6JLH: SCGN

Structure of SCGN in complex with a Snap25 peptide. Determined by X-ray diffraction at 2.37 Å resolution. Released 11 Mar 2020.

Method: X-ray diffraction
Resolution: 2.37 Å
Organisms: Danio rerio, Homo sapiens
Chains: 4
Atoms: 4,637
Mol. weight: 65.91 kDa
Ligands: CA
Released: 11 Mar 2020

Explore 6JLH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6JLH contains 34 α-helices and 12 β-strands across 4 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: 16 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	11
β-strand	28	1	1
α-helix	31-44	14
α-helix	49-50	2
α-helix	52-66	15
β-strand	74	1	1
α-helix	76-83	8
α-helix	86-88	3
α-helix	90-94	5
α-helix	103-113	11
β-strand	121	1	2
α-helix	123-136	14
α-helix	143-157	15
β-strand	165	1	2
α-helix	167-173	7
α-helix	180-183	4
α-helix	191-205	15
β-strand	212-213	2	3
α-helix	216-226	11
α-helix	235-249	15
β-strand	257-258	2	3
α-helix	259-266	8

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-16	14

Chain C: 16 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	13-20	8
β-strand	28	1	4
α-helix	31-44	14
α-helix	49-50	2
α-helix	52-66	15
β-strand	74	1	4
α-helix	76-83	8
α-helix	84-86	3
α-helix	88-92	5
α-helix	103-113	11
β-strand	121	1	5
α-helix	123-136	14
α-helix	143-157	15
β-strand	165	1	5
α-helix	167-173	7
α-helix	181-183	3
α-helix	191-205	15
β-strand	212-213	2	6
α-helix	216-226	11
α-helix	235-249	15
β-strand	257-258	2	6
α-helix	259-266	8

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-14	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Secretagogin	A, C	protein	261	Danio rerio	Q5XJX1 (AlphaFold model)
Synaptosomal-associated protein 25	B, D	protein	17	Homo sapiens	P60880 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6JLH_1 Secretagogin (chains A, C)
NLDAAGFLQIWQHFDADDNGYIEGKELDDFFRHMLKKLQPKDKITDERVQQIKKSFMSAY
DATFDGRLQIEELANMILPQEENFLLIFRREAPLDNSVEFMKIWRKYDADSSGYISAAEL
KNFLKDLFLQHKKKIPPNKLDEYTDAMMKIFDKNKDGRLDLNDLARILALQENFLLQFKM
DASSQVERKRDFEKIFAHYDVSRTGALEGPEVDGFVKDMMELVRPSISGGDLDKFRECLL
THCDMNKDGKIQKSELALCLG

Sequence of entity 2 (B, D), FASTA

>6JLH_2 Synaptosomal-associated protein 25 (chains B, D)
SGIIGNLRHMALDMGNE

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	12

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

Primary citation

Structural and mechanistic insights into secretagogin-mediated exocytosis. Qin, J., Liu, Q., Liu, Z. et al. Proc Natl Acad Sci U S A (2020) 117:6559-6570. DOI 10.1073/pnas.1919698117 · PubMed

Other PDB entries of the same protein (UniProt Q5XJX1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2BE4 2.1 Å, X-ray structure an ef-hand protein from danio rerio Dr.36843
2Q4U 2.1 Å, Ensemble refinement of the crystal structure of an EF-hand protein from Danio rerio…

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