7P02: Antibody fragment scFv16

Human Neurokinin 1 receptor (NK1R) substance P Gs complex. Determined by electron microscopy at 2.87 Å resolution. Released 15 Dec 2021.

Method: Electron microscopy
Resolution: 2.87 Å
Organisms: Mus musculus, Homo sapiens
Chains: 6
Atoms: 9,062
Mol. weight: 153.74 kDa
Ligands: CLR
Released: 15 Dec 2021

Explore 7P02 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7P02 contains 41 α-helices and 63 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: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	7-32	26
β-strand	34-37	4	13
β-strand	39-40	2	14
α-helix	46-48	3
β-strand	202-207	6	13
β-strand	210-215	6	13
α-helix	225-228	4
β-strand	236	1	13
β-strand	239-242	4	14
α-helix	247-261	15
α-helix	263-265	3
β-strand	269	1	13
β-strand	270	1	15
β-strand	272-275	4	14
α-helix	277-286	10
α-helix	291-294	4
α-helix	297-300	4
α-helix	309-310	2
α-helix	315-334	20
β-strand	342	1	15
α-helix	354-373	20

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	9-25	17
α-helix	30-33	4
α-helix	34-36	3
α-helix	38-39	2
β-strand	47-52	6	6
β-strand	58-63	6	7
β-strand	69-74	6	7
β-strand	78-83	6	7
α-helix	84-86	3
β-strand	88-94	7	7
β-strand	100-105	6	8
β-strand	111-116	6	8
β-strand	121-125	5	8
β-strand	134-139	6	8
β-strand	146-151	6	9
β-strand	156-161	6	9
β-strand	166-170	5	9
β-strand	175-180	6	9
β-strand	187-192	6	10
β-strand	198-203	6	10
β-strand	207-212	6	10
β-strand	218-223	6	10
β-strand	229-234	6	11
β-strand	240-245	6	11
β-strand	250-254	5	11
β-strand	259-264	6	11
β-strand	273-278	6	12
β-strand	284-289	6	12
β-strand	294-298	5	12
β-strand	303-308	6	12
β-strand	317-320	4	6
β-strand	327-330	4	6
β-strand	335-339	5	6

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	13-24	12
α-helix	30-43	14

Chain H: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	20-24	5	1
β-strand	27-29	3	2
β-strand	35-42	8	1
α-helix	46-48	3
β-strand	50-56	7	2
β-strand	62-68	7	2
β-strand	75-77	3	2
α-helix	79-81	3
β-strand	85-90	6	1
α-helix	91-93	3
β-strand	95-100	6	1
α-helix	105-107	3
β-strand	109-116	8	2
β-strand	128	1	2
β-strand	132-136	5	2
α-helix	154-156	3
β-strand	157-158	2	3
β-strand	163-165	3	4
β-strand	172-178	7	3
β-strand	183	1	5
β-strand	189	1	5
β-strand	191-196	6	4
β-strand	203-207	5	4
β-strand	211-212	2	4
α-helix	213	1
β-strand	220-224	5	3
β-strand	228-233	6	3
β-strand	242-248	7	4
α-helix	254	1
β-strand	260-263	4	4

Chain R: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	29-59	31
α-helix	67-81	15
α-helix	82-86	5
α-helix	87-95	9
α-helix	102-108	7
α-helix	111-135	25
α-helix	140-143	4
α-helix	144-167	24
β-strand	169-173	5	16
β-strand	178-182	5	16
α-helix	191-201	11
α-helix	202-206	5
α-helix	207-224	18
α-helix	238-273	36
α-helix	275-278	4
α-helix	282-295	14
α-helix	297-308	12
α-helix	310-318	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antibody fragment scFv16	H	protein	298	Mus musculus
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	354	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)
Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s)…	A	protein	246	Homo sapiens	P63092 (AlphaFold model), P63096 (AlphaFold model)
Substance-P receptor	R	protein	382	Homo sapiens	P25103
Protachykinin-1	P	protein	12	Homo sapiens	P20366

Sequence of entity 1 (H), FASTA

>7P02_1 Antibody fragment scFv16 (chains H)
MKFLVNVALVFMVVYISYIYADYKDDDDKHHHHHHHHHHLEVLFQGPDVQLVESGGGLVQ
PGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRD
DPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSSGGGGSGGGGSGG
GGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMS
NLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLELKAAA

Sequence of entity 2 (B), FASTA

>7P02_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHHHHHGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMR
TRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYA
PSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTC
ALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHE
SDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLL
AGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>7P02_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (A), FASTA

>7P02_4 Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
MGCTLSAEDKAAVERSKMIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQMRILHGGS
GGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQE
ALNLFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEP
GEDPRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTCAVDTENARRIFNDCRDIIQRMHL
RQYELL

Sequence of entity 5 (R), FASTA

>7P02_5 Substance-P receptor (chains R)
MKFLVNVALVFMVVYISYIYADYKDDDDKHHHHHHHHHHLEVLFQGPMDNVLPVDSDLSP
NISTNTSEPNQFVQPAWQIVLWAAAYTVIVVTSVVGNVVVMWIILAHKRMRTVTNYFLVN
LAFAEASMAAFNTVVNFTYAVHNEWYYGLFYCKFHNFFPIAAVFASIYSMTAVAFDRYMA
IIHPLQPRLSATATKVVICVIWVLALLLAFPQGYYSTTETMPSRVVCMIEWPEHPNKIYE
KVYHICVTVLIYFLPLLVIGYAYTVVGITLWASEIPGDSSDRYHEQVSAKRKVVKMMIVV
VCTFAICWLPFHIFFLLPYINPDLYLKKFIQQVYLAIMWLAMSSTMYNPIIYCCLNDRFR
LGFKHAFRCCPFISAGDYEGLE

Sequence of entity 6 (P), FASTA

>7P02_6 Protachykinin-1 (chains P)
RPKPQQFFGLMX

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	1

Primary citation

Structures of neurokinin 1 receptor in complex with G q and G s proteins reveal substance P binding mode and unique activation features. Thom, C., Ehrenmann, J., Vacca, S. et al. Sci Adv (2021) 7:eabk2872-eabk2872. DOI 10.1126/sciadv.abk2872 · PubMed

Other PDB entries of the same protein (UniProt P62873 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QEH 1.43 Å, Crystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor
8QEG 1.7 Å, Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
9YDQ 1.94 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE and allosteric…
9YDP 1.95 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE
6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
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

Browse structure collections

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