9C5V: Denticleless protein homolog

Name: PDB 9C5V: Cryo EM structure of a DCAF2:degrader:BRD4 ternary complex
Published: 2025-10-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Cryo EM structure of a DCAF2:degrader:BRD4 ternary complex. Determined by electron microscopy at 3.36 Å resolution. Released 1 Oct 2025.

Method: Electron microscopy
Resolution: 3.36 Å
Organism: Homo sapiens
Chains: 4
Atoms: 12,967
Mol. weight: 207.29 kDa
Ligands: A1AUO
Released: 1 Oct 2025

Explore 9C5V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9C5V contains 26 α-helices and 110 β-strands across 3 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: 3 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
β-strand	32-33	2	1
β-strand	40-41	2	2
β-strand	43	1	3
β-strand	49	1	3
β-strand	66-67	2	4
β-strand	70	1	4
β-strand	75-80	6	4
β-strand	90-95	6	4
β-strand	101-106	6	5
β-strand	112-117	6	5
β-strand	122-126	5	5
β-strand	131-135	5	5
β-strand	143-148	6	6
β-strand	155-160	6	6
β-strand	164-169	6	6
α-helix	173-174	2
β-strand	178	1	5
β-strand	183-186	4	6
β-strand	219-226	8	7
β-strand	229-234	6	7
β-strand	240-244	5	7
α-helix	255-258	4
β-strand	260-262	3	7
β-strand	274-279	6	8
β-strand	285-290	6	8
β-strand	294-299	6	8
β-strand	309-312	4	8
β-strand	323-325	3	9
β-strand	331-334	4	9
β-strand	341-345	5	9
β-strand	354-357	4	9
β-strand	363-368	6	2
β-strand	376-380	5	2
β-strand	384-388	5	2
β-strand	389-390	2	1
β-strand	408-411	4	9

Chain B: 13 helices, 76 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	10
β-strand	18-19	2	11
β-strand	30-34	5	11
β-strand	38-44	7	11
β-strand	49-56	8	11
β-strand	61-67	7	12
α-helix	75	1
β-strand	76-81	6	12
β-strand	85-94	10	12
β-strand	97-107	11	12
α-helix	114	1
β-strand	115	1	13
α-helix	116	1
β-strand	121-124	4	14
β-strand	130-134	5	14
β-strand	136	1	13
β-strand	139-144	6	14
β-strand	155-158	4	14
β-strand	164-169	6	15
β-strand	177-184	8	15
β-strand	187-194	8	15
β-strand	195-196	2	16
β-strand	201-202	2	16
β-strand	210-211	2	15
β-strand	216-221	6	17
β-strand	229-233	5	17
β-strand	236-241	6	17
β-strand	244-248	5	17
β-strand	261-263	3	18
β-strand	270-273	4	18
β-strand	279-290	12	18
β-strand	294-307	14	18
β-strand	311-316	6	19
β-strand	321-326	6	19
β-strand	331-336	6	19
β-strand	347-353	7	19
β-strand	362-365	4	20
β-strand	374-377	4	20
α-helix	382-384	3
β-strand	386	1	21
β-strand	389-392	4	20
β-strand	424-427	4	22
β-strand	432	1	23
β-strand	434-437	4	22
β-strand	457	1	23
β-strand	521-522	2	24
β-strand	525-526	2	24
β-strand	602	1	25
β-strand	614	1	25
β-strand	710-713	4	20
β-strand	716	1	21
β-strand	720-727	8	26
β-strand	732-742	11	26
β-strand	764-765	2	26
β-strand	785-795	11	26
β-strand	801-806	6	26
β-strand	811-813	3	27
β-strand	817-820	4	27
β-strand	827-835	9	27
β-strand	846-855	10	27
β-strand	857-860	4	27
β-strand	865-866	2	27
β-strand	874-875	2	28
β-strand	880-881	2	28
β-strand	888-893	6	28
β-strand	899-905	7	28
β-strand	914-917	4	29
β-strand	920-923	4	29
β-strand	933-935	3	29
β-strand	942-944	3	29
β-strand	947	1	30
β-strand	954-959	6	31
β-strand	964-969	6	31
β-strand	974-978	5	31
α-helix	987-990	4
β-strand	991	1	30
β-strand	993-998	6	31
β-strand	1004-1009	6	10
β-strand	1028-1032	5	10
β-strand	1037-1042	6	10
α-helix	1045-1061	17
α-helix	1063-1064	2
α-helix	1070-1074	5
α-helix	1083-1085	3
β-strand	1088-1089	2	10
α-helix	1092-1095	4
α-helix	1096-1099	4
α-helix	1102-1107	6
α-helix	1126-1138	13

Chain D: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	61-64	4
α-helix	65-69	5
α-helix	70-75	6
α-helix	81-84	4
α-helix	86-87	2
α-helix	96-100	5
α-helix	107-115	9
α-helix	122-138	17
α-helix	141	1
α-helix	145-163	19

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)
Bromodomain-containing protein 4	D	protein	129	Homo sapiens	O60885 (AlphaFold model)
DET1- and DDB1-associated protein 1	C	protein	102	Homo sapiens	Q9BW61 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9C5V_1 Denticleless protein homolog (chains A)
MLFNSVLRQPQLGVLRNGWSSQYPLQSLLTGYQCSGNDEHTSYGETGVPVPPFGCTFSSA
PNMEHVLAVANEEGFVRLYNTESQSFRKKCFKEWMAHWNAVFDLAWVPGELKLVTAAGDQ
TAKFWDVKAGELIGTCKGHQCSLKSVAFSKFEKAVFCTGGRDGNIMVWDTRCNKKDGFYR
QVNQISGAHNTSDKQTPSKPKKKQNSKGLAPSVDFQQSVTVVLFQDENTLVSAGAVDGII
KVWDLRKNYTAYRQEPIASKSFLYPGSSTRKLGYSSLILDSTGSTLFANCTDDNIYMFNM
TGLKTSPVAIFNGHQNSTFYVKSSLSPDDQFLVSGSSDEAAYIWKVSTPWQPPTVLLGHS
QEVTSVCWCPSDFTKIATCSDDNTLKIWRLNRGLEEKPGGDKLSTVGWASQKKKESRPGL
VTVTSSQSTPAKAPRAKCNPSNSSPSSAACAPSCAGDLENLYFQSHHHHHH

Sequence of entity 2 (B), FASTA

>9C5V_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 (D), FASTA

>9C5V_3 Bromodomain-containing protein 4 (chains D)
MHHHHHHETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKII
KTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKI
NELPTEETE

Sequence of entity 4 (C), FASTA

>9C5V_4 DET1- and DDB1-associated protein 1 (chains C)
MADFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLH
QQWDKKNAAKKRDQEQVELEGESSAPPRKVARTDSPDMHEDT

Ligands and cofactors

ID	Name	Formula	Copies
A1AUO	N-({4-[(4-{[1'-(chloroacetyl)-3'-oxo-3',4'-dihydro-1'H-spiro[cyclopentane-1,2'-…	C46 H48 Cl2 N8 O4 S	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:

9C5U 3.05 Å, Cryo EM structure of DCAF2:Compound 1 complex
9UWG 3.21 Å, Structure of the human DCAF2-DDB1 complex
9C5T 3.36 Å, Cryo EM structure of DCAF2
6QC0 3.5 Å, PCNA complex with Cdt2 C-terminal PIP-box peptide

Browse structure collections

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