7W3N: Ufm1 fused to UFBP1 UFIM

Crystal structure of Ufm1 fused to UFBP1 UFIM. Determined by X-ray diffraction at 1.6 Å resolution. Released 7 Dec 2022.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 1
Atoms: 831
Mol. weight: 10.08 kDa
Released: 7 Dec 2022

Explore 7W3N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7W3N contains 4 α-helices and 6 β-strands across 1 chain. 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, 6 β-strands

Element	Residues	Length	Sheet
α-helix	-9--7	3
β-strand	3-10	8	1
β-strand	18-24	7	1
β-strand	28	1	2
α-helix	29-40	12
α-helix	44-46	3
β-strand	47-51	5	1
β-strand	62	1	2
α-helix	63-70	8
β-strand	73-78	6	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
UFBP1 peptide,Ubiquitin-fold modifier 1	A	protein	94	Homo sapiens	P61960 (AlphaFold model), Q96HY6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7W3N_1 UFBP1 peptide,Ubiquitin-fold modifier 1 (chains A)
GPEAFVVEEEGMSKVSFKITLTSDPRLPYKVLSVPESTPFTAVLKFAAEEFKVPAATSAI
ITNDGIGINPAQTAGNVFLKHGSELRIIPRDRVG

Primary citation

The UFM1 system regulates ER-phagy through the ufmylation of CYB5R3. Ishimura, R., El-Gowily, A.H., Noshiro, D. et al. Nat Commun (2022) 13:7857-7857. DOI 10.1038/s41467-022-35501-0 · PubMed

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

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
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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