4A09: HsDDB1-drDDB2

Structure of hsDDB1-drDDB2 bound to a 15 bp CPD-duplex (purine at D-1 position) at 3.1 A resolution (CPD 2). Determined by X-ray diffraction at 3.1 Å resolution. Released 30 Nov 2011.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: HOMO SAPIENS, DANIO RERIO, SYNTHETIC CONSTRUCT
Chains: 4
Atoms: 12,113
Mol. weight: 182.21 kDa
Ligands: CA
Released: 30 Nov 2011

Explore 4A09 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4A09 contains 21 α-helices and 130 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: 17 helices, 100 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
α-helix	114	1
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	163-169	7	6
α-helix	170	1
β-strand	177-184	8	6
β-strand	187-196	10	6
β-strand	201-204	4	6
α-helix	208-209	2
β-strand	210-211	2	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	253-255	3
β-strand	258-263	6	8
β-strand	270-275	6	8
β-strand	279-288	10	8
β-strand	296-307	12	8
β-strand	311-318	8	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	386-392	7	10
β-strand	394	1	11
β-strand	396-402	7	12
β-strand	410-413	4	13
β-strand	422	1	14
β-strand	424-428	5	13
β-strand	433-439	7	13
β-strand	442-445	4	13
β-strand	457-463	7	15
β-strand	467-472	6	15
β-strand	475-479	5	15
β-strand	486-491	6	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	565	1	18
β-strand	566-570	5	17
β-strand	576-578	3	17
β-strand	581	1	18
β-strand	588-596	9	19
β-strand	599-606	8	19
β-strand	610-616	7	19
β-strand	623-630	8	19
α-helix	635-636	2
β-strand	637-642	6	20
β-strand	647-652	6	20
β-strand	657-662	6	20
β-strand	665-670	6	20
β-strand	671	1	11
β-strand	678-682	5	12
β-strand	684	1	14
β-strand	690-694	5	12
β-strand	699-704	6	12
α-helix	705-706	2
β-strand	710-716	7	10
β-strand	720-727	8	21
β-strand	732-743	12	21
β-strand	749-751	3	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	811-819	9	22
β-strand	828-835	8	22
β-strand	846-854	9	22
β-strand	857-866	10	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	954-961	8	25
β-strand	964-969	6	25
β-strand	973-979	7	25
α-helix	986-989	4
β-strand	991	1	24
β-strand	992-999	8	25
β-strand	1004-1009	6	1
β-strand	1028-1032	5	1
β-strand	1037-1042	6	1
α-helix	1045-1061	17
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
α-helix	1126-1136	11

Chain B: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	105-113	9
α-helix	119-133	15
α-helix	134-136	3
β-strand	138-143	6	27
β-strand	150-155	6	28
β-strand	162-167	6	28
β-strand	172-176	5	28
β-strand	184-186	3	28
β-strand	195-200	6	29
β-strand	207-212	6	29
β-strand	216-221	6	29
β-strand	226-231	6	29
β-strand	240-246	7	30
β-strand	251-256	6	30
β-strand	260-265	6	30
β-strand	270-275	6	30
β-strand	281-287	7	31
β-strand	290-298	9	31
β-strand	302-307	6	31
β-strand	310	1	31
β-strand	317-322	6	31
β-strand	327-332	6	32
β-strand	339-344	6	32
β-strand	348-353	6	32
β-strand	356	1	32
β-strand	362-365	4	32
α-helix	375-377	3
β-strand	380-381	2	33
β-strand	387-391	5	33
β-strand	406-410	5	33
β-strand	416-420	5	33
β-strand	431-434	4	27
β-strand	441-445	5	27
β-strand	448-453	6	27

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(gpgptpgpapapap(ttd)papgpcpapgpgp)-3'	G	DNA	14	SYNTHETIC CONSTRUCT
5'-d(cpcptpgpcptpcpcptptptpcpapcpcpc)-3'	H	DNA	16	SYNTHETIC CONSTRUCT

Sequence of entity 1 (A), FASTA

>4A09_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

>4A09_2 DNA DAMAGE-BINDING PROTEIN 2 (chains B)
MHHHHHHRRLVPRGSGGRTGGQKKVGQTSILHYIYKSSLGQSIHAQLRQCLQEPFIRSLK
SYKLHRTASPFDRRVTSLEWHPTHPTTVAVGSKGGDIILWDYDVQNKTSFIQGMGPGDAI
TGMKFNQFNTNQLFVSSIRGATTLRDFSGSVIQVFAKTDSWDYWYCCVDVSVSRQMLATG
DSTGRLLLLGLDGHEIFKEKLHKAKVTHAEFNPRCDWLMATSSVDATVKLWDLRNIKDKN
SYIAEMPHEKPVNAAYFNPTDSTKLLTTDQRNEIRVYSSYDWSKPDQIIIHPHRQFQHLT
PIKATWHPMYDLIVAGRYPDDQLLLNDKRTIDIYDANSGGLVHQLRDPNAAGIISLNKFS
PTGDVLASGMGFNILIWNREDT

Sequence of entity 3 (G), FASTA

>4A09_3 5'-D(*GP*GP*TP*GP*AP*AP*AP*(TTD)P*AP*GP*CP*AP*GP*GP)-3' (chains G)
GGTGAAATAGCAGG

Sequence of entity 4 (H), FASTA

>4A09_4 5'-D(*CP*CP*TP*GP*CP*TP*CP*CP*TP*TP*TP*CP*AP*CP*CP*C)-3' (chains H)
CCTGCTCCTTTCACCC

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

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

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