4CYM: Complex of human VARP-ANKRD1 with Rab32-GppCp
Complex of human VARP-ANKRD1 with Rab32-GppCp. Determined by X-ray diffraction at 2.8 Å resolution. Released 4 Jun 2014.
- Method
- X-ray diffraction
- Resolution
- 2.8 Å
- Organism
- HOMO SAPIENS
- Chains
- 6
- Atoms
- 8,282
- Mol. weight
- 144.85 kDa
- Ligands
- GCP, MG
- Released
- 4 Jun 2014
Explore 4CYM in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4CYM contains 57 α-helices and 30 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: 8 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 23-31 | 9 | 1 |
| α-helix | 38-47 | 10 | |
| β-strand | 60-68 | 9 | 1 |
| β-strand | 74-82 | 9 | 1 |
| α-helix | 84-88 | 5 | |
| α-helix | 92-96 | 5 | |
| β-strand | 101-107 | 7 | 1 |
| α-helix | 111-115 | 5 | |
| α-helix | 117-127 | 11 | |
| β-strand | 129 | 1 | 2 |
| β-strand | 135 | 1 | 2 |
| α-helix | 136-137 | 2 | |
| β-strand | 138-143 | 6 | 1 |
| α-helix | 155-164 | 10 | |
| β-strand | 167-173 | 7 | 1 |
| β-strand | 174 | 1 | 3 |
| β-strand | 179 | 1 | 3 |
| α-helix | 181-195 | 15 | |
Chain B: 9 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 24-31 | 8 | 4 |
| α-helix | 38-47 | 10 | |
| β-strand | 60-68 | 9 | 4 |
| β-strand | 74-82 | 9 | 4 |
| α-helix | 84-88 | 5 | |
| α-helix | 92-96 | 5 | |
| β-strand | 101-107 | 7 | 4 |
| α-helix | 111-115 | 5 | |
| α-helix | 117-127 | 11 | |
| β-strand | 129 | 1 | 5 |
| α-helix | 134 | 1 | |
| β-strand | 135 | 1 | 5 |
| α-helix | 136-137 | 2 | |
| β-strand | 138-143 | 6 | 4 |
| α-helix | 155-164 | 10 | |
| β-strand | 169-173 | 5 | 4 |
| β-strand | 174 | 1 | 6 |
| β-strand | 179 | 1 | 6 |
| α-helix | 181-195 | 15 | |
Chain C: 9 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 23-31 | 9 | 7 |
| α-helix | 38-47 | 10 | |
| β-strand | 60-68 | 9 | 7 |
| β-strand | 74-82 | 9 | 7 |
| α-helix | 84-88 | 5 | |
| α-helix | 92-96 | 5 | |
| β-strand | 101-107 | 7 | 7 |
| α-helix | 111-115 | 5 | |
| α-helix | 117-127 | 11 | |
| β-strand | 129 | 1 | 8 |
| α-helix | 134 | 1 | |
| β-strand | 135 | 1 | 8 |
| α-helix | 136-137 | 2 | |
| β-strand | 138-143 | 6 | 7 |
| α-helix | 155-164 | 10 | |
| β-strand | 167-173 | 7 | 7 |
| β-strand | 174 | 1 | 9 |
| β-strand | 179 | 1 | 9 |
| α-helix | 181-195 | 15 | |
Chain D: 10 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 466-473 | 8 | |
| α-helix | 476-484 | 9 | |
| α-helix | 499-506 | 8 | |
| α-helix | 509-517 | 9 | |
| α-helix | 532-538 | 7 | |
| α-helix | 542-551 | 10 | |
| α-helix | 568-574 | 7 | |
| α-helix | 578-586 | 9 | |
| α-helix | 601-604 | 4 | |
| α-helix | 608-615 | 8 | |
Chain E: 10 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 466-473 | 8 | |
| α-helix | 476-484 | 9 | |
| α-helix | 499-506 | 8 | |
| α-helix | 509-517 | 9 | |
| α-helix | 532-538 | 7 | |
| α-helix | 542-551 | 10 | |
| α-helix | 568-574 | 7 | |
| α-helix | 578-586 | 9 | |
| α-helix | 602-604 | 3 | |
| α-helix | 608-615 | 8 | |
Chain F: 11 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 461-463 | 3 | |
| α-helix | 466-473 | 8 | |
| α-helix | 476-484 | 9 | |
| α-helix | 499-506 | 8 | |
| α-helix | 509-517 | 9 | |
| α-helix | 532-538 | 7 | |
| α-helix | 542-551 | 10 | |
| α-helix | 568-574 | 7 | |
| α-helix | 578-586 | 9 | |
| α-helix | 602-604 | 3 | |
| α-helix | 608-615 | 8 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ras-related protein rab-32 | A, B, C | protein | 230 | HOMO SAPIENS | Q13637 (AlphaFold model) |
| Ankyrin repeat domain-containing protein 27 | D, E, F | protein | 203 | HOMO SAPIENS | Q96NW4 (AlphaFold model) |
Sequence of entity 1 (A, B, C), FASTA
>4CYM_1 RAS-RELATED PROTEIN RAB-32 (chains A, B, C)
GPLGSMAGGGAGDPGLGAAAAPAPETREHLFKVLVIGELGVGKTSIIKRYVHQLFSQHYR
ATIGVDFALKVLNWDSRTLVRLQLWDIAGLERFGNMTRVYYKEAVGAFVVFDISRSSTFE
AVLKWKSDLDSKVHLPNGSPIPAVLLANKCDQNKDSSQSPSQVDQFCKEHGFAGWFETSA
KDNINIEEAARFLVEKILVNHQSFPNEENDVDKIKLDQETLRAENKSQCC
Sequence of entity 2 (D, E, F), FASTA
>4CYM_2 ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27 (chains D, E, F)
GPLGSMDPSVVTPFSRDDRGHTPLHVAAVCGQASLIDLLVSKGAMVNATDYHGATPLHLA
CQKGYQSVTLLLLHYKASAEVQDNNGNTPLHLACTYGHEDCVKALVYYDVESCRLDIGNE
KGDTPLHIAARWGYQGVIETLLQNGASTEIQNRLKETPLKCALNSKILSVMEAYHLSFER
RQKSSEAPVQSPQRSVDHHHHHH
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| GCP | Phosphomethylphosphonic acid guanylate ester | C11 H18 N5 O13 P3 | 3 |
| MG | Magnesium ion | Mg | 3 |
Primary citation
Varp is Recruited on to Endosomes by Direct Interaction with Retromer, Where Together They Function in Export to the Cell Surface. Hesketh, G.G., Perez-Dorado, I., Jackson, L.P. et al. Dev Cell (2014) 29:591. DOI 10.1016/J.DEVCEL.2014.04.010 · PubMed
Other PDB entries of the same protein (UniProt Q13637 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6FF8 2.13 Å, Crystal structure of uncomplexed Rab32 in the active GTP-bound state at 2.13 Angstrom…
- 5OEC 2.3 Å, Human Rab32 (18-201):GDP in complex with Salmonella GtgE (21-214) C45A mutant
- 5OED 2.9 Å, Human Rab32:GDP in complex with Salmonella GtgE C45A mutant
- 4CZ2 2.97 Å, Complex of human VARP-ANKRD1 with Rab32-GppCp. Selenomet derivative.
Browse structure collections
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