8JBF: Senktide

Senktide bound to active human neurokinin 3 receptor in complex with Gq. Determined by electron microscopy at 3.0 Å resolution. Released 28 Feb 2024.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Homo sapiens, Rattus norvegicus, Mus musculoides
Chains: 6
Atoms: 8,784
Mol. weight: 168.54 kDa
Released: 28 Feb 2024

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

Secondary structure: helices and β-sheets

8JBF contains 38 α-helices and 70 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: 19 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	82-99	18
α-helix	106-111	6
α-helix	122-133	12
α-helix	134-138	5
α-helix	141-144	4
α-helix	157-161	5
α-helix	164-185	22
α-helix	197-219	23
β-strand	223-224	2	1
β-strand	227	1	2
β-strand	229	1	2
β-strand	234-235	2	1
α-helix	241-247	7
α-helix	249-251	3
α-helix	252-257	6
α-helix	258-275	18
α-helix	290-294	5
α-helix	297-306	10
α-helix	313-323	11
α-helix	326-331	6
α-helix	334-347	14
α-helix	351-359	9
α-helix	361-368	8

Chain C: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-25	17
α-helix	27-31	5
β-strand	33-40	8	19
α-helix	46-49	4
β-strand	184-191	8	19
β-strand	194-201	8	19
α-helix	211-213	3
β-strand	220-226	7	19
α-helix	233-244	12
β-strand	253-259	7	19
α-helix	261-268	8
α-helix	275-278	4
α-helix	280-282	3
α-helix	299-318	20
β-strand	327-330	4	19
α-helix	338-357	20

Chain D: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	5-23	19
α-helix	30-33	4
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	120-125	6	5
β-strand	134-140	7	5
β-strand	146-153	8	6
β-strand	156-161	6	6
β-strand	166-169	4	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	249-254	6	8
β-strand	259-265	7	8
α-helix	272	1
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	1	10
β-strand	319-320	2	3
β-strand	327-330	4	3
β-strand	331	1	10
β-strand	336-339	4	3

Chain E: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	12	1	12
β-strand	18-24	7	11
α-helix	29-31	3
β-strand	33-39	7	13
β-strand	45-51	7	13
β-strand	58-60	3	13
β-strand	65	1	11
β-strand	68-73	6	11
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-94	3	14
β-strand	95	1	13
β-strand	97-99	3	13
β-strand	110-111	2	13
β-strand	115-117	3	14
β-strand	119	1	12
β-strand	141	1	15
β-strand	146-148	3	16
β-strand	155-160	6	15
β-strand	166	1	17
β-strand	172	1	17
β-strand	174-178	5	18
β-strand	179	1	16
β-strand	186-190	5	18
β-strand	194-195	2	18
α-helix	196	1
β-strand	203-207	5	15
β-strand	211-216	6	15
α-helix	221-223	3
β-strand	226-227	2	16
β-strand	229-231	3	18
β-strand	239	1	18
β-strand	243-246	4	16

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	9-18	10
α-helix	30-43	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuromedin-K receptor	B	protein	394	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)
Senktide	A	protein	8	Homo sapiens
Guanine nucleotide-binding protein Gq subunit alpha	C	protein	361	Homo sapiens

Sequence of entity 1 (B), FASTA

>8JBF_1 Neuromedin-K receptor (chains B)
MATLPAAETWIDGGGGVGADAVNLTASLAAGAATGAVETGWLQLLDQAGNLSSSPSALGL
PVASPAPSQPWANLTNQFVQPSWRIALWSLAYGVVVAVAVLGNLIVIWIILAHKRMRTVT
NYFLVNLAFSDASMAAFNTLVNFIYALHSEWYFGANYCRFQNFFPITAVFASIYSMTAIA
VDRYMAIIDPLKPRLSATATKIVIGSIWILAFLLAFPQCLYSKTKVMPGRTLCFVQWPEG
PKQHFTYHIIVIILVYCFPLLIMGITYTIVGITLWGGEIPGDTCDKYHEQLKAKRKVVKM
MIIVVMTFAICWLPYHIYFILTAIYQQLNRWKYIQQVYLASFWLAMSSTMYNPIIYCCLN
KRFRAGFKRAFRWCPFIKVSSYDELELKTTRFHP

Sequence of entity 2 (D), FASTA

>8JBF_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains D)
HMHHHHHGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRR
TLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSG
NYVACGGLDNICSIYNLKTRDGDVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALW
DIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDI
NAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGY
DDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGGGSG
GGGSSGVSGWRLFKKIS

Sequence of entity 3 (E), FASTA

>8JBF_3 ScFv16 nanobody (chains E)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAVQLVESGGGLVQPGGSRKLSCS
ASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQM
TSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSAGGGGSGGGGSGGGGSSDIVMTQ
ATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDR
FSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLELVDENLYFQGASHHHH
HHHH

Sequence of entity 4 (G), FASTA

>8JBF_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (A), FASTA

>8JBF_5 Senktide (chains A)
DDFFGLMA

Sequence of entity 6 (C), FASTA

>8JBF_6 Guanine nucleotide-binding protein Gq subunit alpha (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
8JBH 2.9 Å, Substance P bound to active human neurokinin 3 receptor in complex with Gq

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