3NOB: K11-linked di-ubiquitin

Structure of K11-linked di-ubiquitin. Determined by X-ray diffraction at 2.19 Å resolution. Released 11 Aug 2010.

Method: X-ray diffraction
Resolution: 2.19 Å
Organism: Homo sapiens
Chains: 8
Atoms: 5,005
Mol. weight: 71.09 kDa
Released: 11 Aug 2010

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

Secondary structure: helices and β-sheets

3NOB contains 28 α-helices and 58 β-strands across 8 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: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	1
β-strand	12-17	6	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	1
β-strand	48-49	2	1
α-helix	50-51	2
β-strand	55	1	2
α-helix	57-59	3
β-strand	66-71	6	1
α-helix	72-73	2
β-strand	74	1	3

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	4
β-strand	12-16	5	4
β-strand	22	1	5
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	4
β-strand	48-49	2	4
α-helix	50-51	2
β-strand	55	1	5
β-strand	66-71	6	4

Chains C and H: 3 helices, 7 β-strands

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

Chain D: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	8
β-strand	12-17	6	8
β-strand	22	1	9
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-44	4	8
β-strand	49	1	8
α-helix	50-51	2
β-strand	55	1	9
β-strand	66-71	6	8

Chain E: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	10
β-strand	12-17	6	10
β-strand	22	1	11
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	10
β-strand	48-49	2	10
α-helix	50-51	2
β-strand	55	1	11
α-helix	57-59	3
β-strand	66-71	6	10

Chain F: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	12
β-strand	12-16	5	12
β-strand	22	1	13
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	12
β-strand	48-49	2	12
α-helix	50-51	2
β-strand	55	1	13
β-strand	66-71	6	12
β-strand	74	1	3

Chain G: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	14
β-strand	12-16	5	14
β-strand	22	1	15
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	14
β-strand	48-49	2	14
α-helix	50-51	2
β-strand	55	1	15
α-helix	61-62	2
β-strand	66-71	6	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	A, B, C, D, E, F, G, H	protein	78	Homo sapiens	P62979 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>3NOB_1 Ubiquitin (chains A, B, C, D, E, F, G, H)
SHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSD
YNIQKESTLHLVLRLRGG

Primary citation

K11-Linked Polyubiquitination in Cell Cycle Control Revealed by a K11 Linkage-Specific Antibody. Matsumoto, M.L., Wickliffe, K.E., Dong, K.C. et al. Mol Cell (2010) 39:477-484. DOI 10.1016/j.molcel.2010.07.001 · PubMed

Other PDB entries of the same protein (UniProt P62979 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3NHE 1.26 Å, High Resolution Structure (1.26A) of USP2a in Complex with Ubiquitin
6SQO 1.41 Å, Crystal structure of human MDM2 RING domain homodimer bound to UbcH5B-Ub
7F0N 1.6 Å, Structure of deamidated Ubiquitin
8GLP 1.67 Å, mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus…
3NS8 1.71 Å, Crystal structure of an open conformation of Lys48-linked diubiquitin at pH 7.5
3N32 1.79 Å, The crystal structure of human Ubiquitin adduct with Zeise's salt
6SQS 1.83 Å, Crystal structure of cat phospho-Ser429 MDM2 RING domain bound to UbcH5B-Ub
8QOI 1.9 Å, Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical…
9O3W 1.9 Å, Human 80S ribosome bound to IDB-001 stalled on MYC nascent chain
5WVO 2.0 Å, Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated…
3PHW 2.0 Å, OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with Ubiquitin
8YOO 2.0 Å, Cryo-EM structure of the human 80S ribosome with 100 um Tigecycline

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