6X18: GLP-1 peptide hormone

GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor. Determined by electron microscopy at 2.1 Å resolution. Released 9 Sept 2020.

Method: Electron microscopy
Resolution: 2.1 Å
Organisms: Homo sapiens, Lama glama
Chains: 6
Atoms: 10,381
Mol. weight: 163.41 kDa
Released: 9 Sept 2020

Explore 6X18 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6X18 contains 55 α-helices and 58 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: 21 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-39	28
α-helix	40	1
β-strand	41-47	7	1
α-helix	53-62	10
α-helix	93-112	20
α-helix	116-119	4
α-helix	127-134	8
α-helix	144-155	12
α-helix	157-161	5
α-helix	165-167	3
α-helix	175-179	5
α-helix	182-186	5
α-helix	194-199	6
β-strand	207-214	8	1
β-strand	217-224	8	1
α-helix	234-238	5
β-strand	243-248	6	1
α-helix	250-252	3
β-strand	253	1	2
β-strand	264	1	2
α-helix	265-277	13
β-strand	286-291	6	1
α-helix	294-303	10
α-helix	308-310	3
α-helix	313-315	3
α-helix	326-327	2
α-helix	332-350	19
β-strand	359-363	5	1
α-helix	371-390	20

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-51	5	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	89-94	6	4
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
β-strand	134-139	6	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	166-170	5	6
β-strand	176-180	5	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	207-212	6	7
β-strand	218-223	6	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	259-264	6	8
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	304-308	5	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	8-23	16
α-helix	27-29	3
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3

Chain N: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	11	1	11
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	34-39	6	12
β-strand	45-51	7	12
β-strand	58-60	3	12
α-helix	62-64	3
β-strand	68-73	6	10
β-strand	78-83	6	10
α-helix	88-90	3
β-strand	92-98	7	12
β-strand	118	1	12
β-strand	122-124	3	12
β-strand	125	1	11

Chain P: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-33	26

Chain R: 22 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	32-52	21
α-helix	54-55	2
α-helix	61	1
β-strand	62	1	13
α-helix	63-64	2
β-strand	65-66	2	14
β-strand	71-72	2	14
α-helix	73-74	2
β-strand	75	1	13
β-strand	79-84	6	15
α-helix	85-86	2
β-strand	99-105	7	15
β-strand	109-110	2	15
α-helix	111	1
β-strand	112	1	16
β-strand	119	1	16
α-helix	120	1
β-strand	121-122	2	15
α-helix	124-126	3
α-helix	138-168	31
α-helix	170-172	3
α-helix	175-204	30
α-helix	207-215	9
α-helix	224-255	32
α-helix	264-291	28
α-helix	303-337	35
α-helix	345-360	16
α-helix	362-365	4
α-helix	378-392	15
α-helix	394-399	6
α-helix	400-404	5
α-helix	407-418	12

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)
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	58	Homo sapiens	P59768 (AlphaFold model)
Nanobody35	N	protein	128	Lama glama
Glucagon-like peptide-1 (GLP-1)(7-36)NH2	P	protein	30	Homo sapiens	P01275 (AlphaFold model)
Glucagon-like peptide 1 receptor	R	protein	491	Homo sapiens	P43220

Sequence of entity 1 (A), FASTA

>6X18_1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
MGCLGNSKTEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGAGESGKNTIVKQM
RILHVNGFNGEGGEEDPQAARSNSDGEKATKVQDIKNNLKEAIETIVAAMSNLVPPVELA
NPENQFRVDYILSVMNVPDFDFPPEFYEHAKALWEDEGVRACYERSNEYQLIDCAQYFLD
KIDVIKQADYVPSDQDLLRCRVLTSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFND
VTAIIFVVASSSYNMVIREDNQTNRLQAALKLFDSIWNNKWLRDTSVILFLNKQDLLAEK
VLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCY
PHFTCAVDTENIRRVFNDCRDIIQRMHLRQYELL

Sequence of entity 2 (B), FASTA

>6X18_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
QSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>6X18_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
NTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFR

Sequence of entity 4 (N), FASTA

>6X18_4 Nanobody35 (chains N)
QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISY
TGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRGQ
GTQVTVSS

Sequence of entity 5 (P), FASTA

>6X18_5 Glucagon-like peptide-1 (GLP-1)(7-36)NH2 (chains P)
HAEGTFTSDVSSYLEGQAAKEFIAWLVKGR

Sequence of entity 6 (R), FASTA

>6X18_6 Glucagon-like peptide 1 receptor (chains R)
MKTIIALSYIFCLVFADYKDDDDLEVLFQGPARPQGATVSLWETVQKWREYRRQCQRSLT
EDPPPATDLFCNRTFDEYACWPDGEPGSFVNVSCPWYLPWASSVPQGHVYRFCTAEGLWL
QKDNSSLPWRDLSECEESKRGERSSPEEQLLFLYIIYTVGYALSFSALVIASAILLGFRH
LHCTRNYIHLNLFASFILRALSVFIKDAALKWMYSTAAQQHQWDGLLSYQDSLSCRLVFL
LMQYCVAANYYWLLVEGVYLYTLLAFSVFSEQWIFRLYVSIGWGVPLLFVVPWGIVKYLY
EDEGCWTRNSNMNYWLIIRLPILFAIGVNFLIFVRVICIVVSKLKANLMCKTDIKCRLAK
STLTLIPLLGTHEVIFAFVMDEHARGTLRFIKLFTELSFTSFQGLMVAILYCFVNNEVQL
EFRKSWERWRLEHLHIQRDSSMKPLKCPTSSLSSGATAGSSMYTATCQASCSPAGLEVLF
QGPHHHHHHHH

Primary citation

Differential GLP-1R Binding and Activation by Peptide and Non-peptide Agonists. Zhang, X., Belousoff, M.J., Zhao, P. et al. Mol Cell (2020) 80:485. DOI 10.1016/j.molcel.2020.09.020 · 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
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)
7TYF 2.2 Å, Human Amylin1 Receptor in complex with Gs and rat amylin peptide

Browse structure collections

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