3TDU: DCN1-like protein 1

N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex: Structure of a human Cul1WHB-Dcn1P-acetylated Ubc12N complex. Determined by X-ray diffraction at 1.5 Å resolution. Released 12 Oct 2011.

Method: X-ray diffraction
Resolution: 1.5 Å
Organisms: Homo sapiens, HOMO SAPIENS
Chains: 6
Atoms: 5,371
Mol. weight: 68.32 kDa
Released: 12 Oct 2011

Explore 3TDU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3TDU contains 30 α-helices and 17 β-strands across 6 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, 5 β-strands

Element	Residues	Length	Sheet
α-helix	62-72	11
β-strand	73-74	2	1
β-strand	77-81	5	1
α-helix	83-93	11
α-helix	100-108	9
β-strand	117-118	2	1
α-helix	119-129	11
α-helix	134-139	6
α-helix	141-147	7
α-helix	151-165	15
β-strand	173-174	2	2
α-helix	175-185	11
α-helix	193-202	10
β-strand	207-208	2	2
α-helix	210-222	13
α-helix	238-250	13

Chain B: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	62-72	11
β-strand	74	1	3
β-strand	77	1	3
β-strand	80-81	2	4
α-helix	83-93	11
α-helix	100-108	9
β-strand	117-118	2	4
α-helix	119-129	11
α-helix	134-139	6
α-helix	141-147	7
α-helix	151-165	15
β-strand	173-174	2	5
α-helix	175-185	11
α-helix	193-202	10
β-strand	207-208	2	5
α-helix	210-222	13
α-helix	238-251	14

Chains C and D: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	703-722	20
β-strand	724-726	3	6
α-helix	727-738	12
α-helix	746-758	13
β-strand	762-765	4	6
β-strand	768-774	7	6

Chains E and F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DCN1-like protein 1	A, B	protein	200	Homo sapiens	Q96GG9 (AlphaFold model)
Cullin-1	C, D	protein	77	Homo sapiens	Q13616 (AlphaFold model)
NEDD8-conjugating enzyme Ubc12	E, F	protein	16	HOMO SAPIENS	P61081 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3TDU_1 DCN1-like protein 1 (chains A, B)
GSRKKLEQLYNRYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQCEFSK
QEFMDGMTELGCDSIEKLKAQIPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAI
AYWNLVLNGRFKFLDLWNKFLLEHHKRSIPKDTWNLLLDFSTMIADDMSNYDEEGAWPVL
IDDFVEFARPQIAGTKSTTV

Sequence of entity 2 (C, D), FASTA

>3TDU_2 Cullin-1 (chains C, D)
GSNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEK
EYLERVDGEKDTYSYLA

Sequence of entity 3 (E, F), FASTA

>3TDU_3 NEDD8-conjugating enzyme Ubc12 (chains E, F)
XMIKLFSLKQQKKEEE

Primary citation

N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex. Scott, D.C., Monda, J.K., Bennett, E.J. et al. Science (2011) 334:674-678. DOI 10.1126/science.1209307 · PubMed

Other PDB entries of the same protein (UniProt Q96GG9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BG3 1.05 Å, Structure of (3S,4S)-1-benzyl-4-(3-(3-(trifluoromethyl)phenyl)ureido)piperidin-3-yl…
6BG5 1.1 Å, Structure of 1-(benzo[d][1,3]dioxol-5-ylmethyl)-1-(1-propylpiperidin-4-yl)-3-(3-(trifluor…
5V86 1.37 Å, Structure of DCN1 bound to NAcM-OPT
6P5V 1.4 Å, Structure of DCN1 bound to N-((4S,5S)-7-ethyl-4-(4-fluorophenyl)-3-methyl-6-oxo-1-phenyl-…
7KWA 1.57 Å, Structure of DCN1 bound to N-((4S,5S)-3-(aminomethyl)-7-ethyl-4-(4-fluorophenyl)-6-oxo-1-…
5V88 1.6 Å, Structure of DCN1 bound to NAcM-COV
6P5W 1.69 Å, Structure of DCN1 bound to 3-methyl-N-((4S,5S)-3-methyl-6-oxo-1-phenyl-4-(p-tolyl)-4,5,6,…
3TDZ 2.0 Å, N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein…
5V83 2.0 Å, Structure of DCN1 bound to NAcM-HIT
6XOO 2.06 Å, DCN1 bound to DI-1859
6XOP 2.07 Å, DCN1 bound to inhibitor 10
6XOQ 2.07 Å, DCN1 covalently bound to inhibitor 4

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