5HKH: Ufm1

Crystal structure of Ufm1 in complex with UBA5. Determined by X-ray diffraction at 2.55 Å resolution. Released 9 Mar 2016.

Method: X-ray diffraction
Resolution: 2.55 Å
Organism: Homo sapiens
Chains: 3
Atoms: 1,342
Mol. weight: 19.47 kDa
Released: 9 Mar 2016

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

Secondary structure: helices and β-sheets

5HKH contains 7 α-helices and 16 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: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	0	1	1
α-helix	1-2	2
β-strand	3-9	7	2
β-strand	18-24	7	2
β-strand	28	1	3
α-helix	29-39	11
β-strand	48-51	4	2
α-helix	55	1
β-strand	56	1	2
α-helix	57-58	2
β-strand	62	1	3
α-helix	63-70	8
β-strand	73-77	5	2

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	344-345	2	2

Chain C: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
β-strand	18-24	7	1
β-strand	28	1	4
α-helix	29-40	12
β-strand	48-51	4	1
β-strand	56	1	1
β-strand	62	1	4
α-helix	63-70	8
β-strand	73-77	5	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-fold modifier 1	A, C	protein	86	Homo sapiens	P61960 (AlphaFold model)
Asp-asn-glu-trp-gly-ile-glu-leu-val	B	protein	9	Homo sapiens	Q9GZZ9 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5HKH_1 Ubiquitin-fold modifier 1 (chains A, C)
GAMESKVSFKITLTSDPRLPYKVLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGI
NPAQTAGNVFLKHGSELRIIPRDRVG

Sequence of entity 2 (B), FASTA

>5HKH_2 ASP-ASN-GLU-TRP-GLY-ILE-GLU-LEU-VAL (chains B)
DNEWGIELV

Primary citation

Structural and Functional Analysis of a Novel Interaction Motif within UFM1-activating Enzyme 5 (UBA5) Required for Binding to Ubiquitin-like Proteins and Ufmylation. Habisov, S., Huber, J., Ichimura, Y. et al. J Biol Chem (2016) 291:9025-9041. DOI 10.1074/jbc.M116.715474 · PubMed

Other PDB entries of the same protein (UniProt P61960 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7W3N 1.6 Å, Crystal structure of Ufm1 fused to UFBP1 UFIM
8BZR 1.78 Å, UFC1-UFM1 conjugate
5IAA 1.85 Å, Crystal structure of human UBA5 in complex with UFM1
5IA7 2.0 Å, Crystal structure of Ubiquitin fold modifier 1 (Ufm1)
5IA8 2.0 Å, Structure of a Ubiquitin like protein with an E1 fragment
5L95 2.1 Å, Crystal structure of human UBA5 in complex with UFM1 and AMP
6H77 2.1 Å, E1 enzyme for ubiquitin like protein activation in complex with UBL
8OJ5 2.9 Å, 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (in-vitro reconstitution)
9GY4 3.0 Å, 60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF…
8OHD 3.1 Å, 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (native)
8QFC 3.2 Å, UFL1 E3 ligase bound 60S ribosome
8OJ0 3.3 Å, 60S ribosomal subunit bound to the E3-UFM1 complex - state 2 (native)

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