9D1I: Ubiquitin

Name: PDB 9D1I: Structure of Ubiquitin bound to KLHDC3-EloB/C
Published: 2024-11-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure of Ubiquitin bound to KLHDC3-EloB/C. Determined by X-ray diffraction at 2.0 Å resolution. Released 20 Nov 2024.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,527
Mol. weight: 77.52 kDa
Released: 20 Nov 2024

Explore 9D1I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D1I contains 26 α-helices and 66 β-strands across 4 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, 43 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	1
β-strand	15	1	2
β-strand	18-22	5	3
β-strand	25-29	5	3
β-strand	32	1	2
β-strand	43	1	4
α-helix	44-45	2
β-strand	46-50	5	3
β-strand	55-58	4	3
α-helix	59-64	6
α-helix	70-71	2
α-helix	74	1
β-strand	75	1	4
β-strand	78-85	8	5
β-strand	88-95	8	5
β-strand	101	1	5
β-strand	106-109	4	5
β-strand	115-116	2	5
β-strand	121-122	2	6
α-helix	124-127	4
β-strand	128-129	2	7
β-strand	132-136	5	6
β-strand	139-143	5	6
β-strand	146-147	2	7
β-strand	152-153	2	7
β-strand	157-161	5	6
β-strand	166-169	4	6
β-strand	173	1	8
α-helix	176-178	3
β-strand	181	1	9
β-strand	184-188	5	8
β-strand	191-195	5	8
β-strand	198-200	3	9
β-strand	210-212	3	9
β-strand	217-220	4	8
β-strand	225-226	2	8
α-helix	227-228	2
α-helix	236-238	3
β-strand	240	1	10
β-strand	243-247	5	10
β-strand	250-258	9	10
β-strand	263-272	10	10
β-strand	277-281	5	10
β-strand	284	1	1
α-helix	288-289	2
β-strand	291	1	10
β-strand	292	1	11
β-strand	295-299	5	1
β-strand	302-306	5	1
β-strand	309-311	3	11
β-strand	323-325	3	11
β-strand	329-333	5	1
α-helix	338-348	11
α-helix	358-367	10

Chain B: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	12
β-strand	10	1	13
β-strand	12-19	8	12
β-strand	23	1	14
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	12
β-strand	49-50	2	12
α-helix	51-52	2
β-strand	56	1	14
α-helix	64-66	3
β-strand	68	1	15
β-strand	71	1	15
α-helix	72	1
β-strand	73-79	7	12
β-strand	80	1	16
β-strand	85	1	16
α-helix	86-88	3
β-strand	90	1	13
α-helix	91-93	3

Chain C: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	12
β-strand	28-32	5	12
α-helix	33-36	4
α-helix	40-46	7
β-strand	59-61	3	12
α-helix	67-83	17
α-helix	97-110	14

Chain D: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	17
β-strand	12-16	5	17
β-strand	22	1	18
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	17
β-strand	48-49	2	17
α-helix	50-51	2
β-strand	55	1	18
α-helix	57-59	3
β-strand	66-71	6	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kelch domain-containing protein 3	A	protein	383	Homo sapiens	Q9BQ90 (AlphaFold model)
Elongin-B	B	protein	104	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	C	protein	121	Homo sapiens	Q15369 (AlphaFold model)
Ubiquitin	D	protein	76	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9D1I_1 Kelch domain-containing protein 3 (chains A)
XMLRWTVHLEGGPRRVNHAAVAVGHRVYSFGGYCSGEDYETLRQIDVHIFNAVSLRWTKL
PPVKSAIRGQAPVVPYMRYGHSTVLIDDTVLLWGGRNDTEGACNVLYAFDVNTHKWFTPR
VSGTVPGARDGHSACVLGKIMYIFGGYEQQADCFSNDIHKLDTSTMTWTLICTKGSPARW
RDFHSATMLGSHMYVFGGRADRFGPFHSNNEIYCNRIRVFDTRTEAWLDCPPTPVLPEGR
RSHSAFGYNGELYIFGGYNARLNRHFHDLWKFNPVSFTWKKIEPKGKGPCPRRRQCCCIV
GDKIVLFGGTSPSPEEGLGDEFDLIDHSDLHILDFSPSLKTLCKLAVIQYNLDQSCLPHD
IRWELNAMTTNSNISRPIVSSHK

Sequence of entity 2 (B), FASTA

>9D1I_2 Elongin-B (chains B)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK

Sequence of entity 3 (C), FASTA

>9D1I_3 Elongin-C (chains C)
MSYYHHHHHHDYDIPTTENLYGQGAMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQ
FAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLD
C

Sequence of entity 4 (D), FASTA

>9D1I_4 Ubiquitin (chains D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Primary citation

Structural basis for C-degron selectivity across KLHDCX family E3 ubiquitin ligases. Scott, D.C., Chittori, S., Purser, N. et al. Nat Commun (2024) 15:9899-9899. DOI 10.1038/s41467-024-54126-z · PubMed

Other PDB entries of the same protein (UniProt Q9BQ90 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9D1Z 1.88 Å, Structure of G75Q Ubiquitin bound to KLHDC3-EloB/C
9D1Y 2.6 Å, Structure of G75R Ubiquitin bound to KLHDC3-EloB/C

Browse structure collections

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