8IC9: Lys48-linked K48C-diubiquitin

Lys48-linked K48C-diubiquitin. Determined by X-ray diffraction at 1.25 Å resolution. Released 26 Apr 2023.

Method: X-ray diffraction
Resolution: 1.25 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,586
Mol. weight: 34.26 kDa
Released: 26 Apr 2023

Explore 8IC9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8IC9 contains 19 α-helices and 28 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: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	12-16	5	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	61-62	2
β-strand	66-71	6	1

Chains B, C and D: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	12-16	5	1
β-strand	22	1	3
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	3
α-helix	57-59	3
α-helix	61-62	2
β-strand	66-71	6	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polyubiquitin-B	A, C	protein	76	Homo sapiens	P0CG47 (AlphaFold model)
Ubiquitin	B, D	protein	76	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8IC9_1 Polyubiquitin-B (chains A, C)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGCQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 2 (B, D), FASTA

>8IC9_2 Ubiquitin (chains B, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Primary citation

Mutational and Environmental Effects on the Dynamic Conformational Distributions of Lys48-Linked Ubiquitin Chains. Hiranyakorn, M., Yagi-Utsumi, M., Yanaka, S. et al. Int J Mol Sci (2023) 24. DOI 10.3390/ijms24076075 · PubMed

Other PDB entries of the same protein (UniProt P0CG47 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NVG 1.07 Å, Thr12 Phosphorylated Ubiquitin
5TOG 1.08 Å, Room temperature structure of ubiquitin variant u7ub25.2540
5TOF 1.12 Å, Room temperature structure of ubiquitin variant u7ub25
4XOF 1.15 Å, Observing the overall rocking motion of a protein in a crystal - Orthorhombic Ubiquitin…
5GOD 1.15 Å, Lys27-linked di-ubiquitin
5GOB 1.15 Å, Lys6-linked di-ubiquitin
5W46 1.18 Å, Structure of S65D Phosphomimetic Ubiquitin Refined at 1.2 Angstroms Resolution
7S6O 1.25 Å, The crystal structure of Lys48-linked di-ubiquitin
5DK8 1.32 Å, Human ubiquitin in the P1 space group
7CAP 1.33 Å, Cyclic Lys48-linked triubiquitin
5V1Y 1.42 Å, Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex
5KYC 1.43 Å, Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin…

Browse structure collections

About this viewer

MolViewer shows 8IC9 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.