5IA7: Ubiquitin fold modifier 1

Crystal structure of Ubiquitin fold modifier 1 (Ufm1). Determined by X-ray diffraction at 2.0 Å resolution. Released 8 Mar 2017.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,221
Mol. weight: 17.88 kDa
Released: 8 Mar 2017

Explore 5IA7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5IA7 contains 8 α-helices and 14 β-strands across 2 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	5-10	6	1
β-strand	18-22	5	1
β-strand	28	1	2
α-helix	29-40	12
β-strand	49-50	2	1
α-helix	55	1
β-strand	56	1	1
α-helix	57	1
β-strand	62	1	2
α-helix	63-70	8
β-strand	73-76	4	1

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	3
β-strand	18-22	5	3
β-strand	28	1	4
α-helix	29-40	12
β-strand	48-50	3	3
α-helix	55	1
β-strand	56	1	3
α-helix	57-58	2
β-strand	62	1	4
α-helix	63-70	8
β-strand	73-77	5	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-fold modifier 1	A, B	protein	83	Homo sapiens	P61960 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5IA7_1 Ubiquitin-fold modifier 1 (chains A, B)
MSKVSFKITLTSDPRLPYKVLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPA
QTAGNVFLKHGSELRIIPRDRVG

Primary citation

Novel insights into the interaction of UBA5 with UFM1 via a UFM1-interacting sequence. Padala, P., Oweis, W., Mashahreh, B. et al. Sci Rep (2017) 7:508-508. DOI 10.1038/s41598-017-00610-0 · 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
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
5HKH 2.55 Å, Crystal structure of Ufm1 in complex with UBA5
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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