-1074	5
β-strand	1076	1	27
β-strand	1083	1	27
α-helix	1084-1085	2
β-strand	1086	1	26
β-strand	1090	1	1
α-helix	1096-1099	4
α-helix	1102-1108	7
α-helix	1130-1136	7

Chain B: 11 helices, 104 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	28
β-strand	17-22	6	29
β-strand	29-34	6	29
β-strand	38-45	8	29
β-strand	48-51	4	29
β-strand	55-56	2	29
β-strand	61-67	7	30
α-helix	75	1
β-strand	76-81	6	30
β-strand	85-92	8	30
β-strand	99-102	4	30
α-helix	114	1
β-strand	115	1	31
β-strand	122-124	3	31
β-strand	130-136	7	31
β-strand	139-144	6	31
β-strand	155-156	2	31
β-strand	163-169	7	32
α-helix	170	1
β-strand	177-183	7	32
β-strand	188-196	9	32
β-strand	201-204	4	32
β-strand	210-211	2	32
β-strand	218-221	4	33
β-strand	229-232	4	33
β-strand	237-241	5	33
β-strand	244-248	5	33
β-strand	258-263	6	34
β-strand	270-275	6	34
β-strand	280-289	10	34
β-strand	295-306	12	34
β-strand	313-316	4	35
β-strand	321-325	5	35
β-strand	331-336	6	35
β-strand	342	1	36
β-strand	345	1	36
β-strand	347-353	7	35
β-strand	362-365	4	37
β-strand	374-379	6	37
α-helix	382-384	3
β-strand	386-392	7	37
β-strand	394	1	38
β-strand	400	1	39
β-strand	410-413	4	40
β-strand	422	1	41
β-strand	424-429	6	40
β-strand	432-437	6	40
β-strand	459-460	2	42
β-strand	467-471	5	42
β-strand	476-480	5	42
β-strand	486-490	5	42
β-strand	500-503	4	43
β-strand	507-512	6	43
β-strand	515-522	8	43
β-strand	525-533	9	43
β-strand	538-542	5	44
β-strand	555-560	6	44
β-strand	564-565	2	45
β-strand	567-570	4	44
β-strand	576-578	3	44
β-strand	581-582	2	45
α-helix	587	1
β-strand	588-594	7	46
β-strand	601-606	6	46
β-strand	610-615	6	46
β-strand	629-630	2	46
β-strand	637-641	5	47
β-strand	648-652	5	47
β-strand	657-658	2	47
β-strand	669-670	2	47
β-strand	671	1	38
β-strand	678-680	3	39
β-strand	684	1	41
β-strand	691-694	4	39
β-strand	699-702	4	39
β-strand	710-716	7	37
β-strand	720-727	8	48
β-strand	732-741	10	48
β-strand	751	1	48
β-strand	786-795	10	48
β-strand	801-806	6	48
β-strand	811-819	9	49
β-strand	828-835	8	49
β-strand	846-853	8	49
β-strand	858-866	9	49
β-strand	872-875	4	50
β-strand	880-884	5	50
β-strand	887-890	4	50
β-strand	892-893	2	51
β-strand	899-900	2	51
β-strand	914-916	3	52
β-strand	921-925	5	52
β-strand	930-935	6	52
β-strand	937	1	53
β-strand	939	1	53
β-strand	942-944	3	52
β-strand	947	1	54
β-strand	954-961	8	55
β-strand	964-969	6	55
β-strand	973-979	7	55
β-strand	991	1	54
β-strand	992-999	8	55
β-strand	1004-1008	5	28
β-strand	1029-1032	4	28
β-strand	1037-1042	6	28
α-helix	1045-1055	11
α-helix	1059-1061	3
α-helix	1070-1073	4
β-strand	1076	1	56
β-strand	1083	1	56
β-strand	1086	1	55
β-strand	1090	1	28
α-helix	1091-1093	3
α-helix	1096-1099	4
α-helix	1130-1136	7

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A, B	protein	1140	Homo sapiens	Q16531 (AlphaFold model)
DET1- and DDB1-associated protein 1	C, D	protein	19	Homo sapiens	Q9BW61 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6DSZ_1 DNA damage-binding protein 1 (chains A, B)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 2 (C, D), FASTA

>6DSZ_2 DET1- and DDB1-associated protein 1 (chains C, D)
MADFLKGLPVYNKSNFSRF

Primary citation

Structural insights into DDA1 function as a core component of the CRL4-DDB1 ubiquitin ligase. Shabek, N., Ruble, J., Waston, C.J. et al. Cell Discov (2018) 4:67-67. DOI 10.1038/s41421-018-0064-8 · 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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