9IVD: CyclinD1 bound AMBRA1-DDB1

Cryo-EM structure of CyclinD1 bound AMBRA1-DDB1. Determined by electron microscopy at 3.55 Å resolution. Released 23 Apr 2025.

Method: Electron microscopy
Resolution: 3.55 Å
Organism: Homo sapiens
Chains: 3
Atoms: 8,628
Mol. weight: 205.44 kDa
Released: 23 Apr 2025

Explore 9IVD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9IVD contains 17 α-helices and 112 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: 10 helices, 74 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	12
β-strand	18-21	4	13
β-strand	30-33	4	13
β-strand	38-44	7	13
β-strand	49-56	8	13
β-strand	61-67	7	14
β-strand	76-81	6	14
β-strand	85-89	5	14
β-strand	92-94	3	15
β-strand	97-99	3	15
β-strand	102-107	6	14
α-helix	113-114	2
β-strand	115	1	16
α-helix	116	1
β-strand	121-124	4	17
β-strand	131-134	4	17
β-strand	136	1	16
β-strand	139-142	4	17
β-strand	155-158	4	17
β-strand	163-169	7	18
α-helix	170	1
β-strand	177-183	7	18
β-strand	189-194	6	18
β-strand	195-196	2	19
β-strand	201-202	2	19
β-strand	210-211	2	18
β-strand	219-221	3	20
β-strand	229-233	5	20
β-strand	236-240	5	20
β-strand	245-248	4	20
β-strand	258-263	6	21
β-strand	270-275	6	21
β-strand	278-285	8	21
β-strand	289	1	22
β-strand	295	1	22
β-strand	300-304	5	21
α-helix	310-311	2
β-strand	314-318	5	23
β-strand	321-324	4	23
β-strand	332-336	5	23
β-strand	347-352	6	23
β-strand	362-365	4	24
β-strand	374-377	4	24
β-strand	381	1	25
β-strand	384	1	25
β-strand	387-390	4	24
β-strand	712-715	4	24
β-strand	720-726	7	26
β-strand	732	1	27
β-strand	733-742	10	26
β-strand	763-765	3	26
β-strand	785-793	9	26
β-strand	795	1	27
β-strand	803-806	4	26
β-strand	811-819	9	28
β-strand	828-835	8	28
β-strand	846-847	2	28
β-strand	850-853	4	28
β-strand	858-860	3	28
β-strand	866	1	28
β-strand	870-873	4	29
β-strand	880-884	5	29
β-strand	888-893	6	29
β-strand	899-904	6	29
β-strand	916	1	30
β-strand	921-922	2	30
β-strand	931-935	5	30
β-strand	942-947	6	30
β-strand	954-959	6	31
β-strand	965-969	5	31
β-strand	973-977	5	31
β-strand	997-998	2	31
β-strand	1004-1009	6	12
β-strand	1028-1032	5	12
β-strand	1037-1042	6	12
α-helix	1047-1057	11
β-strand	1077	1	32
β-strand	1082	1	32
β-strand	1089	1	12
α-helix	1092-1095	4
α-helix	1096-1098	3
α-helix	1105-1107	3
α-helix	1126-1129	4
α-helix	1132-1136	5

Chain B: 7 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	9-17	9
α-helix	25-35	11
β-strand	41-46	6	1
β-strand	48	1	2
β-strand	56-61	6	3
β-strand	67-72	6	3
β-strand	76-81	6	3
β-strand	86	1	2
β-strand	87-90	4	3
β-strand	103	1	4
β-strand	111	1	4
β-strand	119-120	2	5
β-strand	123	1	4
β-strand	129	1	4
β-strand	132-133	2	5
β-strand	143-145	3	6
β-strand	152-154	3	6
β-strand	155	1	7
β-strand	160	1	7
β-strand	163	1	6
β-strand	174	1	7
β-strand	183-185	3	8
β-strand	194	1	9
β-strand	197-201	5	8
α-helix	202	1
β-strand	859-863	5	8
β-strand	866	1	9
α-helix	871-873	3
β-strand	882	1	8
β-strand	887	1	8
α-helix	892-894	3
β-strand	897	1	10
β-strand	903-906	4	10
β-strand	920-925	6	10
β-strand	937-939	3	10
β-strand	944-949	6	11
β-strand	955-960	6	11
β-strand	974-980	7	11
β-strand	992-993	2	11
β-strand	997-998	2	11
α-helix	1015	1
β-strand	1016	1	1
α-helix	1017	1
β-strand	1024-1027	4	1
β-strand	1033-1039	7	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
G1/S-specific cyclin-D1	E	protein	295	Homo sapiens	P24385 (AlphaFold model)
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 (E), FASTA

>9IVD_1 G1/S-specific cyclin-D1 (chains E)
MEHQLLCCEVETIRRAYPDANLLNDRVLRAMLKAEETCAPSVSYFKCVQKEVLPSMRKIV
ATWMLEVCEEQKCEEEVFPLAMNYLDRFLSLEPVKKSRLQLLGATCMFVASKMKETIPLT
AEKLCIYTDNSIRPEELLQMELLLVNKLKWNLAAMTPHDFIEHFLSKMPEAEENKQIIRK
HAQTFVALCATDVKFISNPPSMVAAGSVVAAVQGLNLRSPNNFLSYYRLTRFLSRVIKCD
PDCLRACQEQIEALLESSLRQAQQNMDPKAAEEEEEEEEEVDLACTPTDVRDVDI

Sequence of entity 2 (B), FASTA

>9IVD_2 Activating molecule in BECN1-regulated autophagy protein 1 (chains B)
MKVVPEKNAVRILWGRERGARAMGAQRLLQELVEDKTRWMKWEGKRVELPDSPRSTFLLA
FSPDRTLLASTHVNHNIYITEVKTGKCVHSLIGHRRTPWCVTFHPTISGLIASGCLDGEV
RIWDLHGGSESWFTDSNNAIASLAFHPTAQLLLIATANEIHFWDWSRREPFAVVKTASEM
ERVRLVRFDPLGHYLLTAIVNPSNSNIANTTYRLQWWDFTKFDLPEISNASVNVLVQNCK
IYNDASCDISADGQLLAAFIPSSQRGFPDEGILAVYSLAPHNLGEMLYTKRFGPNAISVS
LSPMGRYVMVGLASRRILLHPSTEHMVAQVFRLQQAHGGETSMRRVFNVLYPMPADQRRH
VSINSARWLPEPGLGLAYGTNKGDLVICRPEALNSG

Sequence of entity 3 (A), FASTA

>9IVD_3 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

Mechanism of D-type cyclin recognition by the AMBRA1 E3 ligase receptor. Wang, Y., Liu, M., Wang, S. et al. Sci Adv (2025) 11:eadu8708-eadu8708. DOI 10.1126/sciadv.adu8708 · PubMed

Other PDB entries of the same protein (UniProt P24385 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9CSK 2.25 Å, Crystal structure of CDK4 cyclin D1 in complex with atirmociclib
2W96 2.3 Å, Crystal Structure of CDK4 in complex with a D-type cyclin
6P8E 2.3 Å, Crystal structure of CDK4 in complex with CyclinD1 and P27
2W9Z 2.45 Å, Crystal Structure of CDK4 in complex with a D-type cyclin
5VZU 2.7 Å, Crystal structure of the Skp1-FBXO31-cyclin D1 complex
2W99 2.8 Å, Crystal Structure of CDK4 in complex with a D-type cyclin
6P8G 2.8 Å, Crystal structure of CDK4 in complex with CyclinD1 and P27
2W9F 2.85 Å, Crystal Structure of CDK4 in complex with a D-type cyclin
6P8F 2.89 Å, Crystal structure of CDK4 in complex with CyclinD1 and P27
6P8H 3.19 Å, Crystal structure of CDK4 in complex with CyclinD1 and P21

Browse structure collections

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