8JPC: NTSR1-GRK2-Galpha(q) complexes 2

cryo-EM structure of NTSR1-GRK2-Galpha(q) complexes 2. Determined by electron microscopy at 3.07 Å resolution. Released 9 Aug 2023.

Method: Electron microscopy
Resolution: 3.07 Å
Organisms: synthetic construct, Homo sapiens, Bos taurus
Chains: 4
Atoms: 9,589
Mol. weight: 169.54 kDa
Ligands: ALF, MG, GDP, STU
Released: 9 Aug 2023

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

Secondary structure: helices and β-sheets

8JPC contains 77 α-helices and 29 β-strands across 3 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 G: 39 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	4-18	15
α-helix	24-27	4
α-helix	34-36	3
α-helix	37-39	3
α-helix	40-48	9
α-helix	55-59	5
α-helix	62-75	14
α-helix	80-93	14
α-helix	98-109	12
α-helix	110-114	5
α-helix	115-119	5
α-helix	126-137	12
α-helix	147-156	10
α-helix	157-161	5
α-helix	162-167	6
α-helix	170-182	13
α-helix	188-190	3
β-strand	191-200	10	1
β-strand	203-210	8	1
β-strand	216-223	8	1
α-helix	224-229	6
α-helix	233-247	15
β-strand	254	1	2
β-strand	257-262	6	1
β-strand	266-272	7	1
β-strand	278	1	2
α-helix	279-286	8
α-helix	291-310	20
β-strand	313-314	2	3
α-helix	320-322	3
β-strand	323-325	3	2
β-strand	331-333	3	2
β-strand	340-341	2	3
α-helix	359-362	4
α-helix	371-386	16
α-helix	399-402	4
α-helix	403-407	5
α-helix	419-428	10
α-helix	444-448	5
α-helix	451-453	3
α-helix	458-463	6
α-helix	467-468	2
α-helix	482-485	4
α-helix	490-493	4
α-helix	500-503	4
α-helix	504-506	3
β-strand	511-512	2	1
α-helix	514-524	11
α-helix	526-547	22
β-strand	561-567	7	4
β-strand	577-583	7	4
β-strand	587-591	5	4
β-strand	597-602	6	4
α-helix	603-605	3
β-strand	606-614	9	4
β-strand	617-624	8	4
β-strand	629-633	5	4
α-helix	637-658	22

Chain Q: 22 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	39	1
β-strand	40-46	7	5
α-helix	52-63	12
α-helix	69-97	29
α-helix	99-101	3
α-helix	104-115	12
α-helix	126-137	12
α-helix	139-146	8
α-helix	148-150	3
α-helix	157-163	7
α-helix	165-168	4
α-helix	176-180	5
β-strand	190-192	3	5
β-strand	195	1	6
β-strand	200	1	6
β-strand	201-205	5	5
α-helix	210-213	4
α-helix	214-219	6
β-strand	223-231	9	5
α-helix	232-235	4
β-strand	238	1	7
α-helix	239	1
β-strand	246	1	7
α-helix	247-260	14
α-helix	262-264	3
β-strand	268-274	7	5
α-helix	276-285	10
α-helix	288-291	4
α-helix	298	1
α-helix	302-315	14
β-strand	324-328	5	5
α-helix	334-351	18

Chain R: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	60-87	28
α-helix	101-117	17
α-helix	120-123	4
α-helix	138-171	34
α-helix	173-179	7
α-helix	182-191	10
α-helix	192-196	5
α-helix	197-200	4
α-helix	202-205	4
α-helix	219-221	3
α-helix	230-241	12
α-helix	242-246	5
α-helix	247-270	24
α-helix	292-327	36
α-helix	336-367	32
α-helix	369-377	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NTS(8-13)	L	protein	6	synthetic construct
Neurotensin receptor type 1	R	protein	418	Homo sapiens	P30989 (AlphaFold model)
Beta-adrenergic receptor kinase 1	G	protein	688	Bos taurus	P21146 (AlphaFold model)
Guanine nucleotide-binding protein G(q) subunit alpha	Q	protein	353	Homo sapiens	P50148 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>8JPC_1 NTS(8-13) (chains L)
RRPYIL

Sequence of entity 2 (R), FASTA

>8JPC_2 Neurotensin receptor type 1 (chains R)
MRLNSSAPGTPGTPAADPFQRAQAGLEEALLAPGFGNASGNASERVLAAPSSELDVNTDI
YSKVLVTAVYLALFVVGTVGNTVTAFTLARKKSLQSLQSTVHYHLGSLALSDLLTLLLAM
PVELYNFIWVHHPWAFGDAGCRGYYFLRDACTYATALNVASLSVERYLAICHPFKAKTLM
SRSRTKKFISAIWLASALLAVPMLFTMGEQNRSADGQHAGGLVCTPTIHTATVKVVIQVN
TFMSFIFPMVVISVLNTIIANKLTVMVRQAAEQGQVCTVGGEHSTFSMAIEPGRVQALRH
GVRVLRAVVIAFVVCWLPYHVRRLMFCYISDEQWTPFLYDFYHYFYMVTNALFYVSSTIN
PILYNLVSANFRHIFLATLACLCPVWRRRRKRPAFSRKADSVSSNHTLSSNATRETLY

Sequence of entity 3 (G), FASTA

>8JPC_3 Beta-adrenergic receptor kinase 1 (chains G)
ADLEAVLADVSYLMAMEKSKATPAARASKKILLPEPSIRSVMQKYLEDRGEVTFEKIFSQ
KLGYLLFRDFCLKHLEEAKPLVEFYEEIKKYEKLETEEERLVCSREIFDTYIMKELLACS
HPFSKSAIEHVQGHLVKKQVPPDLFQPYIEEICQNLRGDVFQKFIESDKFTRFCQWKNVE
LNIHLTMNDFSVHRIIGRGGFGEVYGCRKADTGKMYAMKCLDKKRIKMKQGETLALNERI
MLSLVSTGDCPFIVCMSYAFHTPDKLSFILDLMNGGDLHYHLSQHGVFSEPDMIFYAAEI
ILGLEHMHNRFVVYRDLKPANILLDEHGHVRISDLGLACDFSKKKPHASVGTHGYMAPEV
LQKGVAYDSSADWFSLGCMLFKLLRGHSPFRQHKTKDKHEIDRMTLTMAVELPDSFSPEL
RSLLEGLLQRDVNRRLGCLGRGAQEVKESPFFRDLDWQMVFLQKYPPPLIPPRGEVNAAD
AFDIGSFDEEDTKGIKLLDSDQELYRNFPLTISERWQQEVAETVFDTINAETDRLEARKK
TKNKQLGHEEDYALGKDCIMHGYMSKMGNPFLTQWQRRYFYLFPNRLEWRGEGEAPQSLL
TMEEIQSVEETQIKERKCLLLKIRGGKQFVLQCDSDPELVQWKKELRDAYREAQQLVQRV
PKMKNKPRSPVVELSKVPLIQRGSANGL

Sequence of entity 4 (Q), FASTA

>8JPC_4 Guanine nucleotide-binding protein G(q) subunit alpha (chains Q)
MGCTLSAEDKAAVERSKMIDRNLREDGERSRRELKLLLLGTGESGKSTFIKQMRIIHGSG
YSDEDKRGFTKLVYQNIFTAMQAMIRAMDTLKIPYKYEHNKAHAQLVREVDVEKVSAFEN
PYVDAIKSLWNDPGIQECYDRRREYQLSDSTKYYLNDLDRVADPAYLPTQQDVLRVRVPT
TGIIEYPFDLQSVIFRMVDVGGQRSERRKWIHCFENVTSIMFLVALSEYDQVLVESDNEN
RMEESKALFRTIITYPWFQNSSVILFLNKKDLLEEKIMYSHLVDYFPEYDGPQRDAQAAR
EFILKMFVDLNPDSDKIIYSHFTCATDTENIRFVFAAVKDTILQLNLKEYNLV

Ligands and cofactors

ID	Name	Formula	Copies
ALF	Tetrafluoroaluminate ion	Al F4	1
MG	Magnesium ion	Mg	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
STU	Staurosporine	C28 H26 N4 O3	1
SRW	2-[{2-(1-fluorocyclopropyl)-4-[4-(2-methoxyphenyl)piperidin-1-yl]quinazolin-6-y…	C26 H31 F N4 O2	1

Primary citation

GPCR activation and GRK2 assembly by a biased intracellular agonist. Duan, J., Liu, H., Zhao, F. et al. Nature (2023) 620:676-681. DOI 10.1038/s41586-023-06395-9 · PubMed

Other PDB entries of the same protein (UniProt P30989 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9P7Z 2.1 Å, NTSR1-Gi-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
9YCX 2.1 Å, Neurotensin Receptor 1 (NTSR1) bound to Octotensin in complex with Gi3 in the…
9YCY 2.2 Å, Neurotensin Receptor 1 (NTSR1) bound to Octotensin in complex with Gi3 in the Canonical…
9VAW 2.24 Å, Cryo-EM structure of human Neurotensin Receptor 1 (hNTSR1)-Gq (delipidated) complex in…
9P80 2.3 Å, NTSR1-Gi-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
20ZG 2.4 Å, Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the…
20ZH 2.4 Å, Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the…
7UL2 2.4 Å, CryoEM Structure of Inactive NTSR1 Bound to SR48692 and Nb6
9P82 2.4 Å, NTSR1-Gi-NTS(8-13) GTP-Bound Complex in the Canonical, AHD Closed State (C-Closed-GTP)
20ZC 2.6 Å, Cryo-EM structure of human Neurotensin Receptor 1 (hNTSR1)-Gi1 (delipidated) complex in…
9P81 2.6 Å, NTSR1-Gi-NTS(8-13), GTP-bound Complex in the Canonical, AHD Open State (C-Open-GTP)
8ZYT 2.65 Å, Cryo-EM structure of neurotensin receptor 1 in complex with beta-arrestin1 and SBI-553…

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