7M4R: MAGUK p55 subfamily member 5

Structural basis for SARS-CoV-2 envelope protein in recognition of human cell junction protein PALS1. Determined by electron microscopy at 3.65 Å resolution. Released 31 Mar 2021.

Method: Electron microscopy
Resolution: 3.65 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 3
Atoms: 5,092
Mol. weight: 91.62 kDa
Released: 31 Mar 2021

Explore 7M4R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M4R contains 24 α-helices and 46 β-strands across 3 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: 13 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	249-251	3
β-strand	255-257	3	1
β-strand	260-261	2	2
β-strand	269-271	3	3
β-strand	274	1	4
β-strand	277	1	4
β-strand	280-283	4	3
α-helix	288-292	5
β-strand	303-304	2	1
β-strand	307-308	2	1
α-helix	314-321	8
β-strand	326-327	2	2
β-strand	330-332	3	1
β-strand	350-351	2	5
β-strand	356	1	6
α-helix	358-360	3
β-strand	373	1	6
β-strand	379-383	5	5
β-strand	389-394	6	5
β-strand	405-408	4	5
β-strand	469-472	4	7
β-strand	482-485	4	8
α-helix	492-502	11
β-strand	507	1	9
α-helix	533-542	10
β-strand	547	1	10
β-strand	550-551	2	11
β-strand	554-555	2	11
β-strand	558	1	10
α-helix	561-567	7
β-strand	572	1	9
β-strand	574-576	3	8
α-helix	582-587	6
β-strand	594-598	5	8
α-helix	602-608	7
α-helix	621-632	12
β-strand	642-644	3	8
α-helix	648-661	14
α-helix	662-664	3
β-strand	667-670	4	7
α-helix	671-674	4

Chain B: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	348-350	3	12
β-strand	356	1	13
β-strand	373	1	13
β-strand	379-383	5	12
β-strand	390-392	3	12
α-helix	397-399	3
β-strand	405-407	3	12
β-strand	467-468	2	5
β-strand	469-472	4	14
β-strand	483-485	3	15
α-helix	492-501	10
β-strand	507-509	3	16
β-strand	512-513	2	17
α-helix	533-542	10
β-strand	548-551	4	17
β-strand	554-558	5	17
α-helix	561-568	8
β-strand	572-574	3	16
α-helix	579-581	3
α-helix	583-587	5
β-strand	594-596	3	15
α-helix	602-608	7
α-helix	621-630	10
β-strand	641-642	2	15
α-helix	648-650	3
α-helix	652-661	10
β-strand	667-670	4	14
α-helix	671-674	4

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	73-74	2	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MAGUK p55 subfamily member 5	A, B	protein	393	Homo sapiens	Q8N3R9 (AlphaFold model)
Envelope small membrane protein	C	protein	18	Severe acute respiratory syndrome coronavirus 2	P0DTC4 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7M4R_1 MAGUK p55 subfamily member 5 (chains A, B)
SNAPITDERVYESIGQYGGETVKIVRIEKARDIPLGATVRNEMDSVIISRIVKGGAAEKS
GLLHEGDEVLEINGIEIRGKDVNEVFDLLSDMHGTLTFVLIPSQQIKPPPAKETVIHVKA
HFDYDPSDDPYVPCRELGLSFQKGDILHVISQEDPNWWQAYREGDEDNQPLAGLVPGKEE
ILTYEEMSLYHQPANRKRPIILIGPQNCGQNELRQRLMNKEKDRFASAVPHTTRSRRDQE
VAGRDYHFVSRQAFEADIAAGKFIEHGEFEKNLYGTSIDSVRQVINSGKICLLSLRTQSL
KTLRNSDLKPYIIFIAPPSQERLRALLAKEGKNPKPEELREIIEKTREMEQNNGHYFDTA
IVNSDLDKAYQELLRLINKLDTEPQWVPSTWLR

Sequence of entity 2 (C), FASTA

>7M4R_2 Envelope small membrane protein (chains C)
VYSRVKNLNSSRVPDLLV

Primary citation

Structural basis for SARS-CoV-2 envelope protein recognition of human cell junction protein PALS1. Chai, J., Cai, Y., Pang, C. et al. Nat Commun (2021) 12:3433-3433. DOI 10.1038/s41467-021-23533-x · 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
7NTK 1.9 Å, PALS1 PDZ1 domain with SARS-CoV-2_E PBM complex
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
1Y76 Solution Structure of Patj/Pals1 L27 Domain Complex

Browse structure collections

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