4LHY: GDP-bound Rab8:Rabin8
Crystal structure of GDP-bound Rab8:Rabin8. Determined by X-ray diffraction at 3.1 Å resolution. Released 9 Oct 2013.
- Method
- X-ray diffraction
- Resolution
- 3.1 Å
- Organism
- Homo sapiens
- Chains
- 6
- Atoms
- 4,788
- Mol. weight
- 79.43 kDa
- Ligands
- GDP
- Released
- 9 Oct 2013
Explore 4LHY in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4LHY contains 22 α-helices and 16 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: 7 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8-14 | 7 | 1 |
| α-helix | 21-28 | 8 | |
| β-strand | 43-52 | 10 | 1 |
| β-strand | 55-64 | 10 | 1 |
| α-helix | 68-70 | 3 | |
| α-helix | 71-79 | 9 | |
| β-strand | 83-89 | 7 | 1 |
| α-helix | 93-109 | 17 | |
| β-strand | 115-121 | 7 | 1 |
| α-helix | 126-128 | 3 | |
| α-helix | 133-142 | 10 | |
| β-strand | 146-150 | 5 | 1 |
| β-strand | 151 | 1 | 2 |
| β-strand | 156 | 1 | 2 |
| α-helix | 158-175 | 18 | |
Chain B: 6 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-15 | 9 | 3 |
| α-helix | 21-28 | 8 | |
| β-strand | 43-52 | 10 | 3 |
| β-strand | 55-64 | 10 | 3 |
| α-helix | 68-70 | 3 | |
| α-helix | 71-79 | 9 | |
| β-strand | 83-89 | 7 | 3 |
| α-helix | 93-109 | 17 | |
| β-strand | 115-121 | 7 | 3 |
| α-helix | 133-143 | 11 | |
| β-strand | 146-150 | 5 | 3 |
| β-strand | 151 | 1 | 4 |
| β-strand | 156 | 1 | 4 |
| α-helix | 158-175 | 18 | |
Chain C: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 160-172 | 13 | |
| α-helix | 177-227 | 51 | |
Chain D: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 159-163 | 5 | |
| α-helix | 167-170 | 4 | |
| α-helix | 172-223 | 52 | |
Chain E: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 158-230 | 73 | |
Chain F: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 162-220 | 59 | |
| α-helix | 221-225 | 5 | |
| α-helix | 226-231 | 6 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ras-related protein Rab-8A | A, B | protein | 186 | Homo sapiens | P61006 (AlphaFold model) |
| Rab-3A-interacting protein | C, D, E, F | protein | 78 | Homo sapiens | Q96QF0 (AlphaFold model) |
Sequence of entity 1 (A, B), FASTA
>4LHY_1 Ras-related protein Rab-8A (chains A, B)
GHMAKTYDYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIK
LQIWDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMI
LGNKCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDKKLE
GNSPQG
Sequence of entity 2 (C, D, E, F), FASTA
>4LHY_2 Rab-3A-interacting protein (chains C, D, E, F)
GPGYERLKEELAKAQRELKLKDEECERLSKVRDQLGQELEELTASLFEEAHKMVREANIK
QATAEKQLKEAQGKIDVL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| GDP | Guanosine-5'-diphosphate | C10 H15 N5 O11 P2 | 2 |
Water and common crystallization additives (SO4) are not listed.
Primary citation
Intermediates in the Guanine Nucleotide Exchange Reaction of Rab8 Protein Catalyzed by Guanine Nucleotide Exchange Factors Rabin8 and GRAB. Guo, Z., Hou, X., Goody, R.S. et al. J Biol Chem (2013) 288:32466-32474. DOI 10.1074/jbc.M113.498329 · PubMed
Other PDB entries of the same protein (UniProt P61006 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4LHW 1.55 Å, Crystal structure of Rab8 in its active GppNHp-bound form
- 6SQ2 1.68 Å, Structure of a phosphomimetic switch 2 variant of Rab8a in complex with the phospho-Rab…
- 6WHE 1.73 Å, Structure of phosphomimetic Rab8a GTPase (T72E) in the GTP-bound state
- 6RIR 1.77 Å, Crystal structure of phosphorylated Rab8a in complex with the Rab-binding domain of RILPL2
- 9M0O 1.83 Å, Crystal structure of OPTN 138-170 in complex with GTP-bound RAB8A1-176 (Q67L)
- 7LWB 1.9 Å, Crystal Structure of phospho-Rab8a with the RH2 domain (117-165) of RILPL2
- 6ZSI 1.91 Å, The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members.
- 9IKQ 1.93 Å, Crystal structure of OPTN LZD in complex with GTP-bound Rab8a(Q67L)
- 4LHV 1.95 Å, Crystal structure of Rab8 in its inactive GDP-bound form
- 3QBT 2.0 Å, Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp
- 6ZSJ 2.0 Å, The mechanism of activation of the actin binding protein EHBP1 by Rab8 family members.
- 6YX5 2.14 Å, Structure of DrrA from Legionella pneumophilia in complex with human Rab8a
Browse structure collections
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