7LPS: DDB1-CRBN-ALV1 complex

Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2). Determined by X-ray diffraction at 3.78 Å resolution. Released 2 Jun 2021.

Method: X-ray diffraction
Resolution: 3.78 Å
Organism: Homo sapiens
Chains: 12
Atoms: 37,550
Mol. weight: 703.34 kDa
Ligands: ZN, RN9
Released: 2 Jun 2021

Explore 7LPS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7LPS contains 124 α-helices and 353 β-strands across 12 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: 13 helices, 67 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	38-44	7	2
β-strand	49-56	8	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	4
β-strand	130-136	7	4
β-strand	139-144	6	4
β-strand	155-158	4	4
β-strand	163-169	7	5
α-helix	170	1
β-strand	177-184	8	5
β-strand	187-196	10	5
β-strand	201-204	4	5
β-strand	210-211	2	5
β-strand	218-221	4	6
β-strand	229-232	4	6
β-strand	237-240	4	6
β-strand	245-248	4	6
α-helix	251-253	3
β-strand	258-263	6	7
β-strand	270-275	6	7
β-strand	279-285	7	7
β-strand	300-307	8	7
β-strand	311-318	8	8
β-strand	321-326	6	8
β-strand	331-335	5	8
β-strand	348-353	6	8
α-helix	357	1
α-helix	359	1
β-strand	361-365	5	9
β-strand	374-379	6	9
α-helix	382-384	3
β-strand	386-392	7	9
β-strand	710-716	7	9
β-strand	720-727	8	10
β-strand	732-743	12	10
β-strand	749-751	3	10
β-strand	762-765	4	10
β-strand	785-795	11	10
β-strand	801-806	6	10
α-helix	807-808	2
β-strand	811-819	9	11
β-strand	828-835	8	11
β-strand	837	1	12
β-strand	840	1	12
β-strand	846-854	9	11
β-strand	857-866	10	11
β-strand	870-876	7	13
β-strand	879-884	6	13
β-strand	887-893	7	13
β-strand	899-906	8	13
β-strand	913-917	5	14
β-strand	920-924	5	14
β-strand	929-936	8	14
β-strand	941-949	9	14
β-strand	956-959	4	15
β-strand	964-969	6	15
β-strand	973-978	6	15
α-helix	986-989	4
β-strand	991	1	14
β-strand	993-999	7	15
β-strand	1006-1009	4	1
β-strand	1025-1031	7	1
β-strand	1037-1042	6	1
α-helix	1045-1059	15
α-helix	1063-1064	2
α-helix	1070-1073	4
β-strand	1076-1077	2	16
β-strand	1082-1083	2	16
β-strand	1086	1	15
β-strand	1088-1090	3	1
α-helix	1091-1095	5
α-helix	1102-1108	7
α-helix	1126-1137	12

Chain B: 18 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	52-56	5
α-helix	58-60	3
α-helix	63-64	2
β-strand	65-66	2	17
α-helix	73-74	2
β-strand	78-83	6	17
β-strand	96-101	6	17
α-helix	104-115	12
β-strand	119-127	9	17
β-strand	132-147	16	17
α-helix	149-151	3
β-strand	154-172	19	17
β-strand	178-184	7	17
α-helix	185-186	2
β-strand	188	1	18
α-helix	193-196	4
α-helix	203-205	3
α-helix	220-231	12
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-262	13
α-helix	277-286	10
α-helix	292-300	9
β-strand	303	1	18
α-helix	304-317	14
β-strand	320-323	4	19
β-strand	330-333	4	19
α-helix	334-336	3
β-strand	337	1	20
β-strand	346-350	5	20
β-strand	356-362	7	20
β-strand	368-375	8	20
β-strand	384-391	8	20
β-strand	397-404	8	20
β-strand	413-418	6	20
α-helix	419-421	3
β-strand	422-425	4	19

Chains C, F, I and L: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	140-141	2	21
β-strand	148-149	2	21
α-helix	152-163	12

Chain D: 13 helices, 67 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	22
β-strand	17-21	5	23
β-strand	30-35	6	23
β-strand	38-44	7	23
β-strand	49-56	8	23
β-strand	61-67	7	24
β-strand	76-81	6	24
β-strand	85-94	10	24
β-strand	97-107	11	24
β-strand	115	1	25
β-strand	121-124	4	25
β-strand	130-136	7	25
β-strand	139-144	6	25
β-strand	155-158	4	25
β-strand	163-169	7	26
α-helix	170	1
β-strand	177-184	8	26
β-strand	187-196	10	26
β-strand	201-204	4	26
β-strand	210-211	2	26
β-strand	218-221	4	27
β-strand	229-232	4	27
β-strand	237-240	4	27
β-strand	245-248	4	27
α-helix	251-253	3
β-strand	258-263	6	28
β-strand	270-275	6	28
β-strand	279-285	7	28
β-strand	300-307	8	28
β-strand	313-318	6	29
β-strand	321-325	5	29
β-strand	331-335	5	29
β-strand	348-353	6	29
α-helix	357	1
α-helix	359	1
β-strand	361-365	5	30
β-strand	374-379	6	30
α-helix	382-384	3
β-strand	386-392	7	30
β-strand	710-716	7	30
β-strand	720-727	8	31
β-strand	732-743	12	31
β-strand	749-751	3	31
β-strand	762-765	4	31
β-strand	785-795	11	31
β-strand	801-806	6	31
α-helix	807-808	2
β-strand	811-819	9	32
β-strand	828-835	8	32
β-strand	837	1	33
β-strand	840	1	33
β-strand	846-854	9	32
β-strand	857-866	10	32
β-strand	870-876	7	34
β-strand	879-884	6	34
β-strand	887-893	7	34
β-strand	899-906	8	34
β-strand	913-917	5	35
β-strand	920-924	5	35
β-strand	929-936	8	35
β-strand	941-949	9	35
β-strand	956-959	4	36
β-strand	964-969	6	36
β-strand	973-978	6	36
α-helix	986-989	4
β-strand	991	1	35
β-strand	993-999	7	36
β-strand	1004-1009	6	22
β-strand	1025-1032	8	22
β-strand	1037-1042	6	22
α-helix	1045-1059	15
α-helix	1063-1064	2
α-helix	1070-1073	4
β-strand	1076-1077	2	37
β-strand	1082-1083	2	37
β-strand	1086	1	36
β-strand	1088-1090	3	22
α-helix	1091-1095	5
α-helix	1102-1108	7
α-helix	1126-1137	12

Chain E: 17 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	52-56	5
α-helix	58-60	3
α-helix	63-64	2
β-strand	65-66	2	38
α-helix	73-74	2
β-strand	78-83	6	38
β-strand	96-101	6	38
α-helix	104-115	12
β-strand	119-127	9	38
β-strand	132-147	16	38
β-strand	154-172	19	38
β-strand	178-184	7	38
α-helix	185-186	2
β-strand	188	1	39
α-helix	193-196	4
α-helix	203-205	3
α-helix	220-231	12
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-262	13
α-helix	277-286	10
α-helix	292-300	9
β-strand	303	1	39
α-helix	304-317	14
β-strand	320-323	4	40
β-strand	330-333	4	40
α-helix	334-336	3
β-strand	337	1	41
β-strand	346-350	5	41
β-strand	356-362	7	41
β-strand	368-375	8	41
β-strand	384-391	8	41
β-strand	397-404	8	41
β-strand	413-418	6	41
α-helix	419-421	3
β-strand	422-425	4	40

Chain G: 13 helices, 67 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	43
β-strand	17-21	5	44
β-strand	30-35	6	44
β-strand	38-44	7	44
β-strand	49-56	8	44
β-strand	61-67	7	45
β-strand	76-81	6	45
β-strand	85-94	10	45
β-strand	97-107	11	45
β-strand	115	1	46
β-strand	121-124	4	46
β-strand	130-136	7	46
β-strand	139-144	6	46
β-strand	155-158	4	46
β-strand	163-169	7	47
α-helix	170	1
β-strand	177-184	8	47
β-strand	187-196	10	47
β-strand	201-204	4	47
β-strand	210-211	2	47
β-strand	218-221	4	48
β-strand	229-232	4	48
β-strand	237-240	4	48
β-strand	245-248	4	48
α-helix	251-253	3
β-strand	258-263	6	49
β-strand	270-275	6	49
β-strand	279-285	7	49
β-strand	300-307	8	49
β-strand	313-318	6	50
β-strand	321-325	5	50
β-strand	331-335	5	50
β-strand	348-353	6	50
α-helix	357	1
α-helix	359	1
β-strand	361-365	5	51
β-strand	374-379	6	51
α-helix	382-384	3
β-strand	386-391	6	51
β-strand	711-716	6	51
β-strand	720-727	8	52
β-strand	732-743	12	52
β-strand	749-751	3	52
β-strand	762-765	4	52
β-strand	785-795	11	52
β-strand	801-806	6	52
α-helix	807-808	2
β-strand	811-819	9	53
β-strand	828-835	8	53
β-strand	837	1	54
β-strand	840	1	54
β-strand	846-854	9	53
β-strand	857-866	10	53
β-strand	870-876	7	55
β-strand	879-884	6	55
β-strand	887-893	7	55
β-strand	899-906	8	55
β-strand	913-917	5	56
β-strand	920-924	5	56
β-strand	929-936	8	56
β-strand	941-949	9	56
β-strand	956-959	4	57
β-strand	964-969	6	57
β-strand	973-978	6	57
α-helix	986-989	4
β-strand	991	1	56
β-strand	993-999	7	57
β-strand	1004-1009	6	43
β-strand	1025-1032	8	43
β-strand	1037-1042	6	43
α-helix	1045-1059	15
α-helix	1063-1064	2
α-helix	1070-1073	4
β-strand	1076-1077	2	58
β-strand	1082-1083	2	58
β-strand	1086	1	57
β-strand	1088-1090	3	43
α-helix	1091-1095	5
α-helix	1102-1108	7
α-helix	1126-1137	12

Chain H: 18 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	52-55	4
α-helix	58-60	3
α-helix	63-64	2
β-strand	65-66	2	59
α-helix	73-74	2
β-strand	78-83	6	59
β-strand	96-101	6	59
α-helix	104-115	12
β-strand	119-127	9	59
β-strand	132-147	16	59
α-helix	149-151	3
β-strand	154-172	19	59
β-strand	178-184	7	59
α-helix	185-186	2
β-strand	188	1	60
α-helix	193-196	4
α-helix	203-205	3
α-helix	220-231	12
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-262	13
α-helix	277-286	10
α-helix	292-300	9
β-strand	303	1	60
α-helix	304-317	14
β-strand	320-323	4	61
β-strand	330-333	4	61
α-helix	334-336	3
β-strand	337	1	62
β-strand	346-350	5	62
β-strand	356-362	7	62
β-strand	368-375	8	62
β-strand	384-391	8	62
β-strand	397-404	8	62
β-strand	413-418	6	62
α-helix	419-421	3
β-strand	422-425	4	61

Chain J: 11 helices, 68 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	64
β-strand	17-21	5	65
β-strand	30-35	6	65
β-strand	38-44	7	65
β-strand	49-56	8	65
β-strand	61-67	7	66
β-strand	76-81	6	66
β-strand	85-94	10	66
β-strand	95	1	24
β-strand	97-107	11	66
β-strand	115	1	67
β-strand	121-124	4	67
β-strand	130-136	7	67
β-strand	139-144	6	67
β-strand	155-158	4	67
β-strand	163-169	7	68
β-strand	177-184	8	68
β-strand	187-196	10	68
β-strand	201-204	4	68
β-strand	210-211	2	68
β-strand	218-221	4	69
β-strand	229-232	4	69
β-strand	237-241	5	69
β-strand	244-248	5	69
α-helix	251-253	3
β-strand	258-263	6	70
β-strand	270-275	6	70
β-strand	279-285	7	70
β-strand	300-307	8	70
β-strand	311-318	8	71
β-strand	321-326	6	71
β-strand	331-335	5	71
β-strand	348-353	6	71
β-strand	362-365	4	72
β-strand	374-379	6	72
α-helix	382-384	3
β-strand	386-392	7	72
β-strand	710-716	7	72
β-strand	720-727	8	73
β-strand	732-743	12	73
α-helix	744	1
β-strand	749-751	3	73
β-strand	762-765	4	73
β-strand	785-795	11	73
β-strand	801-806	6	73
α-helix	807-808	2
β-strand	811-819	9	74
β-strand	828-835	8	74
β-strand	837	1	75
β-strand	840	1	75
β-strand	846-854	9	74
β-strand	857-866	10	74
β-strand	870-876	7	76
β-strand	879-884	6	76
β-strand	887-893	7	76
β-strand	899-906	8	76
β-strand	913-917	5	77
β-strand	920-924	5	77
β-strand	929-936	8	77
β-strand	941-949	9	77
β-strand	956-959	4	78
β-strand	964-969	6	78
β-strand	973-979	7	78
α-helix	986-989	4
β-strand	991	1	77
β-strand	992-999	8	78
β-strand	1004-1009	6	64
β-strand	1025-1032	8	64
β-strand	1037-1042	6	64
α-helix	1045-1059	15
α-helix	1063-1064	2
α-helix	1070-1073	4
β-strand	1076-1077	2	79
β-strand	1082-1083	2	79
β-strand	1086	1	78
β-strand	1088-1090	3	64
α-helix	1091-1095	5
α-helix	1102-1108	7
α-helix	1126-1137	12

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A, D, G, J	protein	1140	Homo sapiens	Q16531 (AlphaFold model)
Protein cereblon	B, E, H, K	protein	390	Homo sapiens	Q96SW2 (AlphaFold model)
Zinc finger protein Helios	C, F, I, L	protein	29	Homo sapiens	Q9UKS7 (AlphaFold model)

Sequence of entity 1 (A, D, G, J), FASTA

>7LPS_1 DNA damage-binding protein 1 (chains A, D, G, J)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 2 (B, E, H, K), FASTA

>7LPS_2 Protein cereblon (chains B, E, H, K)
INFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQE
VSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFK
VLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQK
YQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAA
CLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPM
AAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATK
KDMSPQKFWGLTRSALLPTIPDTEDEISPD

Sequence of entity 3 (C, F, I, L), FASTA

>7LPS_3 Zinc finger protein Helios (chains C, F, I, L)
GERPFHCNQCGASFTQKGNLLRHIKLHSG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8
RN9	3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)p…	C25 H23 Cl N4 O5	4

Primary citation

Acute pharmacological degradation of Helios destabilizes regulatory T cells. Wang, E.S., Verano, A.L., Nowak, R.P. et al. Nat Chem Biol (2021) 17:711-717. DOI 10.1038/s41589-021-00802-w · 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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