4Q9U: Rab5, Rabex-5delta and Rabaptin-5C21 complex
Crystal structure of the Rab5, Rabex-5delta and Rabaptin-5C21 complex. Determined by X-ray diffraction at 4.62 Å resolution. Released 23 Jul 2014.
- Method
- X-ray diffraction
- Resolution
- 4.62 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 9,679
- Mol. weight
- 155.6 kDa
- Released
- 23 Jul 2014
Explore 4Q9U in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4Q9U contains 48 α-helices and 14 β-strands across 8 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: 14 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 138-146 | 9 | |
| α-helix | 152-170 | 19 | |
| α-helix | 175-195 | 21 | |
| α-helix | 204-206 | 3 | |
| α-helix | 207-223 | 17 | |
| α-helix | 231-243 | 13 | |
| α-helix | 262-280 | 19 | |
| α-helix | 284-306 | 23 | |
| α-helix | 316-326 | 11 | |
| α-helix | 331-340 | 10 | |
| α-helix | 344-348 | 5 | |
| α-helix | 352-367 | 16 | |
| α-helix | 378-386 | 9 | |
| α-helix | 393-435 | 43 | |
Chain B: 6 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-27 | 6 | 1 |
| α-helix | 35-39 | 5 | |
| β-strand | 61-62 | 2 | 2 |
| β-strand | 69-70 | 2 | 2 |
| β-strand | 72-75 | 4 | 1 |
| α-helix | 86-88 | 3 | |
| β-strand | 95-101 | 7 | 1 |
| α-helix | 105-121 | 17 | |
| β-strand | 129 | 1 | 3 |
| β-strand | 130-133 | 4 | 1 |
| α-helix | 138-140 | 3 | |
| α-helix | 145-154 | 10 | |
| β-strand | 158 | 1 | 3 |
| α-helix | 170-178 | 9 | |
Chain C: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 553-606 | 54 | |
| α-helix | 611-632 | 22 | |
Chain D: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 560-631 | 72 | |
Chain E: 15 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 135-146 | 12 | |
| α-helix | 153-169 | 17 | |
| α-helix | 170-172 | 3 | |
| α-helix | 175-197 | 23 | |
| α-helix | 204-223 | 20 | |
| α-helix | 231-244 | 14 | |
| α-helix | 262-276 | 15 | |
| α-helix | 277-279 | 3 | |
| α-helix | 284-305 | 22 | |
| α-helix | 319-326 | 8 | |
| α-helix | 331-341 | 11 | |
| α-helix | 344-348 | 5 | |
| α-helix | 351-367 | 17 | |
| α-helix | 378-386 | 9 | |
| α-helix | 393-436 | 44 | |
Chain F: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-24 | 3 | 4 |
| α-helix | 36-40 | 5 | |
| β-strand | 58-59 | 2 | 4 |
| β-strand | 72-74 | 3 | 4 |
| β-strand | 95-99 | 5 | 4 |
| α-helix | 106-121 | 16 | |
| β-strand | 127-132 | 6 | 4 |
| α-helix | 145-154 | 10 | |
| β-strand | 159-161 | 3 | 4 |
| α-helix | 170-178 | 9 | |
Chain G: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 553-603 | 51 | |
| α-helix | 609-627 | 19 | |
| α-helix | 629-633 | 5 | |
Chain H: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 554 | 1 | |
| α-helix | 555-559 | 5 | |
| α-helix | 560-631 | 72 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Rab5 GDP/GTP exchange factor | A, E | protein | 317 | Homo sapiens | Q9UJ41 (AlphaFold model) |
| Ras-related protein Rab-5A | B, F | protein | 171 | Homo sapiens | P20339 (AlphaFold model) |
| Rab GTPase-binding effector protein 1 | C, D, G, H | protein | 92 | Homo sapiens | Q15276 (AlphaFold model) |
Sequence of entity 1 (A, E), FASTA
>4Q9U_1 Rab5 GDP/GTP exchange factor (chains A, E)
MGHHHHHHSIETDRVSKEFIEFLKTFHKTGQEIYKQTKLFLEGMHYKRDLSIEEQSECAQ
DFYHNVAERMQTRGKVPPERVEKIMDQIEKYIMTRLYKYVFCPETTDDEKKDLAIQKRIR
ALRWVTPQMLCVPVNEDIPEVSDMVVKAITDIIEMDSKRVPRDKLACITKCSKHIFNAIK
ITKNEPASADDFLPTLIYIVLKGNPPRLQSNIQYITRFCNPSRLMTGEDGYYFTNLCCAV
AFIEKLDAQSLNLSQEDFDRYMSGQTSPRKQMYKNLDLLSQLNERQERIMNEAKKLEKDL
IDWTDGIAREVQDIVEK
Sequence of entity 2 (B, F), FASTA
>4Q9U_2 Ras-related protein Rab-5A (chains B, F)
SGNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEI
WDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGN
KADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPKN
Sequence of entity 3 (C, D, G, H), FASTA
>4Q9U_3 Rab GTPase-binding effector protein 1 (chains C, D, G, H)
METRDQVKKLQLMLRQANDQLEKTMKDKQELEDFIKQSSEDSSHQISALVLRAQASEILL
EELQQGLSQAKRDVQEQMAVLMQSREQVSEEL
Primary citation
Molecular mechanism for Rabex-5 GEF activation by Rabaptin-5. Zhang, Z., Zhang, T., Wang, S. et al. Elife (2014) 3:e02687-e02687. DOI 10.7554/eLife.02687 · PubMed
Other PDB entries of the same protein (UniProt Q9UJ41 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4N3X 2.0 Å, Crystal structure of Rabex-5 CC domain
- 2C7N 2.1 Å, Human Rabex-5 residues 1-74 in complex with Ubiquitin
- 2OT3 2.1 Å, Crystal structure of rabex-5 VPS9 domain in complex with nucleotide free RAB21
- 4N3Y 2.2 Å, Crystal structure of Rabex-5CC and Rabaptin-5C21 complex
- 1TXU 2.35 Å, Crystal Structure of the Vps9 Domain of Rabex-5
- 2C7M 2.4 Å, Human Rabex-5 residues 1-74 in complex with Ubiquitin
- 4N3Z 3.1 Å, Crystal structure of Rabex-5delta and Rabaptin-5C21 complex
Browse structure collections
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