5LOB: Ca2+-bound Rabphilin3A C2B- SNAP25 complex
Structure of the Ca2+-bound Rabphilin3A C2B- SNAP25 complex (C2 space group). Determined by X-ray diffraction at 3.3 Å resolution. Released 21 Jun 2017.
- Method
- X-ray diffraction
- Resolution
- 3.3 Å
- Organism
- Rattus norvegicus
- Chains
- 7
- Atoms
- 5,922
- Mol. weight
- 101.13 kDa
- Ligands
- CA
- Released
- 21 Jun 2017
Explore 5LOB in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5LOB contains 16 α-helices and 27 β-strands across 7 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: 3 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 543-551 | 9 | 1 |
| β-strand | 556-565 | 10 | 1 |
| α-helix | 567-569 | 3 | |
| β-strand | 578-584 | 7 | 2 |
| β-strand | 593-595 | 3 | 2 |
| β-strand | 606-613 | 8 | 1 |
| β-strand | 625-631 | 7 | 2 |
| α-helix | 637-638 | 2 | |
| β-strand | 639-646 | 8 | 2 |
| α-helix | 653-663 | 11 | |
| β-strand | 669-674 | 6 | 1 |
| β-strand | 676 | 1 | 2 |
Chain B: 4 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 543-551 | 9 | 3 |
| β-strand | 556-565 | 10 | 3 |
| α-helix | 567-569 | 3 | |
| β-strand | 578-584 | 7 | 4 |
| β-strand | 593-595 | 3 | 4 |
| α-helix | 596-599 | 4 | |
| β-strand | 606-614 | 9 | 3 |
| β-strand | 624-631 | 8 | 4 |
| α-helix | 637-638 | 2 | |
| β-strand | 639-647 | 9 | 4 |
| α-helix | 653-663 | 11 | |
| β-strand | 669-674 | 6 | 3 |
Chain C: 4 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 543-551 | 9 | 5 |
| β-strand | 556-565 | 10 | 5 |
| α-helix | 567-569 | 3 | |
| β-strand | 576 | 1 | 6 |
| β-strand | 578-584 | 7 | 7 |
| β-strand | 593-595 | 3 | 7 |
| α-helix | 596-599 | 4 | |
| β-strand | 602 | 1 | 6 |
| β-strand | 606-613 | 8 | 5 |
| β-strand | 624-631 | 8 | 7 |
| α-helix | 637-638 | 2 | |
| β-strand | 639-647 | 9 | 7 |
| α-helix | 653-663 | 11 | |
| β-strand | 669-674 | 6 | 5 |
Chain D: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-77 | 74 | |
Chain E: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 141-143 | 3 | |
| α-helix | 144-193 | 50 | |
Chain F: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-80 | 69 | |
Chain G: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 144-193 | 50 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Rabphilin-3A | A, B, C | protein | 162 | Rattus norvegicus | P47709 (AlphaFold model) |
| Synaptosomal-associated protein 25 | D, F | protein | 100 | Rattus norvegicus | P60881 (AlphaFold model) |
| Synaptosomal-associated protein 25 | E, G | protein | 96 | Rattus norvegicus | P60881 (AlphaFold model) |
Sequence of entity 1 (A, B, C), FASTA
>5LOB_1 Rabphilin-3A (chains A, B, C)
HMASMTGGQQMGRGSDFGDIEERGKILVSLMYSTQQGGLIVGIIRCVHLAAMDANGYSDP
FVKLWLKPDMGKKAKHKTQIKKKTLNPEFNEEFFYDIKHSDLAKKSLDISVWDYDIGKSN
DYIGGCQLGISAKGERLKHWYECLKNKDKKIERWHQLQNENH
Sequence of entity 2 (D, F), FASTA
>5LOB_2 Synaptosomal-associated protein 25 (chains D, F)
XXXXXGSHMASMTGGQQMGRGSEFMRNELEEMQRRADQLADESLESTRRMLQLVEESKDA
GIRTLVMLDEQGEQLDRVEEGMNHINQDMKEAEKNLKDLG
Sequence of entity 3 (E, G), FASTA
>5LOB_3 Synaptosomal-associated protein 25 (chains E, G)
XXXXXXXXXXXXXXGSHMASMTGGQQMGRGSEFARENEMDENLEQVSGIIGNLRHMALDM
GNEIDTQNRQIDRIMEKADSNKTRIDEANQRATKML
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CA | Calcium ion | Ca | 6 |
Water and common crystallization additives (GOL, SO4) are not listed.
Primary citation
Structural characterization of the Rabphilin-3A-SNAP25 interaction. Ferrer-Orta, C., Perez-Sanchez, M.D., Coronado-Parra, T. et al. Proc Natl Acad Sci U S A (2017) 114:E5343-E5351. DOI 10.1073/pnas.1702542114 · PubMed
Other PDB entries of the same protein (UniProt P47709 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 2CM5 1.28 Å, crystal structure of the C2B domain of rabphilin
- 4NS0 1.8 Å, The C2A domain of Rabphilin 3A in complex with PI(4,5)P2
- 2CM6 1.85 Å, crystal structure of the C2B domain of rabphilin3A
- 2CHD 1.92 Å, Crystal structure of the C2A domain of Rabphilin-3A
- 4NP9 1.92 Å, Structure of Rabphilin C2A domain bound to IP3
- 4LT7 2.5 Å, Crystal structure of the c2a domain of rabphilin-3a in complex with a calcium
- 5LO8 2.5 Å, The C2B domain of Rabphilin 3A in complex with PI(4,5)P2
- 1ZBD 2.6 Å, Structural basis of rab effector specificity: crystal structure of the small G protein…
- 5LOW 2.8 Å, Structure of the Ca2+-bound Rabphilin 3A C2B domain SNAP25 complex (P21 space group)
- 3RPB The C2B-domain of rabphilin: structural variations in a janus-faced domain
Browse structure collections
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