5F3X: Harmonin NPDZ1

Crystal structure of Harmonin NPDZ1 in complex with ANKS4B SAM-PBM. Determined by X-ray diffraction at 2.65 Å resolution. Released 16 Mar 2016.

Method: X-ray diffraction
Resolution: 2.65 Å
Organisms: Homo sapiens, Mus musculus
Chains: 4
Atoms: 4,081
Mol. weight: 62.94 kDa
Released: 16 Mar 2016

Explore 5F3X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5F3X contains 37 α-helices and 18 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: 11 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	57-62	6
α-helix	63-65	3
α-helix	68-77	10
β-strand	85-91	7	1
β-strand	100-105	6	1
α-helix	106-108	3
β-strand	110-117	8	1
α-helix	122-126	5
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	185-188	4

Chain B: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	350-352	3
α-helix	353-360	8
α-helix	364-366	3
α-helix	367-372	6
α-helix	377-381	5
α-helix	385-390	6
α-helix	395-413	19
β-strand	421-422	2	1

Chain C: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-16	14
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	68-77	10
α-helix	79-80	2
β-strand	85-91	7	3
β-strand	100-105	6	3
α-helix	106-108	3
β-strand	110-117	8	3
α-helix	122-126	5
β-strand	132-137	6	3
β-strand	140-141	2	3
α-helix	147-154	8
β-strand	159-166	8	3
β-strand	169-172	4	4
α-helix	179-180	2
β-strand	181-184	4	4
α-helix	185-191	7

Chain D: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	353-360	8
α-helix	364-366	3
α-helix	367-372	6
α-helix	377-381	5
α-helix	385-390	6
α-helix	395-413	19
β-strand	421-422	2	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Harmonin	A, C	protein	196	Homo sapiens	Q9Y6N9 (AlphaFold model)
Ankyrin repeat and SAM domain-containing protein 4B	B, D	protein	81	Mus musculus	Q8K3X6 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5F3X_1 Harmonin (chains A, C)
GSMDRKVAREFRHKVDFLIENDAEKDYLYDVLRMYHQTMDVAVLVGDLKLVINEPSRLPL
FDAIRPLIPLKHQVEYDQLTPRRSRKLKEVRLDRLHPEGLGLSVRGGLEFGCGLFISHLI
KGGQADSVGLQVGDEIVRINGYSISSCTHEEVINLIRTKKTVSIKVRHIGLIPVKSSPDE
PLTWQYVDQFVSESGG

Sequence of entity 2 (B, D), FASTA

>5F3X_2 Ankyrin repeat and SAM domain-containing protein 4B (chains B, D)
GSEEDAVDATPLEVFLQSQHLEEFLPIFMREQIDLEALLLCSDEDLQNIHMQLGPRKKVL
SAIDKRKQVLQQPGQLVDTSL

Primary citation

Mechanistic Basis of Organization of the Harmonin/USH1C-Mediated Brush Border Microvilli Tip-Link Complex. Li, J., He, Y., Lu, Q. et al. Dev Cell (2016) 36:179-189. DOI 10.1016/j.devcel.2015.12.020 · 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…
3K1R 2.3 Å, Structure of harmonin NPDZ1 in complex with the SAM-PBM of Sans
5MV9 2.6 Å, Structure of human Myosin 7a C-terminal MyTH4-FERM domain in complex with harmonin-a…
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…

Browse structure collections

About this viewer

MolViewer shows 5F3X directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.