2CM6: C2B domain of rabphilin3A

crystal structure of the C2B domain of rabphilin3A. Determined by X-ray diffraction at 1.85 Å resolution. Released 4 Dec 2006.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: RATTUS NORVEGICUS
Chains: 2
Atoms: 2,397
Mol. weight: 38.47 kDa
Ligands: PO4, CA
Released: 4 Dec 2006

Explore 2CM6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2CM6 contains 13 α-helices and 18 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: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	527-530	4
β-strand	543-551	9	1
β-strand	556-565	10	1
α-helix	567-569	3
β-strand	578-585	8	2
β-strand	593-595	3	2
α-helix	597-600	4
β-strand	606-614	9	1
α-helix	617-620	4
β-strand	624-631	8	2
α-helix	637-638	2
β-strand	639-647	9	2
α-helix	652-663	12
β-strand	669-674	6	1
β-strand	676	1	2

Chain B: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	1526-1529	4
β-strand	1543-1551	9	3
β-strand	1556-1565	10	3
α-helix	1567-1569	3
β-strand	1578-1585	8	4
α-helix	1589-1591	3
β-strand	1593-1595	3	4
α-helix	1596-1599	4
β-strand	1606-1614	9	3
α-helix	1617-1620	4
β-strand	1624-1631	8	4
α-helix	1637-1638	2
β-strand	1639-1646	8	4
α-helix	1652-1663	12
β-strand	1669-1674	6	3
β-strand	1676	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rabphilin-3A	A, B	protein	166	RATTUS NORVEGICUS	P47709 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2CM6_1 RABPHILIN-3A (chains A, B)
GSARGMALYEEEQVERIGDIEERGKILVSLMYSTQQGGLIVGIIRCVHLAAMDANGYSDP
FVKLWLKPDMGKKAKHKTQIKKKTLNPEFNEEFFYDIKHSDLAKKSLDISVWDYDIGKSN
DYIGGCQLGISAKGERLKHWYECLKNKDKKIERWHQLQNENHVSSD

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1
CA	Calcium ion	Ca	4

Primary citation

The C2A-C2B Linker Defines the High Affinity Ca2+ Binding Mode of Rabphilin-3A. Montaville, P., Schlicker, C., Leonov, A. et al. J Biol Chem (2007) 282:5015. DOI 10.1074/JBC.M606746200 · 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
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)
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

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