5JON: Unliganded form of HCN2 CNBD

Crystal structure of the unliganded form of HCN2 CNBD. Determined by X-ray diffraction at 2.04 Å resolution. Released 30 Nov 2016.

Method: X-ray diffraction
Resolution: 2.04 Å
Organisms: Escherichia coli O157:H7, Mus musculus
Chains: 2
Atoms: 8,340
Mol. weight: 115.7 kDa
Released: 30 Nov 2016

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

Secondary structure: helices and β-sheets

5JON contains 64 α-helices and 66 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: 31 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	-362--359	4	1
α-helix	-352--338	15
β-strand	-334--331	4	1
α-helix	-326--319	8
β-strand	-310--306	5	1
α-helix	-305--303	3
α-helix	-302--297	6
β-strand	-293	1	2
α-helix	-292--290	3
α-helix	-286--283	4
β-strand	-280	1	3
α-helix	-278--273	6
β-strand	-271--270	2	4
β-strand	-267--266	2	4
β-strand	-263--258	6	1
β-strand	-255--251	5	5
β-strand	-241	1	6
α-helix	-240--238	3
α-helix	-237--229	9
β-strand	-224--222	3	5
α-helix	-215--206	10
β-strand	-202--197	6	7
β-strand	-194--187	8	7
α-helix	-183--169	15
α-helix	-159--151	9
β-strand	-147--142	6	5
α-helix	-140--138	3
α-helix	-137--131	7
β-strand	-127--124	4	5
α-helix	-123--121	3
β-strand	-120	1	6
β-strand	-119	1	8
β-strand	-116	1	8
α-helix	-115--114	2
α-helix	-112	1
β-strand	-111--110	2	9
β-strand	-109--103	7	1
β-strand	-102	1	2
α-helix	-96--90	7
α-helix	-89--85	5
α-helix	-82--73	10
β-strand	-68--67	2	1
β-strand	-65	1	3
α-helix	-64--58	7
α-helix	-54--43	12
β-strand	-41--40	2	9
α-helix	-39--38	2
α-helix	-33--17	17
α-helix	-12-494	14
α-helix	497-514	18
α-helix	516-518	3
α-helix	523-530	8
β-strand	534-538	5	10
β-strand	543-545	3	11
β-strand	553-559	7	10
β-strand	562-565	4	11
β-strand	571-574	4	11
β-strand	579-580	2	10
α-helix	582-585	4
β-strand	594-597	4	11
β-strand	601-607	7	10
α-helix	608-617	10
α-helix	619-631	13

Chain B: 33 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	-367--366	2
β-strand	-363--359	5	12
α-helix	-352--338	15
β-strand	-335--331	5	12
α-helix	-326--318	9
β-strand	-310--306	5	12
α-helix	-305--303	3
α-helix	-302--297	6
β-strand	-293	1	13
α-helix	-292--290	3
α-helix	-286--283	4
β-strand	-280	1	14
α-helix	-278--274	5
β-strand	-271--270	2	15
β-strand	-267--266	2	15
β-strand	-263--258	6	12
β-strand	-255--251	5	16
β-strand	-241	1	17
α-helix	-240--238	3
α-helix	-237--229	9
β-strand	-224--222	3	16
α-helix	-215--213	3
α-helix	-211--206	6
β-strand	-202--198	5	18
β-strand	-193--187	7	18
α-helix	-183--169	15
α-helix	-159--151	9
β-strand	-147--142	6	16
α-helix	-140--138	3
α-helix	-137--131	7
β-strand	-127--124	4	16
α-helix	-123--121	3
β-strand	-120	1	17
β-strand	-119	1	19
β-strand	-116	1	19
α-helix	-115--114	2
α-helix	-112	1
β-strand	-111--110	2	20
β-strand	-109--103	7	12
β-strand	-102	1	13
α-helix	-96--90	7
α-helix	-89--85	5
α-helix	-82--75	8
β-strand	-68--67	2	12
β-strand	-65	1	14
α-helix	-64--58	7
α-helix	-54--43	12
β-strand	-41--40	2	20
α-helix	-39--38	2
α-helix	-33--18	16
α-helix	-12-494	14
α-helix	497-514	18
α-helix	516-519	4
α-helix	523-531	9
β-strand	534-538	5	21
β-strand	543-545	3	22
β-strand	550	1	23
β-strand	553-559	7	21
β-strand	562-565	4	22
β-strand	571-574	4	22
β-strand	579-580	2	21
α-helix	582-586	5
β-strand	590	1	23
β-strand	594-597	4	22
β-strand	601-607	7	21
α-helix	608-617	10
α-helix	619-629	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltose-binding periplasmic protein,Potassium/sodium hyperpolarization-activated cyclic…	A, B	protein	517	Escherichia coli O157:H7, Mus musculus	O88703 (AlphaFold model), P0AEY0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5JON_1 Maltose-binding periplasmic protein,Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 (chains A, B)
GKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDI
IFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNK
DLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIK
DVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSK
VNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPL
GAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDE
ALKDAQTNAAELNGPLREEIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDY
IIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGSYFGEICLLTRGRRTASVRADTYCRL
YSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKN

Primary citation

Structure and dynamics underlying elementary ligand binding events in human pacemaking channels. Goldschen-Ohm, M.P., Klenchin, V.A., White, D.S. et al. Elife (2016) 5. DOI 10.7554/eLife.20797 · PubMed

Other PDB entries of the same protein (UniProt O88703 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3BPZ 1.65 Å, HCN2-I 443-460 E502K in the presence of cAMP
5KHH 1.77 Å, HCN2 CNBD in complex with inosine-3', 5'-cyclic monophosphate (cIMP)
1Q3E 1.9 Å, HCN2J 443-645 in the presence of cGMP
3ETQ 1.9 Å, X-ray structure of cysteine-free fragment of mHCN2 C-terminal region from amino acids…
1Q43 2.0 Å, HCN2I 443-640 in the presence of cAMP, selenomethionine derivative
5KHJ 2.01 Å, HCN2 CNBD in complex with uridine-3', 5'-cyclic monophosphate (cUMP)
5KHK 2.07 Å, HCN2 CNBD in complex with 2-aminopurine riboside-3', 5'-cyclic monophosphate (2-NH2-cPuMP)
5KHI 2.1 Å, HCN2 CNBD in complex with purine riboside-3', 5'-cyclic monophosphate (cPuMP)
5KHG 2.24 Å, HCN2 CNBD in complex with cytidine-3', 5'-cyclic monophosphate (cCMP)
2Q0A 2.25 Å, Structure and rearrangements in the carboxy-terminal region of SpIH channels
1Q5O 2.3 Å, HCN2J 443-645 in the presence of cAMP, selenomethionine derivative
3FFQ 2.4 Å, HCN2I 443-640 apo-state

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