7NTK: PALS1 PDZ1 domain with SARS-CoV-2_E PBM complex

PALS1 PDZ1 domain with SARS-CoV-2_E PBM complex. Determined by X-ray diffraction at 1.9 Å resolution. Released 16 Jun 2021.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 8
Atoms: 3,155
Mol. weight: 41.66 kDa
Ligands: FLC
Released: 16 Jun 2021

Explore 7NTK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7NTK contains 11 α-helices and 29 β-strands across 8 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, 7 β-strands

Element	Residues	Length	Sheet
α-helix	251-253	3
β-strand	255-261	7	1
β-strand	269-274	6	1
β-strand	277-283	7	1
α-helix	288-292	5
β-strand	300-304	5	1
β-strand	307-308	2	1
α-helix	314-322	9
β-strand	324	1	2
β-strand	326-333	8	1

Chain B: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	251-253	3
β-strand	255-261	7	2
β-strand	269-274	6	2
β-strand	277-283	7	2
α-helix	288-292	5
β-strand	300-304	5	2
β-strand	307-308	2	2
α-helix	314-322	9
β-strand	326-333	8	2

Chains C, E, G and H: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	209-210	2	1

Chain D: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	255-261	7	3
β-strand	269-274	6	3
β-strand	277-283	7	3
α-helix	288-292	5
α-helix	299	1
β-strand	300-304	5	3
β-strand	307-308	2	3
α-helix	314-322	9
β-strand	326-333	8	3

Chain F: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	255-261	7	4
β-strand	269-274	6	4
β-strand	277-283	7	4
α-helix	288-292	5
β-strand	300-304	5	4
β-strand	307-308	2	4
α-helix	314-322	9
β-strand	326-333	8	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MAGUK p55 subfamily member 5	A, B, D, F	protein	87	Homo sapiens	Q8N3R9 (AlphaFold model)
Envelope small membrane protein	C, E, G, H	protein	8	Severe acute respiratory syndrome coronavirus 2	P0DTC4 (AlphaFold model)

Sequence of entity 1 (A, B, D, F), FASTA

>7NTK_1 MAGUK p55 subfamily member 5 (chains A, B, D, F)
GPLGSKIVRIEKARDIPLGATVRNEMDSVIISRIVKGGAAEKSGLLHEGDEVLEINGIEI
RGKDVNEVFDLLSDMHGTLTFVLIPSQ

Sequence of entity 2 (C, E, G, H), FASTA

>7NTK_2 Envelope small membrane protein (chains C, E, G, H)
SRVPDLLV

Ligands and cofactors

ID	Name	Formula	Copies
FLC	Citrate anion	C6 H5 O7	1

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

Primary citation

Structural basis of coronavirus E protein interactions with human PALS1 PDZ domain. Javorsky, A., Humbert, P.O., Kvansakul, M. Commun Biol (2021) 4:724-724. DOI 10.1038/s42003-021-02250-7 · PubMed

Other PDB entries of the same protein (UniProt Q8N3R9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4UU5 1.23 Å, Crystal structure of the PDZ domain of PALS1 in complex with the crb peptide
7NTJ 1.74 Å, PALS1 PDZ1 domain with SARS-CoV-1_E PBM complex
4UU6 1.8 Å, Crystal structure of the PDZ domain of PALS1
3UIT 2.05 Å, Overall structure of Patj/Pals1/Mals complex
7QCS 2.8 Å, PALS1/MPP5 PDZ domain in complex with SARS-CoV-2_E PBM peptide
4WSI 2.95 Å, Crystal Structure of PALS1/Crb complex
7M4R 3.65 Å, Structural basis for SARS-CoV-2 envelope protein in recognition of human cell junction…
1Y76 Solution Structure of Patj/Pals1 L27 Domain Complex

Browse structure collections

About this viewer

MolViewer shows 7NTK 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.