7NVK: UBA5 fragment fused to the N-terminus of UFC1

Crystal structure of UBA5 fragment fused to the N-terminus of UFC1. Determined by X-ray diffraction at 2.65 Å resolution. Released 29 Sept 2021.

Method: X-ray diffraction
Resolution: 2.65 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,488
Mol. weight: 25.92 kDa
Released: 29 Sept 2021

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

Secondary structure: helices and β-sheets

7NVK contains 10 α-helices and 7 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 AAA: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	48-59	12
α-helix	62-70	9
α-helix	72-74	3
α-helix	83-106	24
β-strand	112-116	5	1
β-strand	122	1	2
β-strand	123-130	8	1
β-strand	135-140	6	1
β-strand	143	1	2
α-helix	152-153	2
β-strand	167	1	3
α-helix	169-171	3
β-strand	173	1	3
α-helix	179-186	8
α-helix	192-194	3
α-helix	195-200	6
α-helix	201-213	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like modifier-activating enzyme 5,Ubiquitin-fold modifier-conjugating enzyme 1	AAA	protein	226	Homo sapiens	Q9GZZ9 (AlphaFold model), Q9Y3C8 (AlphaFold model)

Sequence of entity 1 (AAA), FASTA

>7NVK_1 Ubiquitin-like modifier-activating enzyme 5,Ubiquitin-fold modifier-conjugating enzyme 1 (chains AAA)
GSEVSEEELKNFSGPVPDLPEGITVAYTIPKKQEDSVTELTVEDSGESLEDLMAKMKNMM
ADEATRRVVSEIPVLKTNAGPRDRELWVQRLKEEYQSLIRYVENNKNADNDWFRLESNKE
GTRWFGKCWYIHDLLKYEFDIEFDIPITYPTTAPEIAVPELDGKTAKMYRGGKICLTDHF
KPLWARNVPKFGLAHLMALGLGPWLAVEIPDLIQKGVIQHKEKCNQ

Primary citation

Structural basis for UFM1 transfer from UBA5 to UFC1. Kumar, M., Padala, P., Fahoum, J. et al. Nat Commun (2021) 12:5708-5708. DOI 10.1038/s41467-021-25994-6 · PubMed

Other PDB entries of the same protein (UniProt Q9GZZ9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5IAA 1.85 Å, Crystal structure of human UBA5 in complex with UFM1
7NW1 1.95 Å, Crystal structure of UFC1 in complex with UBA5
3H8V 2.0 Å, Human Ubiquitin-activating Enzyme 5 in Complex with ATP
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
3GUC 2.25 Å, Human Ubiquitin-activating Enzyme 5 in Complex with AMPPNP
5HKH 2.55 Å, Crystal structure of Ufm1 in complex with UBA5
6H78 2.7 Å, E1 enzyme for ubiquitin like protein activation.
6H8C Structure of the human GABARAPL2 protein in complex with the UBA5 LIR motif
7OVC Structure of the human UFC1 protein in complex with the UBA5 C-terminal UFC1-binding…

Browse structure collections

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