9C5U: Cryo EM structure of DCAF2:Compound 1 complex

Name: PDB 9C5U: Cryo EM structure of DCAF2:Compound 1 complex
Published: 2025-10-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Cryo EM structure of DCAF2:Compound 1 complex. Determined by electron microscopy at 3.05 Å resolution. Released 1 Oct 2025.

Method: Electron microscopy
Resolution: 3.05 Å
Organism: Homo sapiens
Chains: 3
Atoms: 12,013
Mol. weight: 191.08 kDa
Ligands: A1AUM
Released: 1 Oct 2025

Explore 9C5U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9C5U contains 21 α-helices and 125 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: 6 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
α-helix	26-31	6
β-strand	32-34	3	1
α-helix	36-38	3
β-strand	39-40	2	1
β-strand	43	1	2
β-strand	49	1	2
β-strand	52-57	6	3
β-strand	66-71	6	3
β-strand	75-80	6	3
β-strand	90-95	6	3
β-strand	101-106	6	4
α-helix	107	1
β-strand	112-117	6	4
β-strand	121-126	6	4
β-strand	131-137	7	4
β-strand	143-148	6	5
β-strand	155-160	6	5
β-strand	164-169	6	5
β-strand	178-179	2	4
β-strand	183-186	4	5
β-strand	219-224	6	6
β-strand	229-234	6	6
β-strand	240-244	5	6
α-helix	255-256	2
β-strand	260-262	3	6
β-strand	274-279	6	7
β-strand	285-290	6	7
β-strand	294-299	6	7
β-strand	309-311	3	7
β-strand	323-325	3	1
β-strand	331-334	4	1
β-strand	336	1	1
β-strand	342-345	4	1
α-helix	352-353	2
β-strand	354-357	4	1
β-strand	359	1	1
β-strand	363-368	6	1
β-strand	375-380	6	1
β-strand	385-390	6	1
β-strand	407-411	5	1

Chain B: 15 helices, 90 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	8
β-strand	17-21	5	9
β-strand	30-35	6	9
β-strand	38-44	7	9
β-strand	49-56	8	9
β-strand	61-67	7	10
β-strand	76-81	6	10
β-strand	85-94	10	10
β-strand	97-107	11	10
α-helix	114	1
β-strand	115	1	11
α-helix	116	1
β-strand	121-124	4	12
β-strand	130-134	5	12
β-strand	136	1	11
β-strand	139-144	6	12
β-strand	155-158	4	12
β-strand	164-169	6	13
α-helix	170	1
β-strand	177-184	8	13
β-strand	187-194	8	13
β-strand	195-196	2	14
β-strand	201-202	2	14
β-strand	210-212	3	13
β-strand	216-221	6	15
β-strand	229-233	5	15
β-strand	236-241	6	15
β-strand	244-248	5	15
α-helix	253-255	3
β-strand	261-263	3	16
β-strand	270-273	4	16
β-strand	279-289	11	16
β-strand	295-307	13	16
β-strand	313-318	6	17
β-strand	321-325	5	17
β-strand	331-336	6	17
β-strand	347-353	7	17
β-strand	361-365	5	18
β-strand	372	1	19
β-strand	374-378	5	18
β-strand	379	1	20
α-helix	382-384	3
β-strand	386	1	20
β-strand	389-392	4	18
β-strand	410	1	21
β-strand	425-428	4	22
β-strand	433-436	4	22
β-strand	439	1	23
β-strand	442	1	23
β-strand	459	1	21
β-strand	522	1	24
β-strand	525	1	24
α-helix	587-588	2
β-strand	590	1	25
β-strand	594-595	2	26
β-strand	600-604	5	26
β-strand	605	1	25
β-strand	612-615	4	26
β-strand	639-640	2	27
β-strand	649-650	2	27
β-strand	657-660	4	28
β-strand	667-670	4	28
α-helix	671	1
β-strand	710-713	4	18
β-strand	716	1	20
β-strand	720-727	8	29
β-strand	732-743	12	29
β-strand	749-751	3	29
β-strand	762-765	4	29
β-strand	785-795	11	29
β-strand	801-806	6	29
β-strand	811-819	9	30
β-strand	828-835	8	30
β-strand	845-853	9	30
β-strand	858-862	5	30
β-strand	865-866	2	30
β-strand	873-875	3	31
β-strand	880-882	3	31
β-strand	888-893	6	31
β-strand	899-905	7	31
β-strand	913-917	5	32
β-strand	920-924	5	32
β-strand	931-936	6	32
β-strand	941-947	7	32
β-strand	954-959	6	33
β-strand	964-969	6	33
β-strand	974-979	6	33
α-helix	987-990	4
β-strand	991	1	32
β-strand	992-998	7	33
β-strand	1004-1009	6	8
β-strand	1014	1	19
β-strand	1024-1032	9	8
β-strand	1037-1043	7	8
α-helix	1045-1061	17
α-helix	1070-1074	5
α-helix	1083-1085	3
β-strand	1086	1	33
β-strand	1088-1090	3	8
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1107	6
β-strand	1113-1114	2	34
β-strand	1122-1123	2	34
α-helix	1126-1138	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Denticleless protein homolog	A	protein	471	Homo sapiens	Q9NZJ0 (AlphaFold model)
DNA damage-binding protein 1	B	protein	1140	Homo sapiens	Q16531 (AlphaFold model)
DET1- and DDB1-associated protein 1	C	protein	102	Homo sapiens	Q9BW61 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9C5U_1 Denticleless protein homolog (chains A)
MLFNSVLRQPQLGVLRNGWSSQYPLQSLLTGYQCSGNDEHTSYGETGVPVPPFGCTFSSA
PNMEHVLAVANEEGFVRLYNTESQSFRKKCFKEWMAHWNAVFDLAWVPGELKLVTAAGDQ
TAKFWDVKAGELIGTCKGHQCSLKSVAFSKFEKAVFCTGGRDGNIMVWDTRCNKKDGFYR
QVNQISGAHNTSDKQTPSKPKKKQNSKGLAPSVDFQQSVTVVLFQDENTLVSAGAVDGII
KVWDLRKNYTAYRQEPIASKSFLYPGSSTRKLGYSSLILDSTGSTLFANCTDDNIYMFNM
TGLKTSPVAIFNGHQNSTFYVKSSLSPDDQFLVSGSSDEAAYIWKVSTPWQPPTVLLGHS
QEVTSVCWCPSDFTKIATCSDDNTLKIWRLNRGLEEKPGGDKLSTVGWASQKKKESRPGL
VTVTSSQSTPAKAPRAKCNPSNSSPSSAACAPSCAGDLENLYFQSHHHHHH

Sequence of entity 2 (B), FASTA

>9C5U_2 DNA damage-binding protein 1 (chains B)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 3 (C), FASTA

>9C5U_3 DET1- and DDB1-associated protein 1 (chains C)
MADFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLH
QQWDKKNAAKKRDQEQVELEGESSAPPRKVARTDSPDMHEDT

Ligands and cofactors

ID	Name	Formula	Copies
A1AUM	1'-acetyl-1',4'-dihydro-3'H-spiro[cyclopentane-1,2'-quinoxalin]-3'-one	C14 H16 N2 O2	1

Primary citation

Structural basis for DCAF2 as a novel E3 ligase for PROTAC-mediated targeted protein degradation. McMahon, E.J., Cioffi, A.G., Visperas, P.R. et al. Structure (2025) 33:2020-2028.e7. DOI 10.1016/j.str.2025.09.006 · PubMed

Other PDB entries of the same protein (UniProt Q9NZJ0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9UWG 3.21 Å, Structure of the human DCAF2-DDB1 complex
9C5T 3.36 Å, Cryo EM structure of DCAF2
9C5V 3.36 Å, Cryo EM structure of a DCAF2:degrader:BRD4 ternary complex
6QC0 3.5 Å, PCNA complex with Cdt2 C-terminal PIP-box peptide

Browse structure collections

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