2FID: Bovine Rabex-5 fragment

Crystal Structure of a Bovine Rabex-5 fragment complexed with ubiquitin. Determined by X-ray diffraction at 2.8 Å resolution. Released 7 Feb 2006.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Bos taurus
Chains: 2
Atoms: 1,089
Mol. weight: 16.77 kDa
Ligands: ZN
Released: 7 Feb 2006

Explore 2FID in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2FID contains 7 α-helices and 9 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	2-6	5	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	1
β-strand	48-49	2	1
α-helix	50-51	2
β-strand	55	1	2
α-helix	56-59	4
β-strand	66-71	6	1

Chain B: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	3
β-strand	26	1	3
α-helix	27	1
α-helix	29-31	3
α-helix	36-70	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	A	protein	76	Bos taurus	P0CH28 (AlphaFold model)
Rab5 GDP/GTP exchange factor	B	protein	70	Bos taurus	O18973 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2FID_1 Ubiquitin (chains A)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 2 (B), FASTA

>2FID_2 Rab5 GDP/GTP exchange factor (chains B)
GAMGSGIHVDQSELLCKKGCGYYGNPAWQGFCSKCWREEYHKARQKQIQEDWELAERLQR
EEEEAFASSQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Structural basis for ubiquitin recognition and autoubiquitination by Rabex-5. Lee, S., Tsai, Y.C., Mattera, R. et al. Nat Struct Mol Biol (2006) 13:264-271. DOI 10.1038/nsmb1064 · 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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