8JBH: Substance P

Substance P bound to active human neurokinin 3 receptor in complex with Gq. Determined by electron microscopy at 2.9 Å resolution. Released 7 Feb 2024.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Homo sapiens, Rattus norvegicus, Mus musculoides
Chains: 6
Atoms: 8,684
Mol. weight: 282.76 kDa
Released: 7 Feb 2024

Explore 8JBH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JBH contains 33 α-helices and 67 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 B: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	82-112	31
α-helix	123-133	11
α-helix	134-139	6
α-helix	140-148	9
α-helix	155-161	7
α-helix	164-188	25
α-helix	193-195	3
α-helix	199-220	22
β-strand	222	1	1
β-strand	236	1	1
α-helix	241-252	12
α-helix	253-257	5
α-helix	258-274	17
α-helix	291-324	34
α-helix	326-330	5
α-helix	334-346	13
α-helix	348-359	12
α-helix	361-366	6

Chain C: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9-32	24
β-strand	34-39	6	16
α-helix	46-51	6
β-strand	184-190	7	16
β-strand	195-201	7	16
α-helix	211-215	5
β-strand	220-226	7	16
α-helix	230-244	15
β-strand	253-259	7	16
α-helix	261-269	9
α-helix	280-282	3
α-helix	299-318	20
β-strand	326	1	16
β-strand	330	1	16
α-helix	338-357	20

Chain D: 2 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-34	5
β-strand	43	1	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	88-94	7	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	165-170	6	6
β-strand	176-180	5	6
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	250-254	5	8
β-strand	259-264	6	8
β-strand	273-278	6	2
β-strand	284-289	6	2
β-strand	294-298	5	2
β-strand	306-308	3	2
β-strand	315	1	9
β-strand	319-320	2	3
β-strand	327-330	4	3
β-strand	331	1	9
β-strand	336-339	4	3

Chain E: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-12	3	11
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	33-39	7	12
β-strand	45-51	7	12
β-strand	58-60	3	12
β-strand	68-69	2	10
β-strand	72-73	2	10
β-strand	78-83	6	10
α-helix	88-90	3
β-strand	92-94	3	11
β-strand	95-99	5	12
β-strand	110-111	2	12
β-strand	115-119	5	11
β-strand	140-141	2	13
β-strand	146	1	14
β-strand	155-161	7	13
β-strand	166	1	15
β-strand	172	1	15
β-strand	174-179	6	14
β-strand	185-190	6	14
β-strand	194-195	2	14
β-strand	205-207	3	13
β-strand	211-216	6	13
α-helix	221-223	3
β-strand	225-227	3	14
β-strand	229-231	3	14
α-helix	237	1
β-strand	239	1	14
β-strand	243-245	3	14

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-43	14
α-helix	53-55	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NK3R-pFastbac1	B	protein	1428	Homo sapiens	P29371 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	D	protein	377	Rattus norvegicus	P54311 (AlphaFold model)
ScFv16 nanobody	E	protein	304	Mus musculoides
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Bos taurus	P63212 (AlphaFold model)
peptide from Protachykinin-1	A	protein	11	Homo sapiens	P20366 (AlphaFold model)
Guanine nucleotide-binding protein Gq subunit alpha (G324)	C	protein	361	Homo sapiens

Sequence of entity 1 (B), FASTA

>8JBH_1 NK3R-pFastbac1 (chains B)
MKTIIALSYIFCLVFAADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKAT
PPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQK
YLMATLPAAETWIDGGGGVGADAVNLTASLAAGAATGAVETGWLQLLDQAGNLSSSPSAL
GLPVASPAPSQPWANLTNQFVQPSWRIALWSLAYGVVVAVAVLGNLIVIWIILAHKRMRT
VTNYFLVNLAFSDASMAAFNTLVNFIYALHSEWYFGANYCRFQNFFPITAVFASIYSMTA
IAVDRYMAIIDPLKPRLSATATKIVIGSIWILAFLLAFPQCLYSKTKVMPGRTLCFVQWP
EGPKQHFTYHIIVIILVYCFPLLIMGITYTIVGITLWGGEIPGDTCDKYHEQLKAKRKVV
KMMIIVVMTFAICWLPYHIYFILTAIYQQLNRWKYIQQVYLASFWLAMSSTMYNPIIYCC
LNKRFRAGFKRAFRWCPFIKVSSYDELELKTTRFHPVFTLEDFVGDWEQTAAYNLDQVLE
QGGVSSLLQNLAVSVTPIQRIVRSGENALKIDIHVIIPYEGLSADQMAQIEEVFKVVYPV
DDHHFKVILPYGTLVIDGVTPNMLNYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLI
TPDGSMLFRVTINSGGSENLYFQGGSAGSAAKIEEGKLVIWINGDKGYNGLAEVGKKFEK
DTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKL
YPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMF
NLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTD
YSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAA
SPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEI
MPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTAKIEEGKLVIWINGDKGYNGLAE
VGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPD
KAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAK
GKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNK
HMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVL
SAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATME
NAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTRITK

Sequence of entity 2 (D), FASTA

>8JBH_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains D)
HMHHHHHGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRR
TLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSG
NYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALW
DIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDI
NAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGY
DDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGGGSG
GGGSSGVSGWRLFKKIS

Sequence of entity 3 (E), FASTA

>8JBH_3 ScFv16 nanobody (chains E)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAVQLVESGGGLVQPGGSRKLSCS
ASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQM
TSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSAGGGGSGGGGSGGGGSSDIVMTQ
ATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDR
FSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLELVDENLYFQGASHHHH
HHHH

Sequence of entity 4 (G), FASTA

>8JBH_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (A), FASTA

>8JBH_5 peptide from Protachykinin-1 (chains A)
RPKPQQFFGLM

Sequence of entity 6 (C), FASTA

>8JBH_6 Guanine nucleotide-binding protein Gq subunit alpha (G324) (chains C)
MGCTLSAEDKAAVERSKMIEKQLQKDKQVYRRTLRLLLLGADNSGKSTIVKQMRIYHVNG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDF
DSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPR
VTRAKYFIRKEFVDISTASGDGRHICYPHFTCAVDTENARRIFNDCKDIILQMNLREYNL
V

Primary citation

Structural insights into neurokinin 3 receptor activation by endogenous and analogue peptide agonists. Sun, W., Yang, F., Zhang, H. et al. Cell Discov (2023) 9:66-66. DOI 10.1038/s41421-023-00564-w · PubMed

Other PDB entries of the same protein (UniProt P29371 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8JBG 2.8 Å, Neurokinin B bound to active human neurokinin 3 receptor in complex with Gq
8JBF 3.0 Å, Senktide bound to active human neurokinin 3 receptor in complex with Gq

Browse structure collections

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