6Y9P: Whirlin PDZ3_C-ter

Crystal structure of Whirlin PDZ3_C-ter in complex with Harmonin a1 C-terminal PDZ binding motif peptide. Determined by X-ray diffraction at 3.17 Å resolution. Released 7 Oct 2020.

Method: X-ray diffraction
Resolution: 3.17 Å
Organisms: Mus musculus, Rattus norvegicus
Chains: 12
Atoms: 4,545
Mol. weight: 76.58 kDa
Released: 7 Oct 2020

Explore 6Y9P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Y9P contains 9 α-helices and 44 β-strands across 12 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: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	813-819	7	1
β-strand	827-830	4	1
β-strand	841-845	5	1
α-helix	850-854	5
α-helix	861	1
β-strand	862-866	5	1
β-strand	869-870	2	1
α-helix	876-888	13
β-strand	894-900	7	1

Chain B: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	814-819	6	2
β-strand	827-830	4	2
β-strand	841-845	5	2
α-helix	850-854	5
β-strand	862-866	5	2
β-strand	869-870	2	2
α-helix	876-888	13
β-strand	894-900	7	2

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	546-547	2	1

Chains D, F, H, J and L: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	545-547	3	2

Chains E and G: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
β-strand	814-819	6	3
β-strand	827-830	4	3
β-strand	841-845	5	3
β-strand	862-866	5	3
β-strand	869-870	2	3
α-helix	876-888	13
β-strand	894-900	7	3

Chain I: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
β-strand	814-818	5	1
β-strand	827-830	4	1
β-strand	841-846	6	1
β-strand	862-866	5	1
β-strand	869-870	2	1
α-helix	876-888	13
β-strand	895-900	6	1

Chain K: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	814-819	6	4
β-strand	827-830	4	4
β-strand	833	1	5
β-strand	841-846	6	4
β-strand	862-866	5	4
β-strand	869-870	2	4
β-strand	875	1	5
α-helix	876-888	13
β-strand	894-900	7	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Whirlin	A, B, E, G, I, K	protein	105	Mus musculus	Q80VW5 (AlphaFold model)
Harmonin a1	C, D, F, H, J, L	protein	11	Rattus norvegicus	Q6PPF3

Sequence of entity 1 (A, B, E, G, I, K), FASTA

>6Y9P_1 Whirlin (chains A, B, E, G, I, K)
GAMGSTSLEPTSTLVRVRKSAATLGIAIEGGANTRQPLPRIVTIQRGGSAHNCGQLKVGH
VILEVNGQTLRGKEHKEAARIIAEAFKTKERDYIDFLVTEFNVML

Sequence of entity 2 (C, D, F, H, J, L), FASTA

>6Y9P_2 Harmonin a1 (chains C, D, F, H, J, L)
PKEYDDELTFF

Primary citation

Deciphering the Unexpected Binding Capacity of the Third PDZ Domain of Whirlin to Various Cochlear Hair Cell Partners. Zhu, Y., Delhommel, F., Cordier, F. et al. J Mol Biol (2020) 432:5920-5937. DOI 10.1016/j.jmb.2020.09.012 · PubMed

Other PDB entries of the same protein (UniProt Q80VW5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Y9Q 1.31 Å, Crystal structure of Whirlin PDZ3_C-ter in complex with Taperin internal PDZ binding…
6Y9O 1.63 Å, Crystal structure of Whirlin PDZ3_C-ter in complex with CASK internal PDZ binding motif…
6Y38 1.7 Å, Crystal structure of Whirlin PDZ3 in complex with Myosin 15a C-terminal PDZ binding…
6FDD 1.75 Å, Crystal Structure of the HHD2 Domain of Whirlin
6FDE 1.85 Å, Crystal Structure of the HHD2 Domain of Whirlin : 3-helix conformation
6Y9N 1.93 Å, Crystal structure of Whirlin PDZ3_C-ter in complex with Myosin 15a C-terminal PDZ…

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