6NIY: PDB entry 6NIY

A high-resolution cryo-electron microscopy structure of a calcitonin receptor-heterotrimeric Gs protein complex. Determined by electron microscopy at 3.34 Å resolution. Released 23 Jan 2019.

Method: Electron microscopy
Resolution: 3.34 Å
Organisms: Homo sapiens, Lama glama, Oncorhynchus sp.
Chains: 6
Atoms: 7,727
Mol. weight: 164.97 kDa
Released: 23 Jan 2019

Explore 6NIY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NIY contains 29 α-helices and 50 β-strands across 6 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: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	12-38	27
β-strand	40-46	7	1
β-strand	208-213	6	1
β-strand	218-223	6	1
α-helix	237-240	4
β-strand	243-248	6	1
α-helix	267-277	11
β-strand	286-291	6	1
α-helix	332-349	18
β-strand	359-360	2	1
α-helix	373-390	18

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-26	23
α-helix	30-34	5
α-helix	38-39	2
β-strand	47-51	5	7
β-strand	58-63	6	8
β-strand	69-74	6	8
β-strand	78-83	6	8
β-strand	88-94	7	8
β-strand	100-105	6	9
β-strand	111-116	6	9
β-strand	121-125	5	9
β-strand	135-139	5	9
β-strand	146-151	6	10
β-strand	156-161	6	10
β-strand	166-170	5	10
β-strand	176-180	5	10
β-strand	189-192	4	11
β-strand	198-202	5	11
β-strand	208-212	5	11
β-strand	218-222	5	11
β-strand	229-234	6	12
β-strand	240-245	6	12
β-strand	250-254	5	12
β-strand	260-264	5	12
β-strand	273-278	6	13
β-strand	284-289	6	13
β-strand	294-298	5	13
β-strand	303-308	6	13
β-strand	315-320	6	7
β-strand	327-331	5	7
β-strand	336-339	4	7

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-44	15
α-helix	53-55	3

Chain N: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	2
β-strand	10-12	3	3
β-strand	17-25	9	2
α-helix	29-31	3
β-strand	34-39	6	4
β-strand	45-50	6	4
β-strand	59-60	2	4
β-strand	65	1	5
β-strand	68	1	5
β-strand	69-73	5	2
β-strand	78-84	7	2
β-strand	92-94	3	3
β-strand	95-98	4	4
β-strand	118	1	4
β-strand	122-126	5	3

Chain P: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	4	1	6
α-helix	5-7	3
α-helix	8-18	11

Chain R: 15 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	139-172	34
α-helix	174-176	3
α-helix	179-204	26
α-helix	218-245	28
α-helix	246-250	5
α-helix	259-263	5
α-helix	264-268	5
α-helix	271-284	14
α-helix	296-298	3
α-helix	299-329	31
α-helix	337-352	16
α-helix	355-358	4
β-strand	361	1	6
α-helix	366-381	16
α-helix	383-392	10
α-helix	396-411	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	A	protein	394	Homo sapiens	P63092 (AlphaFold model)
Nanobody35	N	protein	138	Lama glama
Calcitonin receptor	R	protein	474	Homo sapiens	P30988 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	340	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
Calcitonin	P	protein	32	Oncorhynchus sp.	Q92163

Sequence of entity 1 (A), FASTA

>6NIY_1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
MGCLGNSKTEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGAGESGKSTIVKQM
RILHVNGFNGEGGEEDPQAARSNSDGEKATKVQDIKNNLKEAIETIVAAMSNLVPPVELA
NPENQFRVDYILSVMNVPDFDFPPEFYEHAKALWEDEGVRACYERSNEYQLIDCAQYFLD
KIDVIKQADYVPSDQDLLRCRVLTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFND
VTAIIFVVASSSYNMVIREDNQTNRLQEALNLFKSIWNNRWLRTISVILFLNKQDLLAEK
VLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCY
PHFTCAVDTENIRRVFNDCRDIIQRMHLRQYELL

Sequence of entity 2 (N), FASTA

>6NIY_2 Nanobody35 (chains N)
QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISY
TGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRGQ
GTQVTVSSHHHHHHEPEA

Sequence of entity 3 (R), FASTA

>6NIY_3 Calcitonin receptor (chains R)
MRFTFTSRCLALFLLLNHPTPILPAFSNQTYPTIEPKPFLYVVGRKKMMDAQYKCYDRMQ
QLPAYQGEGPYCNRTWDGWLCWDDTPAGVLSYQFCPDYFPDFDPSEKVTKYCDEKGVWFK
HPENNRTWSNYTMCNAFTPEKLKNAYVLYYLAIVGHSLSIFTLVISLGIFVFFRSLGCQR
VTLHKNMFLTYILNSMIIIIHLVEVVPNGELVRRDPVSCKILHFFHQYMMACNYFWMLCE
GIYLHTLIVVAVFTEKQRLRWYYLLGWGFPLVPTTIHAITRAVYFNDNCWLSVETHLLYI
IHGPVMAALVVNFFFLLNIVRVLVTKMRETHEAESHMYLKAVKATMILVPLLGIQFVVFP
WRPSNKMLGKIYDYVMHSLIHFQGFFVATIYCFCNNEVQTTVKRQWAQFKIQWNQRWGRR
PSNRSARAAAAAAEAGDIPIYICHQEPRNEPANNQGEESAEIIPLNIIEQESSA

Sequence of entity 4 (B), FASTA

>6NIY_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 5 (G), FASTA

>6NIY_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 6 (P), FASTA

>6NIY_6 Calcitonin (chains P)
CSNLSTCVLGKLSQELHKLQTYPRTNTGSGTP

Primary citation

The Molecular Control of Calcitonin Receptor Signaling. Dal Maso, E., Glukhova, A., Zhu, Y. et al. Acs Pharmacol Transl Sci (2019) 2:31-51. DOI 10.1021/acsptsci.8b00056 · PubMed

Other PDB entries of the same protein (UniProt P63092 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7BPH 1.57 Å, Crystal structure of GppNHp-bound GNAS in complex with the cyclic peptide inhibitor GN13
6AU6 1.7 Å, Crystal structure of GDP-bound human GNAS R201C mutant
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
7E5E 1.95 Å, Crystal structure of GDP-bound GNAS in complex with the cyclic peptide inhibitor GD20
7MBX 1.95 Å, Human Cholecystokinin 1 receptor (CCK1R) Gs complex
8F0J 2.0 Å, Calcitonin Receptor in complex with Gs and Pramlintide analogue peptide San45
8F2B 2.0 Å, Amylin 3 Receptor in complex with Gs and Pramlintide analogue peptide San45
9XXT 2.0 Å, Cryo-EM structure of lysophosphatidylserine (18:0)-bound GPR174-Gs complex
6X18 2.1 Å, GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor
6X19 2.1 Å, Non peptide agonist CHU-128, bound to Glucagon-Like peptide-1 (GLP-1) Receptor
9NTU 2.1 Å, Cryo-EM structure of BETP-GLP-1(9-36)-GLP-1R-Gs complex
7RTB 2.14 Å, Peptide-19 bound to the Glucagon-Like Peptide-1 Receptor (GLP-1R)

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