4A08: HsDDB1-drDDB2

Structure of hsDDB1-drDDB2 bound to a 13 bp CPD-duplex (purine at D-1 position) at 3.0 A resolution (CPD 1). Determined by X-ray diffraction at 3.0 Å resolution. Released 30 Nov 2011.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: HOMO SAPIENS, DANIO RERIO, synthetic construct
Chains: 4
Atoms: 11,866
Mol. weight: 181.74 kDa
Ligands: CA
Released: 30 Nov 2011

Explore 4A08 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4A08 contains 23 α-helices and 133 β-strands across 2 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: 19 helices, 103 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	1
β-strand	17-21	5	2
α-helix	29	1
β-strand	30-35	6	2
β-strand	38-43	6	2
β-strand	50-56	7	2
β-strand	61-67	7	3
β-strand	76-81	6	3
β-strand	85-92	8	3
β-strand	99-107	9	3
α-helix	109-110	2
α-helix	113-114	2
β-strand	115	1	4
α-helix	116	1
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	210-211	2	6
β-strand	218-221	4	7
β-strand	229-232	4	7
β-strand	237-241	5	7
β-strand	244-248	5	7
β-strand	258-263	6	8
β-strand	270-275	6	8
β-strand	279-285	7	8
β-strand	300-307	8	8
α-helix	309-310	2
β-strand	311-316	6	9
β-strand	321-326	6	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	386-390	5	10
β-strand	393-394	2	11
β-strand	397-403	7	12
β-strand	409-413	5	13
β-strand	421	1	14
β-strand	424-428	5	13
β-strand	433-437	5	13
β-strand	444-445	2	13
β-strand	457-463	7	15
β-strand	467-472	6	15
β-strand	475-480	6	15
β-strand	485-491	7	15
α-helix	496-498	3
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	565-570	6	17
β-strand	575-581	7	17
α-helix	586-587	2
β-strand	588-596	9	18
β-strand	599-606	8	18
β-strand	610-615	6	18
β-strand	616	1	19
β-strand	623	1	19
β-strand	627-630	4	18
α-helix	635-636	2
β-strand	637-642	6	11
β-strand	647-652	6	11
β-strand	657-662	6	11
β-strand	665-671	7	11
β-strand	678-683	6	12
β-strand	684	1	14
β-strand	688-694	7	12
β-strand	698-703	6	12
β-strand	706	1	20
β-strand	708	1	20
β-strand	712-716	5	10
β-strand	720-727	8	21
β-strand	732-742	11	21
β-strand	750-751	2	21
β-strand	762-765	4	21
β-strand	786-795	10	21
β-strand	801-806	6	21
α-helix	807-808	2
β-strand	811-820	10	22
β-strand	827-835	9	22
β-strand	846-853	8	22
β-strand	858-866	9	22
β-strand	870-876	7	23
β-strand	879-884	6	23
β-strand	887-893	7	23
β-strand	899-905	7	23
β-strand	911-917	7	24
β-strand	920-925	6	24
β-strand	930-936	7	24
β-strand	941-947	7	24
β-strand	948	1	25
β-strand	954-959	6	25
β-strand	965-969	5	25
β-strand	973-979	7	25
β-strand	992-999	8	25
β-strand	1004-1009	6	1
β-strand	1025-1032	8	1
β-strand	1037-1043	7	1
α-helix	1045-1061	17
α-helix	1065-1067	3
α-helix	1070-1073	4
β-strand	1076-1077	2	26
β-strand	1082-1083	2	26
β-strand	1086	1	25
β-strand	1088-1090	3	1
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1108	7
β-strand	1113-1114	2	27
β-strand	1122-1123	2	27
α-helix	1126-1136	11
α-helix	1137-1139	3

Chain B: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	105-114	10
α-helix	119-134	16
β-strand	137-143	7	28
β-strand	150-155	6	29
β-strand	162-167	6	29
β-strand	172-176	5	29
β-strand	184-186	3	29
β-strand	195-200	6	30
β-strand	207-212	6	30
β-strand	216-221	6	30
β-strand	225-232	8	30
β-strand	240-246	7	31
β-strand	251-256	6	31
β-strand	260-265	6	31
β-strand	270-275	6	31
β-strand	281-286	6	32
β-strand	293-298	6	32
β-strand	302-307	6	32
β-strand	317-322	6	32
β-strand	327-332	6	33
β-strand	339-344	6	33
β-strand	348-353	6	33
β-strand	356	1	33
β-strand	362-365	4	33
α-helix	375-377	3
β-strand	378	1	28
β-strand	380-381	2	34
β-strand	387-391	5	34
α-helix	405	1
β-strand	406-410	5	34
β-strand	416-420	5	34
β-strand	429-434	6	28
β-strand	441-445	5	28
β-strand	448-454	7	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A	protein	1159	HOMO SAPIENS	Q16531 (AlphaFold model)
DNA damage-binding protein 2	B	protein	382	DANIO RERIO	Q2YDS1 (AlphaFold model)
5'-d(apcpgpcpgpap(ttd)pgpcpgpcpcp*c)-3'	G	DNA	13	synthetic construct
5'-d(tpgpgpgpcpgpcpcpcptpcpgpcpg)-3'	H	DNA	14	synthetic construct

Sequence of entity 1 (A), FASTA

>4A08_1 DNA DAMAGE-BINDING PROTEIN 1 (chains A)
MHHHHHHVDENLYFQGGGRMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEI
YVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDII
TRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEE
LHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYAVSLREKEFNKGPWKQENVEAEASMVIA
VPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLF
MLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSN
EQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHAS
IDLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCG
NVAHQQLIQITSASVRLVSQEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQI
HPQELRQISHTEMEHEVACLDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEM
LGGEIIPRSILMTTFESSHYLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTF
RSLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTI
GTIDEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQAL
SSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKL
GKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLL
ASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGN
FEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLG
EFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKV
IKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMK
REATADDLIKVVEELTRIH

Sequence of entity 2 (B), FASTA

>4A08_2 DNA DAMAGE-BINDING PROTEIN 2 (chains B)
MHHHHHHRRLVPRGSGGRTGGQKKVGQTSILHYIYKSSLGQSIHAQLRQCLQEPFIRSLK
SYKLHRTASPFDRRVTSLEWHPTHPTTVAVGSKGGDIILWDYDVQNKTSFIQGMGPGDAI
TGMKFNQFNTNQLFVSSIRGATTLRDFSGSVIQVFAKTDSWDYWYCCVDVSVSRQMLATG
DSTGRLLLLGLDGHEIFKEKLHKAKVTHAEFNPRCDWLMATSSVDATVKLWDLRNIKDKN
SYIAEMPHEKPVNAAYFNPTDSTKLLTTDQRNEIRVYSSYDWSKPDQIIIHPHRQFQHLT
PIKATWHPMYDLIVAGRYPDDQLLLNDKRTIDIYDANSGGLVHQLRDPNAAGIISLNKFS
PTGDVLASGMGFNILIWNREDT

Sequence of entity 3 (G), FASTA

>4A08_3 5'-D(*AP*CP*GP*CP*GP*AP*(TTD)P*GP*CP*GP*CP*CP*C)-3' (chains G)
ACGCGATGCGCCC

Sequence of entity 4 (H), FASTA

>4A08_4 5'-D(*TP*GP*GP*GP*CP*GP*CP*CP*CP*TP*CP*GP*CP*G)-3' (chains H)
TGGGCGCCCTCGCG

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2

Water and common crystallization additives (MES) are not listed.

Primary citation

The Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase Architecture, Targeting, and Activation. Scrima, A., Fischer, E.S., Iwai, S. 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

Browse structure collections

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