5LO8: The C2B domain of Rabphilin 3A

The C2B domain of Rabphilin 3A in complex with PI(4,5)P2. Determined by X-ray diffraction at 2.5 Å resolution. Released 21 Jun 2017.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Rattus norvegicus
Chains: 2
Atoms: 2,465
Mol. weight: 39.55 kDa
Ligands: PIO, CA
Released: 21 Jun 2017

Explore 5LO8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5LO8 contains 7 α-helices and 16 β-strands across 2 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: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	543-551	9	1
β-strand	556-565	10	1
β-strand	578-584	7	2
α-helix	585-587	3
β-strand	593-595	3	2
β-strand	606-613	8	1
α-helix	617-620	4
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

Chain B: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	543-551	9	3
β-strand	556-565	10	3
β-strand	578-585	8	4
β-strand	593-595	3	4
β-strand	606-613	8	3
α-helix	617-620	4
β-strand	624-631	8	4
α-helix	637-638	2
β-strand	639-646	8	4
α-helix	654-663	10
β-strand	669-674	6	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rabphilin-3A	A, B	protein	162	Rattus norvegicus	P47709 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5LO8_1 Rabphilin-3A (chains A, B)
HMASMTGGQQMGRGSDFGDIEERGKILVSLMYSTQQGGLIVGIIRCVHLAAMDANGYSDP
FVKLWLKPDMGKKAKHKTQIKKKTLNPEFNEEFFYDIKHSDLAKKSLDISVWDYDIGKSN
DYIGGCQLGISAKGERLKHWYECLKNKDKKIERWHQLQNENH

Ligands and cofactors

ID	Name	Formula	Copies
PIO	[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-d…	C25 H49 O19 P3	2
CA	Calcium ion	Ca	4

Water and common crystallization additives (SO4, GOL) 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
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)
5LOB 3.3 Å, Structure of the Ca2+-bound Rabphilin3A C2B- SNAP25 complex (C2 space group)
3RPB The C2B-domain of rabphilin: structural variations in a janus-faced domain

Browse structure collections

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