6H77: E1 enzyme for ubiquitin like protein activation

E1 enzyme for ubiquitin like protein activation in complex with UBL. Determined by X-ray diffraction at 2.1 Å resolution. Released 31 Oct 2018.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 8
Atoms: 12,866
Mol. weight: 176.82 kDa
Ligands: ATP, MG, ZN
Released: 31 Oct 2018

Explore 6H77 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6H77 contains 72 α-helices and 92 β-strands across 8 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.

Chains A, B, C and D: 15 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	54-61	8
α-helix	68-73	6
β-strand	75-79	5	1
α-helix	83-95	13
β-strand	99-103	5	1
β-strand	107	1	2
α-helix	110-112	3
α-helix	120-122	3
β-strand	126	1	2
α-helix	127-138	12
β-strand	143-147	5	1
α-helix	154-166	13
β-strand	167	1	3
β-strand	173	1	3
α-helix	174-175	2
β-strand	177-180	4	1
α-helix	185-198	14
β-strand	202-207	6	1
β-strand	213-219	7	1
α-helix	233-236	4
α-helix	241-244	4
α-helix	255-274	20
β-strand	282-286	5	1
β-strand	291	1	1
β-strand	294-295	2	1
α-helix	297	1
β-strand	298	1	4
α-helix	299-300	2
α-helix	306-320	15
β-strand	344-345	2	5

Chains Q, R, S and T: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	5
β-strand	18-24	7	5
β-strand	28	1	21
α-helix	29-40	12
α-helix	44-46	3
β-strand	48-51	4	5
β-strand	55	1	9
β-strand	56	1	5
β-strand	62	1	21
α-helix	63-70	8
β-strand	73-77	5	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like modifier-activating enzyme 5	A, B, C, D	protein	311	Homo sapiens	Q9GZZ9 (AlphaFold model)
Ubiquitin-fold modifier 1	Q, R, S, T	protein	78	Homo sapiens	P61960 (AlphaFold model)

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

>6H77_1 Ubiquitin-like modifier-activating enzyme 5 (chains A, B, C, D)
GRVRIEKMSSEVVDSNPYSRLMALKRMGIVSDYEKIRTFAVAIVGVGGVGSVTAEMLTRC
GIGKLLLFDYDKVELANMNRLFFQPHQAGLSKVQAAEHTLRNINPDVLFEVHNYNITTVE
NFQHFMDRISNGGLEEGKPVDLVLSCVDNFEARMTINTACNELGQTWMESGVSENAVSGH
IQLIIPGESACFACAPPLVVAANIDEKTLKREGVCAASLPTTMGVVAGILVQNVLKFLLN
FGTVSFYLGYNAMQDFFPTMSMKPNPQCDDRNCRKQQEEYKKKVAALPKQEVIQEEEEII
HEDNEWGIELV

Sequence of entity 2 (Q, R, S, T), FASTA

>6H77_2 Ubiquitin-fold modifier 1 (chains Q, R, S, T)
MSKVSFKITLTSDPRLPYKVLSVPESTPFTAVLKFAAEEFKVPAATSAIITNDGIGINPA
QTAGNVFLKHGSELRIIP

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	4
MG	Magnesium ion	Mg	8
ZN	Zinc ion	Zn	4

Water and common crystallization additives (EDO, PEG) are not listed.

Primary citation

An N-Terminal Extension to UBA5 Adenylation Domain Boosts UFM1 Activation: Isoform-Specific Differences in Ubiquitin-like Protein Activation. Soudah, N., Padala, P., Hassouna, F. et al. J Mol Biol (2019) 431:463-478. DOI 10.1016/j.jmb.2018.10.007 · 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
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
7NVK 2.65 Å, Crystal structure of UBA5 fragment fused to the N-terminus of UFC1
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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