7BYN: Human KCNQ4 with linopirdine

Cryo-EM structure of human KCNQ4 with linopirdine. Determined by electron microscopy at 3.3 Å resolution. Released 2 Dec 2020.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Aequorea victoria, Homo sapiens
Chains: 8
Atoms: 16,349
Mol. weight: 509.42 kDa
Ligands: PT5, FCC
Released: 2 Dec 2020

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

Secondary structure: helices and β-sheets

7BYN contains 119 α-helices and 16 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.

Chains A and G: 20 helices, 0 β-strands

Element	Residues	Length
α-helix	75-92	18
α-helix	96-98	3
α-helix	99-120	22
α-helix	125-153	29
α-helix	162-170	9
α-helix	173-191	19
α-helix	200-205	6
α-helix	206-211	6
α-helix	212-215	4
α-helix	219-221	3
α-helix	222-233	12
α-helix	235-260	26
α-helix	270-281	12
α-helix	294-307	14
α-helix	310-312	3
α-helix	313-335	23
α-helix	340-354	15
α-helix	359-361	3
α-helix	528-552	25
α-helix	560-586	27

Chains B, D, F and H: 10 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-19	14
β-strand	26-27	2	1
α-helix	29-38	10
α-helix	45-53	9
β-strand	63-64	2	1
α-helix	65-74	10
α-helix	79-91	13
β-strand	99-101	3	2
α-helix	102-111	10
α-helix	115-117	3
α-helix	118-127	10
β-strand	135-137	3	2
α-helix	138-145	8

Chain C: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	75-92	18
α-helix	98-120	23
α-helix	125-153	29
α-helix	162-170	9
α-helix	173-191	19
α-helix	200-205	6
α-helix	206-211	6
α-helix	212-215	4
α-helix	219-221	3
α-helix	222-233	12
α-helix	235-260	26
α-helix	270-281	12
α-helix	294-307	14
α-helix	310-312	3
α-helix	313-335	23
α-helix	340-354	15
α-helix	359-361	3
α-helix	528-551	24
α-helix	560-586	27

Chain E: 20 helices, 0 β-strands

Element	Residues	Length
α-helix	75-91	17
α-helix	96-98	3
α-helix	99-120	22
α-helix	125-153	29
α-helix	162-170	9
α-helix	173-191	19
α-helix	200-205	6
α-helix	206-211	6
α-helix	212-215	4
α-helix	219-221	3
α-helix	222-233	12
α-helix	235-260	26
α-helix	270-281	12
α-helix	294-307	14
α-helix	310-312	3
α-helix	313-335	23
α-helix	340-354	15
α-helix	359-361	3
α-helix	528-552	25
α-helix	560-586	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Green fluorescent protein,Potassium voltage-gated channel subfamily KQT member 4	A, C, E, G	protein	979	Aequorea victoria, Homo sapiens	P42212 (AlphaFold model), P56696 (AlphaFold model)
Calmodulin-3	B, D, F, H	protein	149	Homo sapiens	P0DP25 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>7BYN_1 Green fluorescent protein,Potassium voltage-gated channel subfamily KQT member 4 (chains A, C, E, G)
MHHHHHHHHAADYKDHDIDYKDDDDKSAMVSKGEELFTGVVPILVELDGDVNGHKFSVSG
EGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEG
YVQERTIFFKDDGNYTTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVY
IMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDP
NEKRDHMVLLEFVTAAGITLGMDELYKSGLRSGLEVLFQGPGGRMAEAPPRRLGLGPPPG
DAPRAELVALTAVQSEQGEAGGGGSPRRLGLLGSPLPPGAPLPGPGSGSGSACGQRSSAA
HKRYRRLQNWVYNVLERPRGWAFVYHVFIFLLVFSCLVLSVLSTIQEHQELANECLLILE
FVMIVVFGLEYIVRVWSAGCCCRYRGWQGRFRFARKPFCVIDFIVFVASVAVIAAGTQGN
IFATSALRSMRFLQILRMVRMDRRGGTWKLLGSVVYAHSKELITAWYIGFLVLIFASFLV
YLAEKDANSDFSSYADSLWWGTITLTTIGYGDKTPHTWLGRVLAAGFALLGISFFALPAG
ILGSGFALKVQEQHRQKHFEKRRMPAANLIQAAWRLYSTDMSRAYLTATWYYYDSILPSF
RELALLFEHVQRARNGGLRPLEVRRAPVPDGAPSRYPPVATCHRPGSTSFCPGESSRMGI
KDRIRMGSSQRRTGPSKQHLAPPTMPTSPSSEQVGEATSPTKVQKSWSFNDRTRFRASLR
LKPRTSAEDAPSEEVAEEKSYQCELTVDDIMPAVKTVIRSIRILKFLVAKRKFKETLRPY
DVKDVIEQYSAGHLDMLGRIKSLQTRVDQIVGRGPGDRKAREKGDKGPSDAEVVDEISMM
GRVVKVEKQVQSIEHKLDLLLGFYSRCLRSGTSASLGAVQVPLFDPDITSDYHSPVDHED
ISVSAQTLSISRSVSTNMD

Sequence of entity 2 (B, D, F, H), FASTA

>7BYN_2 Calmodulin-3 (chains B, D, F, H)
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVQMMTAK

Ligands and cofactors

ID	Name	Formula	Copies
PT5	[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4…	C47 H85 O19 P3	4
FCC	1-phenyl-3,3-bis(pyridin-4-ylmethyl)indol-2-one	C26 H21 N3 O	1

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

Primary citation

Structural Basis for the Modulation of Human KCNQ4 by Small-Molecule Drugs. Li, T., Wu, K., Yue, Z. et al. Mol Cell (2021) 81:25. DOI 10.1016/j.molcel.2020.10.037 · PubMed

Other PDB entries of the same protein (UniProt P42212 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6L27 0.77 Å, X-ray crystal structure of the mutant green fluorescent protein
6JGJ 0.78 Å, Crystal structure of the F99S/M153T/V163A/E222Q variant of GFP at 0.78 A
6KL0 0.8 Å, Crystal structure of the S65T/F99S/M153T/V163A variant of perdeuterated GFP at pD 7.0
6JGI 0.85 Å, Crystal structure of the S65T/F99S/M153T/V163A variant of GFP at 0.85 A
6KL1 0.85 Å, Crystal structure of the S65T/F99S/M153T/V163A variant of non-deuterated GFP at pD 8.5
2WUR 0.9 Å, Atomic resolution structure of GFP measured on a rotating anode
6KKZ 0.9 Å, Crystal structure of the S65T/F99S/M153T/V163A variant of perdeuterated GFP at pD 8.5
6JGH 0.94 Å, Crystal structure of the F99S/M153T/V163A/T203I variant of GFP at 0.94 A
4AS8 1.02 Å, X-ray structure of the cyan fluorescent protein Cerulean cryoprotected with ethylene…
5OXC 1.02 Å, Structure of Cerulean Fluorescent Protein at 1.02 Angstrom resolution
7PCA 1.05 Å, Functional and structural characterization of redox sensitive superfolder green…
4GF6 1.1 Å, crystal structure of GFP with cuprum bound at the Incorporated metal Chelating Amino…

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