2FIF: Bovine Rabex-5 fragment
Crystal Structure of a Bovine Rabex-5 fragment complexed with ubiquitin. Determined by X-ray diffraction at 2.49 Å resolution. Released 7 Feb 2006.
- Method
- X-ray diffraction
- Resolution
- 2.49 Å
- Organism
- Bos taurus
- Chains
- 6
- Atoms
- 3,228
- Mol. weight
- 50.39 kDa
- Ligands
- ZN
- Released
- 7 Feb 2006
Explore 2FIF in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
2FIF contains 19 α-helices and 29 β-strands across 6 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 | 2-7 | 6 | 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, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18 | 1 | 3 |
| β-strand | 26 | 1 | 3 |
| α-helix | 27 | 1 | |
| β-strand | 28 | 1 | 4 |
| α-helix | 29-31 | 3 | |
| β-strand | 34 | 1 | 4 |
| α-helix | 36-70 | 35 | |
Chain C: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-7 | 6 | 5 |
| β-strand | 12-16 | 5 | 5 |
| β-strand | 22 | 1 | 6 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 5 |
| β-strand | 48-49 | 2 | 5 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 6 |
| α-helix | 57-59 | 3 | |
| β-strand | 66-71 | 6 | 5 |
Chain D: 3 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18 | 1 | 7 |
| β-strand | 26 | 1 | 7 |
| α-helix | 27 | 1 | |
| β-strand | 28 | 1 | 8 |
| α-helix | 29-31 | 3 | |
| β-strand | 34 | 1 | 8 |
| α-helix | 36-69 | 34 | |
Chain E: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-7 | 6 | 9 |
| β-strand | 12-16 | 5 | 9 |
| β-strand | 22 | 1 | 10 |
| α-helix | 23-31 | 9 | |
| α-helix | 38-40 | 3 | |
| β-strand | 41-45 | 5 | 9 |
| β-strand | 48-49 | 2 | 9 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 10 |
| α-helix | 56-59 | 4 | |
| β-strand | 66-71 | 6 | 9 |
Chain F: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 36-69 | 34 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ubiquitin | A, C, E | protein | 76 | Bos taurus | P0CH28 (AlphaFold model) |
| Rab5 GDP/GTP exchange factor | B, D, F | protein | 70 | Bos taurus | O18973 (AlphaFold model) |
Sequence of entity 1 (A, C, E), FASTA
>2FIF_1 Ubiquitin (chains A, C, E)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
Sequence of entity 2 (B, D, F), FASTA
>2FIF_2 Rab5 GDP/GTP exchange factor (chains B, D, F)
GAMGSGIHVDQSELLCKKGCGYYGNPAWQGFCSKCWREEYHKARQKQIQEDWELAERLQR
EEEEAFASSQ
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 3 |
Water and common crystallization additives (SO4) are not listed.
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
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