5LOW: Rabphilin-3A

Structure of the Ca2+-bound Rabphilin 3A C2B domain SNAP25 complex (P21 space group). Determined by X-ray diffraction at 2.8 Å resolution. Released 21 Jun 2017.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Rattus norvegicus
Chains: 14
Atoms: 11,297
Mol. weight: 192.86 kDa
Ligands: CA
Released: 21 Jun 2017

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

Secondary structure: helices and β-sheets

5LOW contains 32 α-helices and 61 β-strands across 14 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: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	543-548	6	1
β-strand	550-551	2	2
β-strand	556-557	2	2
β-strand	560-565	6	1
α-helix	567-569	3
β-strand	578-585	8	3
β-strand	593-594	2	3
α-helix	597-599	3
β-strand	609-610	2	1
β-strand	613-614	2	2
α-helix	617-622	6
β-strand	624-631	8	3
α-helix	637-638	2
β-strand	639-647	9	3
α-helix	652-663	12
β-strand	669-674	6	1

Chain B: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	543-551	9	4
β-strand	556-565	10	4
β-strand	578-583	6	5
β-strand	584-585	2	6
β-strand	593-595	3	5
β-strand	609-613	5	4
α-helix	617-620	4
β-strand	624-625	2	6
β-strand	628-631	4	5
α-helix	637-638	2
β-strand	639-643	5	5
β-strand	646-647	2	6
α-helix	653-663	11
β-strand	669-674	6	4
β-strand	676	1	5

Chain C: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	543-551	9	7
β-strand	556-565	10	7
α-helix	567-569	3
β-strand	576	1	8
β-strand	578-585	8	9
β-strand	593-595	3	9
α-helix	596-598	3
β-strand	602	1	8
β-strand	606-614	9	7
α-helix	617-620	4
β-strand	624-631	8	9
α-helix	637-638	2
β-strand	639-647	9	9
α-helix	653-663	11
β-strand	669-674	6	7
β-strand	676	1	9

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	7-69	63

Chains E, G and N: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	145-196	52

Chain F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	17-78	62

Chain H: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	543-551	9	10
β-strand	556-565	10	10
β-strand	579-585	7	11
β-strand	593-595	3	11
α-helix	596-598	3
β-strand	606-614	9	10
α-helix	619-622	4
β-strand	624-630	7	11
β-strand	640-647	8	11
α-helix	653-663	11
β-strand	669-674	6	10
β-strand	676	1	11

Chain I: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	543-551	9	12
β-strand	556-563	8	12
β-strand	578-585	8	13
β-strand	593-595	3	13
β-strand	609-614	6	12
α-helix	617-620	4
β-strand	624-631	8	13
α-helix	638	1
β-strand	639-646	8	13
α-helix	653-663	11
β-strand	669-674	6	12
β-strand	676	1	13

4 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
Rabphilin-3A	A, B, C, H, I, J	protein	162	Rattus norvegicus	P47709 (AlphaFold model)
Synaptosomal-associated protein 25	D, F, K, M	protein	95	Rattus norvegicus	P60881 (AlphaFold model)
Synaptosomal-associated protein 25	E, G, L, N	protein	82	Rattus norvegicus	P60881 (AlphaFold model)

Sequence of entity 1 (A, B, C, H, I, J), FASTA

>5LOW_1 Rabphilin-3A (chains A, B, C, H, I, J)
HMASMTGGQQMGRGSDFGDIEERGKILVSLMYSTQQGGLIVGIIRCVHLAAMDANGYSDP
FVKLWLKPDMGKKAKHKTQIKKKTLNPEFNEEFFYDIKHSDLAKKSLDISVWDYDIGKSN
DYIGGCQLGISAKGERLKHWYECLKNKDKKIERWHQLQNENH

Sequence of entity 2 (D, F, K, M), FASTA

>5LOW_2 Synaptosomal-associated protein 25 (chains D, F, K, M)
GSHMASMTGGQQMGRGSEFMRNELEEMQRRADQLADESLESTRRMLQLVEESKDAGIRTL
VMLDEQGEQLDRVEEGMNHINQDMKEAEKNLKDLG

Sequence of entity 3 (E, G, L, N), FASTA

>5LOW_3 Synaptosomal-associated protein 25 (chains E, G, L, N)
GSHMASMTGGQQMGRGSEFARENEMDENLEQVSGIIGNLRHMALDMGNEIDTQNRQIDRI
MEKADSNKTRIDEANQRATKML

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	12

Water and common crystallization additives (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
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…
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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