3EI2: HsDDB1-drDDB2

Structure of hsDDB1-drDDB2 bound to a 16 bp abasic site containing DNA-duplex. Determined by X-ray diffraction at 2.6 Å resolution. Released 20 Jan 2009.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Homo sapiens, Danio rerio
Chains: 4
Atoms: 12,465
Mol. weight: 182.67 kDa
Released: 20 Jan 2009

Explore 3EI2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3EI2 contains 21 α-helices and 129 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: 18 helices, 98 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
β-strand	115	1	4
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	210-212	3	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	251-254	4
β-strand	258-263	6	8
β-strand	270-275	6	8
β-strand	279-288	10	8
β-strand	296-307	12	8
α-helix	310-311	2
β-strand	313-318	6	9
β-strand	321-325	5	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	409-413	5	13
β-strand	424-429	6	13
β-strand	432-439	8	13
β-strand	442-446	5	13
β-strand	457-463	7	14
β-strand	467-472	6	14
β-strand	476-480	5	14
β-strand	486-490	5	14
α-helix	496-498	3
β-strand	500-503	4	15
β-strand	507-512	6	15
β-strand	515-522	8	15
β-strand	525-533	9	15
β-strand	538-542	5	16
β-strand	555-560	6	16
β-strand	565-570	6	16
β-strand	576-581	6	16
α-helix	586-587	2
β-strand	588-596	9	17
β-strand	599-606	8	17
β-strand	610-616	7	17
β-strand	623-630	8	17
α-helix	635-636	2
β-strand	637-643	7	18
β-strand	646-652	7	18
β-strand	657-661	5	18
β-strand	666-670	5	18
β-strand	671	1	11
β-strand	678-682	5	12
β-strand	690-694	5	12
β-strand	699-704	6	12
β-strand	710-716	7	10
β-strand	720-727	8	19
α-helix	728-730	3
β-strand	732-743	12	19
α-helix	744	1
β-strand	749-751	3	19
β-strand	762-765	4	19
β-strand	785-795	11	19
β-strand	801-806	6	19
β-strand	811-819	9	20
β-strand	828-835	8	20
β-strand	846-853	8	20
β-strand	858-866	9	20
β-strand	870-876	7	21
β-strand	879-884	6	21
β-strand	887-893	7	21
β-strand	899-905	7	21
β-strand	911-917	7	22
β-strand	920-925	6	22
β-strand	928	1	23
β-strand	930-936	7	22
β-strand	941-947	7	22
β-strand	952	1	23
β-strand	954-959	6	24
β-strand	964-969	6	24
β-strand	973-979	7	24
α-helix	986-989	4
β-strand	991	1	22
β-strand	992-999	8	24
β-strand	1004-1009	6	1
β-strand	1025-1032	8	1
β-strand	1037-1042	6	1
α-helix	1045-1061	17
α-helix	1063-1064	2
α-helix	1070-1073	4
β-strand	1076-1077	2	25
β-strand	1082-1083	2	25
β-strand	1086	1	24
β-strand	1088-1090	3	1
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1109	8
α-helix	1126-1137	12

Chain B: 3 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	105-113	9
α-helix	119-134	16
β-strand	138-143	6	26
β-strand	150-155	6	27
β-strand	162-167	6	27
β-strand	172-176	5	27
β-strand	183-186	4	27
β-strand	195-200	6	28
β-strand	207-212	6	28
β-strand	216-221	6	28
β-strand	226-229	4	28
β-strand	240-246	7	29
β-strand	251-256	6	29
β-strand	260-265	6	29
β-strand	270-275	6	29
β-strand	281-287	7	30
β-strand	290-298	9	30
β-strand	302-307	6	30
β-strand	317-322	6	30
β-strand	327-332	6	31
β-strand	339-344	6	31
β-strand	348-353	6	31
β-strand	362-365	4	31
α-helix	375-377	3
β-strand	378	1	26
β-strand	380-381	2	32
β-strand	387-391	5	32
β-strand	406-410	5	32
β-strand	416-420	5	32
β-strand	422	1	33
β-strand	425	1	33
β-strand	429-434	6	26
β-strand	441-445	5	26
β-strand	448-453	6	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A	protein	1158	Homo sapiens	Q16531 (AlphaFold model)
DNA damage-binding protein 2	B	protein	383	Danio rerio	Q2YDS1 (AlphaFold model)
5'-D(DAPDAPDAPDTPDGPDAPDAPDTP(3DR)PDAPDAPDGPDCPDAPDGPDG)-3'	G	DNA	16
5'-d(dcpdcpdtpdgpdcpdtpdtpdtpdapdtpdtpdcpdapdtpdtpdt)-3'	H	DNA	16

Sequence of entity 1 (A), FASTA

>3EI2_1 DNA damage-binding protein 1 (chains A)
MHHHHHHRRLVPRGSGGRMSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIY
VVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIIT
RAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEEL
HVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAV
PEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFM
LLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNE
QGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASI
DLPGIKGLWPLRSDPNRETDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGN
VAHQQLIQITSASVRLVSQEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIH
PQELRQISHTEMEHEVACLDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEML
GGEIIPRSILMTTFESSHYLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFR
SLSTTNVFACSDRPTVIYSSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIG
TIDEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALS
SSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLG
KDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLA
SINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNF
EEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGE
FVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVI
KSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKR
EATADDLIKVVEELTRIH

Sequence of entity 2 (B), FASTA

>3EI2_2 DNA damage-binding protein 2 (chains B)
MHHHHHHVDENLYFQGGGRTGGQKKVGQTSILHYIYKSSLGQSIHAQLRQCLQEPFIRSL
KSYKLHRTASPFDRRVTSLEWHPTHPTTVAVGSKGGDIILWDYDVQNKTSFIQGMGPGDA
ITGMKFNQFNTNQLFVSSIRGATTLRDFSGSVIQVFAKTDSWDYWYCCVDVSVSRQMLAT
GDSTGRLLLLGLDGHEIFKEKLHKAKVTHAEFNPRCDWLMATSSVDATVKLWDLRNIKDK
NSYIAEMPHEKPVNAAYFNPTDSTKLLTTDQRNEIRVYSSYDWSKPDQIIIHPHRQFQHL
TPIKATWHPMYDLIVAGRYPDDQLLLNDKRTIDIYDANSGGLVHQLRDPNAAGIISLNKF
SPTGDVLASGMGFNILIWNREDT

Sequence of entity 3 (G), FASTA

>3EI2_3 5'-D(*DAP*DAP*DAP*DTP*DGP*DAP*DAP*DTP*(3DR)P*DAP*DAP*DGP*DCP*DAP*DGP*DG)-3' (chains G)
AAATGAATNAAGCAGG

Sequence of entity 4 (H), FASTA

>3EI2_4 5'-D(*DCP*DCP*DTP*DGP*DCP*DTP*DTP*DTP*DAP*DTP*DTP*DCP*DAP*DTP*DTP*DT)-3' (chains H)
CCTGCTTTATTCATTT

Primary citation

Structural basis of UV DNA-damage recognition by the DDB1-DDB2 complex. Scrima, A., Konickova, R., Czyzewski, B.K. et al. Cell (2008) 135:1213-1223. DOI 10.1016/j.cell.2008.10.045 · 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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