4Z9S: Ubiquitin-40S ribosomal protein S27a

Non-covalent assembly of monoubiquitin that mimics K11 poly-ubiquitin. Determined by X-ray diffraction at 2.3 Å resolution. Released 29 Jul 2015.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Bos taurus
Chains: 4
Atoms: 2,633
Mol. weight: 35.45 kDa
Ligands: SCN, MLA
Released: 29 Jul 2015

Explore 4Z9S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Z9S contains 18 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: 3 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	41-45	5	1
β-strand	48-49	2	1
α-helix	50-51	2
β-strand	55	1	2
β-strand	66-71	6	1

Chains B, C and D: 5 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	41-45	5	3
β-strand	48-49	2	3
α-helix	50-51	2
β-strand	55	1	4
α-helix	57-59	3
β-strand	66-71	6	3
α-helix	72-74	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-40S ribosomal protein S27a	A, B, C, D	protein	76	Bos taurus	P62992 (AlphaFold model)

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

>4Z9S_1 Ubiquitin-40S ribosomal protein S27a (chains A, B, C, D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
SCN	Thiocyanate ion	C N S	9
MLA	Malonic acid	C3 H4 O4	6

Primary citation

Tetrameric Assembly of Monoubiquitin Accurately Mimics the Lys11 Polyubiquitin Chain Structure. Levin-Kravets, O., Shohat, N., Prag, G. Biochemistry (2015) 54:4704-4710. DOI 10.1021/acs.biochem.5b00498 · PubMed

Other PDB entries of the same protein (UniProt P62992 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Q01 0.85 Å, TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 2
5XVE 1.24 Å, Crystal structure of human USP2 C276S mutant in complex with ubiquitin
4M0W 1.4 Å, Crystal Structure of SARS-CoV papain-like protease C112S mutant in complex with ubiquitin
4Y1H 1.4 Å, Crystal structure of K33 linked tri-Ubiquitin
6E2B 1.45 Å, Ubiquitin in complex with Pt(2-phenilpyridine)(PPh3)
5XU8 1.81 Å, Crystal structure of human USP2 in complex with ubiquitin and 6-thioguanine
5MN9 2.05 Å, Crystal structure of MINDY-1 tMIU in complex with K48-diUb
5BZ0 2.1 Å, Crystal structure of IBV papain-like protease PLpro C101S mutant in complex with ubiquitin
7F0U 2.2 Å, porcine epidemic diarrhea virus papain-like protease 2 C44S mutant in complex with mono…
5FER 2.34 Å, Complex of TRIM25 RING with UbcH5-Ub
5JQS 2.65 Å, Crystal structure of deubiquitinase MINDY-1 in complex with Ubiquitin
6DJW 3.8 Å, Crystal Structure of pParkin (REP and RING2 deleted)-pUb-UbcH7 complex

Browse structure collections

About this viewer

MolViewer shows 4Z9S 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.