9C5T: Cryo EM structure of DCAF2

Name: PDB 9C5T: Cryo EM structure of DCAF2
Published: 2025-10-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Cryo EM structure of DCAF2. Determined by electron microscopy at 3.36 Å resolution. Released 1 Oct 2025.

Method: Electron microscopy
Resolution: 3.36 Å
Organism: Homo sapiens
Chains: 2
Atoms: 11,781
Mol. weight: 178.98 kDa
Released: 1 Oct 2025

Explore 9C5T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9C5T contains 21 α-helices and 161 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: 4 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
α-helix	28-31	4
β-strand	32-35	4	1
β-strand	40	1	2
β-strand	43	1	3
β-strand	49	1	3
β-strand	52	1	4
β-strand	57	1	5
β-strand	67-70	4	5
β-strand	71	1	4
β-strand	75-79	5	5
β-strand	90-95	6	5
β-strand	101-106	6	6
α-helix	107	1
β-strand	112-117	6	6
β-strand	121-126	6	6
β-strand	132-137	6	6
β-strand	143-149	7	7
β-strand	152-160	9	7
β-strand	165-169	5	7
β-strand	181-185	5	7
β-strand	219-224	6	8
β-strand	229-234	6	8
β-strand	240-244	5	8
β-strand	260-262	3	8
β-strand	276-279	4	9
β-strand	285-289	5	9
β-strand	294-299	6	9
β-strand	309-312	4	9
β-strand	323-325	3	1
β-strand	331-334	4	1
β-strand	336	1	10
β-strand	341-345	5	1
α-helix	352-353	2
β-strand	354-357	4	1
β-strand	363	1	10
β-strand	367-368	2	11
β-strand	376-378	3	11
β-strand	380	1	10
β-strand	385	1	2
β-strand	386-388	3	11
β-strand	389-390	2	1
β-strand	405-411	7	1

Chain B: 17 helices, 122 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	12
β-strand	8-10	3	12
β-strand	17-21	5	13
β-strand	30-35	6	13
β-strand	38-44	7	13
β-strand	49-56	8	13
β-strand	61-67	7	14
α-helix	75	1
β-strand	76-81	6	14
β-strand	85-92	8	14
β-strand	99-107	9	14
α-helix	114	1
β-strand	115	1	15
α-helix	116	1
β-strand	121-124	4	16
β-strand	130-134	5	16
β-strand	136	1	15
β-strand	139	1	17
β-strand	141-144	4	16
β-strand	155	1	16
β-strand	158	1	17
β-strand	163-169	7	18
α-helix	170	1
β-strand	178-183	6	18
β-strand	189-193	5	18
β-strand	196	1	19
β-strand	201	1	19
β-strand	204	1	18
β-strand	210-211	2	18
β-strand	218-221	4	20
β-strand	229-232	4	20
β-strand	237-241	5	20
β-strand	244-248	5	20
α-helix	251-253	3
β-strand	261-263	3	21
β-strand	270-273	4	21
β-strand	279-288	10	21
β-strand	296-307	12	21
β-strand	311-316	6	22
β-strand	321-326	6	22
β-strand	331	1	23
β-strand	333-336	4	22
β-strand	342	1	24
β-strand	345	1	24
β-strand	347-349	3	22
α-helix	352	1
β-strand	353	1	23
α-helix	354	1
β-strand	362-365	4	25
β-strand	374-377	4	25
α-helix	382-384	3
β-strand	386	1	26
β-strand	388-392	5	25
β-strand	403	1	27
α-helix	405-407	3
β-strand	409	1	28
β-strand	412-413	2	28
β-strand	424-428	5	28
β-strand	433-437	5	28
β-strand	444-445	2	28
β-strand	459	1	29
β-strand	462-464	3	30
β-strand	467-468	2	30
β-strand	471	1	29
β-strand	473	1	31
β-strand	476	1	29
β-strand	497	1	31
β-strand	500-504	5	32
β-strand	507-511	5	32
β-strand	515-516	2	32
β-strand	522	1	33
β-strand	525	1	33
β-strand	532-533	2	32
β-strand	557-558	2	34
β-strand	567-568	2	34
α-helix	587	1
β-strand	588-595	8	35
β-strand	600-606	7	35
β-strand	611-612	2	35
β-strand	614	1	35
β-strand	628-629	2	35
β-strand	637	1	36
β-strand	640-641	2	37
β-strand	648-649	2	37
β-strand	652	1	36
β-strand	657	1	38
β-strand	662	1	39
β-strand	665	1	39
β-strand	670	1	38
β-strand	678-680	3	40
β-strand	692-694	3	40
β-strand	698	1	27
β-strand	699	1	40
β-strand	710-713	4	25
β-strand	716	1	26
β-strand	720	1	41
β-strand	726-727	2	42
β-strand	732-733	2	42
β-strand	738-743	6	41
α-helix	744	1
β-strand	749-751	3	41
β-strand	763-765	3	43
β-strand	785-789	5	41
β-strand	790-794	5	43
β-strand	795	1	42
β-strand	801-806	6	43
β-strand	811-819	9	44
β-strand	828-835	8	44
β-strand	845-851	7	44
β-strand	853	1	45
β-strand	858	1	45
β-strand	862	1	44
β-strand	865-866	2	44
β-strand	870-876	7	46
β-strand	879-884	6	46
β-strand	888-893	6	46
β-strand	899-902	4	46
β-strand	913-917	5	47
β-strand	920-924	5	47
β-strand	930-935	6	47
β-strand	942-947	6	47
β-strand	954-959	6	48
β-strand	965-969	5	48
β-strand	973-979	7	48
β-strand	991	1	47
β-strand	992-999	8	48
β-strand	1004-1010	7	12
β-strand	1025-1032	8	12
β-strand	1037-1042	6	12
α-helix	1045-1061	17
α-helix	1062-1064	3
α-helix	1070-1073	4
β-strand	1076-1077	2	49
β-strand	1082-1083	2	49
β-strand	1086	1	48
β-strand	1088-1090	3	12
α-helix	1091-1095	5
α-helix	1102-1109	8
α-helix	1126-1137	12

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)

Sequence of entity 1 (A), FASTA

>9C5T_1 Denticleless protein homolog (chains A)
MLFNSVLRQPQLGVLRNGWSSQYPLQSLLTGYQCSGNDEHTSYGETGVPVPPFGCTFSSA
PNMEHVLAVANEEGFVRLYNTESQSFRKKCFKEWMAHWNAVFDLAWVPGELKLVTAAGDQ
TAKFWDVKAGELIGTCKGHQCSLKSVAFSKFEKAVFCTGGRDGNIMVWDTRCNKKDGFYR
QVNQISGAHNTSDKQTPSKPKKKQNSKGLAPSVDFQQSVTVVLFQDENTLVSAGAVDGII
KVWDLRKNYTAYRQEPIASKSFLYPGSSTRKLGYSSLILDSTGSTLFANCTDDNIYMFNM
TGLKTSPVAIFNGHQNSTFYVKSSLSPDDQFLVSGSSDEAAYIWKVSTPWQPPTVLLGHS
QEVTSVCWCPSDFTKIATCSDDNTLKIWRLNRGLEEKPGGDKLSTVGWASQKKKESRPGL
VTVTSSQSTPAKAPRAKCNPSNSSPSSAACAPSCAGDLENLYFQSHHHHHH

Sequence of entity 2 (B), FASTA

>9C5T_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

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
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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