6NYC: Munc13-1 C2B-domain, calcium free

Munc13-1 C2B-domain, calcium free. Determined by X-ray diffraction at 1.89 Å resolution. Released 20 Feb 2019.

Method: X-ray diffraction
Resolution: 1.89 Å
Organism: Rattus norvegicus
Chains: 1
Atoms: 982
Mol. weight: 17.29 kDa
Ligands: B3P
Released: 20 Feb 2019

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

Secondary structure: helices and β-sheets

6NYC contains 2 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: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	689-699	11	1
β-strand	712-718	7	2
β-strand	721-724	4	2
β-strand	735-744	10	1
β-strand	750-757	8	2
β-strand	776-784	9	2
α-helix	785-787	3
β-strand	791-797	7	1
α-helix	798	1
β-strand	799	1	2
β-strand	810-818	9	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Munc13-1	A	protein	148	Rattus norvegicus	Q62768 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6NYC_1 Munc13-1 (chains A)
EFAVKQSVLDGTSKWSAKISITVVCAQGLQAKDKTGSSDPYVTVQVGKTKKRTKTIYGNL
NPVWEENFHFECHNSSDRIKVRVWDEDDDIKSRVKQRFKRESDDFLGQTIIEVRTLSGEM
DVWYNLDKRTDKSAVSGAIRLHISVEIK

Ligands and cofactors

ID	Name	Formula	Copies
B3P	2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-pr…	C11 H26 N2 O6	1

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

Primary citation

Munc13 C2B domain is an activity-dependent Ca2+ regulator of synaptic exocytosis. Shin, O.H., Lu, J., Rhee, J.S. et al. Nat Struct Mol Biol (2010) 17:280-288. DOI 10.1038/nsmb.1758 · PubMed

Other PDB entries of the same protein (UniProt Q62768 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6NYT 1.37 Å, Munc13-1 C2B-domain, calcium bound
2CJT 1.44 Å, Structural Basis for a Munc13-1 Homodimer - Munc13-1 - RIM Heterodimer Switch:…
2CJS 1.78 Å, Structural Basis for a Munc13-1 Homodimer - Munc13-1 - RIM Heterodimer Switch:…
3SWH 2.65 Å, Munc13-1, MUN domain, C-terminal module
6A30 2.79 Å, Crystal Structure of Munc13-1 MUN Domain and Synaptobrevin-2 Juxtamembrane Linker Region
5UF7 2.9 Å, Crystal structure of MUNC13-1 mun domain
4Y21 2.9 Å, Crystal Structure of Munc13-1 MUN domain
5UE8 3.35 Å, The crystal structure of Munc13-1 C1C2BMUN domain
7T7X 10.0 Å, Munc13-1 C1-C2B-MUN-C2C Upright conformation spanning two lipid bilayers
7T81 10.0 Å, Model of Munc13-1 C1-C2B-MUN-C2C 2D crystal between lipid bilayers.
1Y8F Solution structure of the munc13-1 C1-domain
2KDU Structural basis of the Munc13-1/Ca2+-Calmodulin interaction: A novel 1-26 calmodulin…

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