4HLQ: Human rab1b
Crystal structure of human rab1b bound to GDP and BEF3 in complex with the GAP domain of TBC1D20 from homo sapiens. Determined by X-ray diffraction at 3.3 Å resolution. Released 16 Jan 2013.
- Method
- X-ray diffraction
- Resolution
- 3.3 Å
- Organism
- Homo sapiens
- Chains
- 10
- Atoms
- 17,765
- Mol. weight
- 276.73 kDa
- Ligands
- MG, GDP, BEF
- Released
- 16 Jan 2013
Explore 4HLQ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4HLQ contains 133 α-helices and 33 β-strands across 10 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: 19 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-41 | 16 | |
| α-helix | 47-55 | 9 | |
| α-helix | 63-74 | 12 | |
| α-helix | 81-84 | 4 | |
| α-helix | 89-92 | 4 | |
| α-helix | 96-104 | 9 | |
| α-helix | 107-109 | 3 | |
| α-helix | 116-136 | 21 | |
| α-helix | 146-156 | 11 | |
| α-helix | 159-170 | 12 | |
| α-helix | 183-190 | 8 | |
| α-helix | 192-199 | 8 | |
| α-helix | 201-210 | 10 | |
| α-helix | 218-223 | 6 | |
| α-helix | 232-244 | 13 | |
| α-helix | 249-260 | 12 | |
| α-helix | 262-266 | 5 | |
| α-helix | 272-280 | 9 | |
| α-helix | 288-301 | 14 | |
Chain B: 7 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-15 | 9 | 1 |
| α-helix | 21-29 | 9 | |
| β-strand | 43-52 | 10 | 1 |
| β-strand | 55-64 | 10 | 1 |
| α-helix | 68-70 | 3 | |
| α-helix | 71-74 | 4 | |
| α-helix | 75-77 | 3 | |
| β-strand | 83-89 | 7 | 1 |
| α-helix | 93-109 | 17 | |
| β-strand | 115-121 | 7 | 1 |
| α-helix | 133-143 | 11 | |
| β-strand | 147-150 | 4 | 1 |
| β-strand | 151 | 1 | 2 |
| β-strand | 157 | 1 | 2 |
| α-helix | 158-173 | 16 | |
Chain C: 18 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-40 | 15 | |
| α-helix | 48-55 | 8 | |
| α-helix | 63-73 | 11 | |
| α-helix | 81-84 | 4 | |
| α-helix | 89-92 | 4 | |
| α-helix | 96-104 | 9 | |
| α-helix | 116-135 | 20 | |
| α-helix | 146-171 | 26 | |
| α-helix | 175-178 | 4 | |
| α-helix | 183-199 | 17 | |
| α-helix | 201-209 | 9 | |
| α-helix | 215-217 | 3 | |
| α-helix | 218-223 | 6 | |
| α-helix | 232-243 | 12 | |
| α-helix | 249-260 | 12 | |
| α-helix | 262-266 | 5 | |
| α-helix | 272-278 | 7 | |
| α-helix | 288-301 | 14 | |
Chain D: 9 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-15 | 9 | 3 |
| α-helix | 21-29 | 9 | |
| α-helix | 37-40 | 4 | |
| β-strand | 44-52 | 9 | 3 |
| β-strand | 55-63 | 9 | 3 |
| α-helix | 68-70 | 3 | |
| α-helix | 71-74 | 4 | |
| α-helix | 75-77 | 3 | |
| β-strand | 83-89 | 7 | 3 |
| α-helix | 93-97 | 5 | |
| α-helix | 99-109 | 11 | |
| β-strand | 115-121 | 7 | 3 |
| α-helix | 133-143 | 11 | |
| β-strand | 147-150 | 4 | 3 |
| α-helix | 158-171 | 14 | |
Chain E: 19 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 28-40 | 13 | |
| α-helix | 47-55 | 9 | |
| α-helix | 63-73 | 11 | |
| α-helix | 81-84 | 4 | |
| α-helix | 96-105 | 10 | |
| α-helix | 116-136 | 21 | |
| α-helix | 146-157 | 12 | |
| α-helix | 159-171 | 13 | |
| α-helix | 175-178 | 4 | |
| α-helix | 183-190 | 8 | |
| α-helix | 192-199 | 8 | |
| α-helix | 201-210 | 10 | |
| α-helix | 215-217 | 3 | |
| α-helix | 218-223 | 6 | |
| α-helix | 232-244 | 13 | |
| α-helix | 249-260 | 12 | |
| α-helix | 262-266 | 5 | |
| α-helix | 274-280 | 7 | |
| α-helix | 288-301 | 14 | |
Chain F: 9 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-15 | 9 | 4 |
| α-helix | 21-30 | 10 | |
| α-helix | 37-40 | 4 | |
| β-strand | 44-52 | 9 | 4 |
| β-strand | 55-63 | 9 | 4 |
| α-helix | 68-70 | 3 | |
| α-helix | 71-74 | 4 | |
| α-helix | 75-78 | 4 | |
| β-strand | 83-89 | 7 | 4 |
| α-helix | 93-97 | 5 | |
| α-helix | 99-109 | 11 | |
| β-strand | 115-121 | 7 | 4 |
| α-helix | 133-142 | 10 | |
| β-strand | 147-150 | 4 | 4 |
| α-helix | 158-173 | 16 | |
Chain G: 19 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-39 | 13 | |
| α-helix | 47-56 | 10 | |
| α-helix | 63-73 | 11 | |
| α-helix | 81-84 | 4 | |
| α-helix | 89-92 | 4 | |
| α-helix | 96-104 | 9 | |
| α-helix | 116-136 | 21 | |
| α-helix | 146-157 | 12 | |
| α-helix | 159-172 | 14 | |
| α-helix | 183-189 | 7 | |
| α-helix | 192-199 | 8 | |
| α-helix | 201-210 | 10 | |
| α-helix | 215-217 | 3 | |
| α-helix | 218-221 | 4 | |
| α-helix | 232-244 | 13 | |
| α-helix | 249-260 | 12 | |
| α-helix | 262-265 | 4 | |
| α-helix | 272-280 | 9 | |
| α-helix | 288-301 | 14 | |
Chain H: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7 | 1 | 5 |
| β-strand | 10-15 | 6 | 5 |
| α-helix | 23-26 | 4 | |
| β-strand | 46-52 | 7 | 5 |
| β-strand | 55-62 | 8 | 5 |
| α-helix | 68-70 | 3 | |
| β-strand | 83-89 | 7 | 5 |
| α-helix | 93-97 | 5 | |
| α-helix | 99-109 | 11 | |
| β-strand | 115-121 | 7 | 5 |
| α-helix | 133-141 | 9 | |
| β-strand | 147-149 | 3 | 5 |
| α-helix | 158-170 | 13 | |
2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| TBC1 domain family member 20 | A, C, E, G, I | protein | 305 | Homo sapiens | Q96BZ9 (AlphaFold model) |
| Ras-related protein Rab-1B | B, D, F, H, J | protein | 175 | Homo sapiens | Q9H0U4 (AlphaFold model) |
Sequence of entity 1 (A, C, E, G, I), FASTA
>4HLQ_1 TBC1 domain family member 20 (chains A, C, E, G, I)
MALRSAQGDGPTSGHWDGGAEKADFNAKRKKKVAEIHQALNSDPTDVAALRRMAISEGGL
LTDEIRRKVWPKLLNVNANDPPPISGKNLRQMSKDYQQVLLDVRRSLRRFPPGMPEEQRE
GLQEELIDIILLILERNPQLHYYQGYHDIVVTFLLVVGERLATSLVEKLSTHHLRDFMDP
TMDNTKHILNYLMPIIDQVNPELHDFMQSAEVGTIFALSWLITWFGHVLSDFRHVVRLYD
FFLACHPLMPIYFAAVIVLYREQEVLDCDCDMASVHHLLSQIPQDLPYETLISRAGDLFV
QFPPS
Sequence of entity 2 (B, D, F, H, J), FASTA
>4HLQ_2 Ras-related protein Rab-1B (chains B, D, F, H, J)
GHMPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKL
QIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLV
GNKSDLTTKKVVDNTTAKEFADSLGIPFLETSAKNATNVEQAFMTMAAEIKKRMG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 5 |
| GDP | Guanosine-5'-diphosphate | C10 H15 N5 O11 P2 | 5 |
| BEF | Beryllium trifluoride ion | Be F3 | 5 |
Water and common crystallization additives (SO4) are not listed.
Primary citation
Catalytic mechanism of a mammalian Rab-RabGAP complex in atomic detail. Gavriljuk, K., Gazdag, E.M., Itzen, A. et al. Proc Natl Acad Sci U S A (2012) 109:21348-21353. DOI 10.1073/pnas.1214431110 · PubMed
Other PDB entries of the same protein (UniProt Q96BZ9 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4HL4 2.2 Å, Crystal structure of the human TBC1D20 RabGAP domain
Browse structure collections
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