7RMI: SP6-11 biased agonist

SP6-11 biased agonist bound to active human neurokinin 1 receptor in complex with miniGs/q70. Determined by electron microscopy at 3.2 Å resolution. Released 3 Nov 2021.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, synthetic construct, Lama glama
Chains: 6
Atoms: 7,205
Mol. weight: 138.48 kDa
Released: 3 Nov 2021

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

Secondary structure: helices and β-sheets

7RMI contains 34 α-helices and 46 β-strands across 5 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: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	26-38	13
β-strand	40-46	7	1
β-strand	208-214	7	1
β-strand	217-223	7	1
α-helix	234-238	5
β-strand	243-249	7	1
α-helix	253-265	3
α-helix	266-277	12
β-strand	286-292	7	1
α-helix	294-301	8
α-helix	332-349	18
β-strand	359-363	5	1
α-helix	371-390	20

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	15-24	10
α-helix	30-33	4
β-strand	47-51	5	3
β-strand	58-63	6	4
β-strand	70-74	5	4
β-strand	78-83	6	4
β-strand	88-94	7	4
α-helix	95	1
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
β-strand	135-139	5	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	166-170	5	6
β-strand	175-180	6	6
α-helix	186	1
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	208-212	5	7
β-strand	218-222	5	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	249-254	6	8
β-strand	260-265	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: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	14-23	10
α-helix	30-42	13

Chain N: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	19-25	7	10
β-strand	34-39	6	11
β-strand	45-51	7	11
β-strand	59-60	2	11
α-helix	62-64	3
β-strand	69-73	5	10
β-strand	78-82	5	10
α-helix	88-90	3
β-strand	92-98	7	11
β-strand	118	1	11
β-strand	122-124	3	11

Chain R: 19 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	29-59	31
α-helix	66-68	3
α-helix	69-80	12
α-helix	81-86	6
α-helix	87-93	7
α-helix	101-134	34
α-helix	140-143	4
α-helix	144-167	24
β-strand	169-174	6	2
β-strand	177-182	6	2
α-helix	184-186	3
α-helix	191-201	11
α-helix	202-206	5
α-helix	207-223	17
α-helix	240-269	30
α-helix	270-272	3
α-helix	275-277	3
α-helix	282-295	14
α-helix	296-298	3
α-helix	300-308	9
α-helix	310-319	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, with certain residues…	A	protein	229	Homo sapiens	P63092 (AlphaFold model)
Substance-P receptor	R	protein	418	Homo sapiens	P25103 (AlphaFold model)
Substance P 6-11	S	protein	7	synthetic construct
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	370	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	68	Homo sapiens	P59768 (AlphaFold model)
Nanobody 35	N	protein	142	Lama glama

Sequence of entity 1 (A), FASTA

>7RMI_1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, with certain residues mutated to match Guanine nucleotide-binding protein G(q) subunit (chains A)
GIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQMRILHGGSGGSGGTSGIFETKFQVD
KVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDFKSIWNNRWLRTI
SVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEF
LRISTASGDGRHYCYPHFTCAVDTENARRIFNDCKDIILQMNLREYNLV

Sequence of entity 2 (R), FASTA

>7RMI_2 Substance-P receptor (chains R)
DYKDDDDASIDMDNVLPVDSDLSPNISTNTSEPNQFVQPAWQIVLWAAAYTVIVVTSVVG
NVVVMWIILAHKRMRTVTNYFLVNLAFAEASMAAFNTVVNFTYAVHNEWYYGLFYCKFHN
FFPIAAVFASIYSMTAVAFDRYMAIIHPLQPRLSATATKVVICVIWVLALLLAFPQGYYS
TTETMPSRVVCMIEWPEHPNKIYEKVYHICVTVLIYFLPLLVIGYAYTVVGITLWASEIP
GDSSDRYHEQVSAKRKVVKMMIVVVCTFAICWLPFHIFFLLPYINPDLYLKKFIQQVYLA
IMWLAMSSTMYNPIIYCCLNDRFRLGFKHAFRCCPFISAGDYEGLEMKSTRYLQTQGSVY
KVSRLETTISTVVGAHEEEPEDGPKATPSSLDLTSNCSSRSDSKTMTESFSFSSNVLS

Sequence of entity 3 (S), FASTA

>7RMI_3 Substance P 6-11 (chains S)
QFFGLMX

Sequence of entity 4 (B), FASTA

>7RMI_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHLEVLFQGPEDQVDPRLIDGKGSSGSELDQLRQEAEQLKNQIRDARKACADATL
SQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKV
HAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCR
FLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKL
WDVREGMCRQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNII
CGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATG
SWDSFLKIWN

Sequence of entity 5 (G), FASTA

>7RMI_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFC

Sequence of entity 6 (N), FASTA

>7RMI_6 Nanobody 35 (chains N)
QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISY
TGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRGQ
GTQVTVSSGSEDQVDPRLIDGK

Primary citation

Selective G protein signaling driven by substance P-neurokinin receptor dynamics. Harris, J.A., Faust, B., Gondin, A.B. et al. Nat Chem Biol (2022) 18:109-115. DOI 10.1038/s41589-021-00890-8 · 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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