8WQR: PDB entry 8WQR

Structure of the DDB1-AMBRA1 E3 ligase receptor complex linked to cell cycle regulation. Determined by electron microscopy at 3.08 Å resolution. Released 20 Dec 2023.

Method: Electron microscopy
Resolution: 3.08 Å
Organism: Homo sapiens
Chains: 2
Atoms: 9,681
Mol. weight: 171.59 kDa
Released: 20 Dec 2023

Explore 8WQR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8WQR contains 18 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: 11 helices, 101 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	8
β-strand	17-18	2	9
β-strand	21-25	5	9
β-strand	28-30	3	9
β-strand	33-34	2	9
β-strand	39-44	6	9
β-strand	49-55	7	9
β-strand	61-67	7	10
β-strand	76-81	6	10
β-strand	86-92	7	10
β-strand	99-105	7	10
β-strand	115	1	11
β-strand	121-124	4	11
β-strand	130-136	7	11
β-strand	139-144	6	11
β-strand	155-158	4	11
β-strand	164-169	6	12
β-strand	177-182	6	12
β-strand	188-194	7	12
β-strand	210-212	3	12
β-strand	219-221	3	13
β-strand	229-231	3	13
β-strand	237-241	5	13
β-strand	244-248	5	13
α-helix	253-255	3
β-strand	258-263	6	14
β-strand	270-275	6	14
β-strand	280-285	6	14
β-strand	300-301	2	14
β-strand	304	1	14
β-strand	313-318	6	15
β-strand	321-325	5	15
β-strand	332-335	4	15
β-strand	348-352	5	15
β-strand	362-365	4	16
β-strand	374-378	5	16
β-strand	387-390	4	16
β-strand	394	1	17
α-helix	395	1
β-strand	409-413	5	18
β-strand	424-428	5	18
β-strand	433-437	5	18
β-strand	444	1	18
β-strand	457-459	3	19
β-strand	462	1	19
β-strand	467-472	6	19
β-strand	476-480	5	19
β-strand	485-490	6	19
β-strand	500	1	20
β-strand	503	1	20
β-strand	507-512	6	20
β-strand	515-522	8	20
β-strand	525-533	9	20
β-strand	538-542	5	21
β-strand	555-560	6	21
β-strand	565-570	6	21
β-strand	575-581	7	21
α-helix	586-587	2
β-strand	588-594	7	22
β-strand	600-606	7	22
β-strand	611-616	6	22
β-strand	626-629	4	22
β-strand	637-641	5	23
β-strand	648-652	5	23
β-strand	657-659	3	23
β-strand	661	1	24
β-strand	666	1	24
β-strand	669-670	2	23
β-strand	671	1	17
β-strand	678-681	4	25
β-strand	684	1	26
β-strand	687	1	26
β-strand	691-694	4	25
β-strand	699-700	2	25
α-helix	709-711	3
β-strand	712-715	4	16
β-strand	724-725	2	27
β-strand	732	1	28
β-strand	734-739	6	27
β-strand	764-765	2	29
β-strand	788-792	5	27
β-strand	794	1	30
β-strand	795	1	28
β-strand	801	1	30
β-strand	805-806	2	29
β-strand	812-817	6	31
β-strand	828-834	7	31
β-strand	846-852	7	31
β-strand	859	1	31
β-strand	883-884	2	32
β-strand	887-888	2	32
β-strand	915-916	2	33
β-strand	921-925	5	33
β-strand	930-936	7	33
β-strand	941-947	7	33
β-strand	954-957	4	34
β-strand	965	1	34
β-strand	967-969	3	34
β-strand	973-977	5	34
β-strand	991	1	33
β-strand	994-999	6	34
β-strand	1004-1008	5	8
β-strand	1029-1032	4	8
β-strand	1037-1043	7	8
α-helix	1045-1053	9
α-helix	1055-1057	3
α-helix	1058-1061	4
α-helix	1070-1074	5
β-strand	1089-1090	2	8
α-helix	1092-1095	4
α-helix	1102-1107	6
α-helix	1128-1134	7

Chain B: 7 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	9-17	9
α-helix	25-37	13
β-strand	44-45	2	1
β-strand	56-61	6	2
β-strand	68-72	5	2
β-strand	76-80	5	2
β-strand	87-92	6	2
β-strand	98-102	5	3
β-strand	110-115	6	3
β-strand	119-124	6	3
β-strand	129-133	5	3
α-helix	138-140	3
β-strand	142-146	5	4
β-strand	151-155	5	4
β-strand	159-163	5	4
β-strand	172-175	4	4
β-strand	183-188	6	5
β-strand	194-200	7	5
α-helix	201-202	2
β-strand	860-866	7	5
α-helix	871-873	3
β-strand	882-887	6	5
β-strand	896-897	2	6
β-strand	904-908	5	6
β-strand	920-924	5	6
α-helix	928-930	3
β-strand	934-939	6	6
β-strand	944-949	6	7
β-strand	955-960	6	7
β-strand	976-981	6	7
α-helix	988-990	3
β-strand	991-997	7	7
β-strand	1011-1016	6	1
β-strand	1024-1028	5	1
β-strand	1033-1036	4	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Activating molecule in BECN1-regulated autophagy protein 1	B	protein	396	Homo sapiens	Q9C0C7 (AlphaFold model)
DNA damage-binding protein 1	A	protein	1140	Homo sapiens	Q16531 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8WQR_1 Activating molecule in BECN1-regulated autophagy protein 1 (chains B)
MKVVPEKNAVRILWGRERGARAMGAQRLLQELVEDKTRWMKWEGKRVELPDSPRSTFLLA
FSPDRTLLASTHVNHNIYITEVKTGKCVHSLIGHRRTPWCVTFHPTISGLIASGCLDGEV
RIWDLHGGSESWFTDSNNAIASLAFHPTAQLLLIATANEIHFWDWSRREPFAVVKTASEM
ERVRLVRFDPLGHYLLTAIVNPSNSNIANTTYRLQWWDFTKFDLPEISNASVNVLVQNCK
IYNDASCDISADGQLLAAFIPSSQRGFPDEGILAVYSLAPHNLGEMLYTKRFGPNAISVS
LSPMGRYVMVGLASRRILLHPSTEHMVAQVFRLQQAHGGETSMRRVFNVLYPMPADQRRH
VSINSARWLPEPGLGLAYGTNKGDLVICRPEALNSG

Sequence of entity 2 (A), FASTA

>8WQR_2 DNA damage-binding protein 1 (chains A)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Primary citation

Structure of the DDB1-AMBRA1 E3 ligase receptor complex linked to cell cycle regulation. Liu, M., Wang, Y., Teng, F. et al. Nat Commun (2023) 14:7631-7631. DOI 10.1038/s41467-023-43174-6 · PubMed

Other PDB entries of the same protein (UniProt Q9C0C7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9IVD 3.55 Å, Cryo-EM structure of CyclinD1 bound AMBRA1-DDB1

Browse structure collections

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