5NLJ: Polyubiquitin-B

Crystal structure of Zn3-E16V human ubiquitin (hUb) mutant adduct, from a solution 70 mM zinc acetate/20% v/v TFE/1.3 mM E16V hUb. Determined by X-ray diffraction at 1.53 Å resolution. Released 26 Apr 2017.

Method: X-ray diffraction
Resolution: 1.53 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,019
Mol. weight: 26.85 kDa
Ligands: ETF, ZN
Released: 26 Apr 2017

Explore 5NLJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NLJ contains 13 α-helices and 21 β-strands across 3 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	2-6	5	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	43-45	3	1
β-strand	48-49	2	1
α-helix	50-51	2
β-strand	55	1	2
α-helix	57-59	3
β-strand	66-69	4	1

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	3
β-strand	12-16	5	3
β-strand	22	1	4
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	3
β-strand	48-49	2	3
α-helix	50-51	2
β-strand	55	1	4
α-helix	57-59	3
β-strand	66-70	5	3

Chain C: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	5
α-helix	11	1
β-strand	12-16	5	5
β-strand	22	1	6
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	5
β-strand	48-49	2	5
α-helix	50-51	2
β-strand	55	1	6
α-helix	57-59	3
β-strand	66-71	6	5

Molecules and chains

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

Sequence of entity 1 (A, B, C), FASTA

>5NLJ_1 Polyubiquitin-B (chains A, B, C)
MQIFVKTLTGKTITLVVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ETF	Trifluoroethanol	C2 H3 F3 O	1
ZN	Zinc ion	Zn	9

Water and common crystallization additives (EDO, PEG, ACT) are not listed.

Primary citation

Aggregation Pathways of Native-Like Ubiquitin Promoted by Single-Point Mutation, Metal Ion Concentration, and Dielectric Constant of the Medium. Fermani, S., Calvaresi, M., Mangini, V. et al. Chemistry (2018) 24:4140-4148. DOI 10.1002/chem.201705543 · 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
8IC9 1.25 Å, Lys48-linked K48C-diubiquitin
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

Browse structure collections

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