1YD8: Complex of human GGA3 gat domain and ubiquitin

Complex of human GGA3 gat domain and ubiquitin. Determined by X-ray diffraction at 2.8 Å resolution. Released 22 Feb 2005.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: Bos taurus, Homo sapiens
Chains: 4
Atoms: 2,808
Mol. weight: 39.58 kDa
Released: 22 Feb 2005

Explore 1YD8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1YD8 contains 10 α-helices and 10 β-strands across 4 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 G and H: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	212-233	22
α-helix	242-266	25
α-helix	275-298	24

Chains U and V: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	12-16	5	1
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-44	4	1
β-strand	49	1	1
β-strand	66-71	6	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquin	U, V	protein	76	Bos taurus	P0CH28 (AlphaFold model)
ADP-ribosylation factor binding protein GGA3	G, H	protein	98	Homo sapiens	Q9NZ52 (AlphaFold model)

Sequence of entity 1 (U, V), FASTA

>1YD8_1 UBIQUIN (chains U, V)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 2 (G, H), FASTA

>1YD8_2 ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA3 (chains G, H)
GAMGIQKVTKRLHTLEEVNNNVRLLSEMLLHYSQEDSSDGDRELMKELFDQCENKRRTLF
KLASETEDNDNSLGDILQASDNLSRVINSYKTIIEGQV

Primary citation

Structural mechanism for ubiquitinated-cargo recognition by the Golgi-localized, {gamma}-ear-containing, ADP-ribosylation-factor-binding proteins. Prag, G., Lee, S., Mattera, R. et al. Proc Natl Acad Sci U S A (2005) 102:2334-2339. DOI 10.1073/pnas.0500118102 · PubMed

Other PDB entries of the same protein (UniProt P0CH28 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2WWZ 1.4 Å, TAB2 NZF DOMAIN IN COMPLEX WITH Lys63-linked di-ubiquitin, P212121
2ZCC 1.4 Å, Ubiquitin crystallized under high pressure
3M3J 1.6 Å, A new crystal form of Lys48-linked diubiquitin
4XYZ 1.65 Å, Crystal structure of K33 linked di-Ubiquitin
1P3Q 1.7 Å, Mechanism of Ubiquitin Recognition by the CUE Domain of VPS9
2D3G 1.7 Å, Double sided ubiquitin binding of Hrs-UIM
6A42 1.7 Å, R1EN(5-223)-ubiquitin fusion
1WRD 1.75 Å, Crystal structure of Tom1 GAT domain in complex with ubiquitin
1UZX 1.85 Å, A complex of the Vps23 UEV with ubiquitin
2HD5 1.85 Å, USP2 in complex with ubiquitin
2QHO 1.85 Å, Crystal structure of the UBA domain from EDD ubiquitin ligase in complex with ubiquitin
2OOB 1.9 Å, crystal structure of the UBA domain from Cbl-b ubiquitin ligase in complex with ubiquitin

Browse structure collections

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