3K1R: Harmonin NPDZ1

Structure of harmonin NPDZ1 in complex with the SAM-PBM of Sans. Determined by X-ray diffraction at 2.3 Å resolution. Released 26 Jan 2010.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,378
Mol. weight: 30.38 kDa
Released: 26 Jan 2010

Explore 3K1R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3K1R contains 21 α-helices and 9 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: 14 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	2-16	15
α-helix	20-36	17
α-helix	39-46	8
α-helix	53-55	3
α-helix	57-62	6
α-helix	63-65	3
α-helix	68-70	3
α-helix	71-77	7
α-helix	85	1
β-strand	86-91	6	1
β-strand	100-105	6	1
α-helix	106-108	3
β-strand	110-117	8	1
α-helix	122-125	4
β-strand	132-137	6	1
β-strand	140-141	2	1
α-helix	147-154	8
β-strand	159-166	8	1
β-strand	169-172	4	2
α-helix	179-180	2
β-strand	181-184	4	2
α-helix	185-191	7

Chain B: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	391-397	7
α-helix	402-404	3
α-helix	405-410	6
α-helix	415-418	4
α-helix	423-428	6
α-helix	433-451	19
α-helix	458	1
β-strand	459-460	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Harmonin	A	protein	192	Homo sapiens	Q9Y6N9 (AlphaFold model)
Usher syndrome type-1G protein	B	protein	74	Homo sapiens	Q495M9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3K1R_1 Harmonin (chains A)
MDRKVAREFRHKVDFLIENDAEKDYLYDVLRMYHQTMDVAVLVGDLKLVINEPSRLPLFD
AIRPLIPLKHQVEYDQLTPRRSRKLKEVRLDRLHPEGLGLSVRGGLEFGCGLFISHLIKG
GQADSVGLQVGDEIVRINGYSISSCTHEEVINLIRTEKTVSIKVRHIGLIPVKSSPDEPL
TWQYVDQFVSES

Sequence of entity 2 (B), FASTA

>3K1R_2 Usher syndrome type-1G protein (chains B)
ETSPLETFLASLHMEDFAALLRQEKIDLEALMLCSDLDLRSISVPLGPREKILGAVRRRR
QAMERPPALEDTEL

Primary citation

The structure of the harmonin/sans complex reveals an unexpected interaction mode of the two Usher syndrome proteins. Yan, J., Pan, L., Chen, X. et al. Proc Natl Acad Sci U S A (2010) 107:4040-4045. DOI 10.1073/pnas.0911385107 · PubMed

Other PDB entries of the same protein (UniProt Q9Y6N9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5XBF 1.8 Å, Crystal Structure of Myo7b C-terminal MyTH4-FERM in complex with USH1C PDZ3
7X2E 1.85 Å, Structure of USH1C PDZ2 and coiled-coil in complex with CDHR2 C-terminal tail
5MV8 1.88 Å, Structure of human Myosin 7b C-terminal MyTH4-FERM domain in complex with harmonin-a…
5MV9 2.6 Å, Structure of human Myosin 7a C-terminal MyTH4-FERM domain in complex with harmonin-a…
5F3X 2.65 Å, Crystal structure of Harmonin NPDZ1 in complex with ANKS4B SAM-PBM
1X5N Solution structure of the second PDZ domain of harmonin protein
2KBQ Solution structure of harmonin N terminal domain
2KBR Solution structure of harmonin N terminal domain in complex with a internal peptide of…
2KBS Solution structure of harmonin PDZ2 in complex with the carboxyl tail peptide of…
2LSR Solution structure of harmonin N terminal domain in complex with a exon68 encoded…

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