4NP9: Rabphilin C2A domain

Structure of Rabphilin C2A domain bound to IP3. Determined by X-ray diffraction at 1.92 Å resolution. Released 25 Dec 2013.

Method: X-ray diffraction
Resolution: 1.92 Å
Organism: Rattus norvegicus
Chains: 1
Atoms: 1,204
Mol. weight: 15.82 kDa
Ligands: I3P
Released: 25 Dec 2013

Explore 4NP9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4NP9 contains 7 α-helices and 9 β-strands across 1 chain. 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, 9 β-strands

Element	Residues	Length	Sheet
β-strand	385-393	9	1
α-helix	394-396	3
β-strand	398-407	10	1
α-helix	409-411	3
β-strand	420-427	8	2
α-helix	432-434	3
β-strand	435-437	3	2
α-helix	438-441	4
β-strand	448-456	9	1
α-helix	460-465	6
β-strand	467-475	9	2
β-strand	481-490	10	2
α-helix	491-493	3
α-helix	494-495	2
β-strand	500-505	6	1
β-strand	507	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rabphilin-3A	A	protein	133	Rattus norvegicus	P47709 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4NP9_1 Rabphilin-3A (chains A)
DQATTLGALEFSLLYDQDNSNLQCTIIRAKGLKPMDSNGLADPYVKLHLLPGASKSNKLR
TKTLRNTRNPVWNETLQYHGITEEDMQRKTLRISVCDEDKFGHNEFIGETRFSLKKLKAN
QRKNFNICLERVI

Ligands and cofactors

ID	Name	Formula	Copies
I3P	D-myo-inositol-1,4,5-triphosphate	C6 H15 O15 P3	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structural insights into the Ca2+ and PI(4,5)P2 binding modes of the C2 domains of rabphilin 3A and synaptotagmin 1. Guillen, J., Ferrer-Orta, C., Buxaderas, M. et al. Proc Natl Acad Sci U S A (2013) 110:20503-20508. DOI 10.1073/pnas.1316179110 · 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
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)
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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