8JPB: NTSR1-GRK2-Galpha(q) complexes 1

cryo-EM structure of NTSR1-GRK2-Galpha(q) complexes 1. Determined by electron microscopy at 3.07 Å resolution. Released 9 Aug 2023.

Method: Electron microscopy
Resolution: 3.07 Å
Organisms: Bos taurus, synthetic construct, Homo sapiens
Chains: 4
Atoms: 9,650
Mol. weight: 169.54 kDa
Ligands: SRW, ALF, MG, GDP
Released: 9 Aug 2023

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

Secondary structure: helices and β-sheets

8JPB contains 74 α-helices and 31 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: 40 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	79-92	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	162-166	5
α-helix	169-182	14
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	289-290	2
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	399-403	5
α-helix	404-407	4
α-helix	419-428	10
α-helix	433-435	3
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	561-568	8	4
β-strand	577-584	8	4
β-strand	587-591	5	4
β-strand	597-602	6	4
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: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	60-87	28
α-helix	101-126	26
α-helix	137-171	35
α-helix	175-180	6
α-helix	184-199	16
α-helix	202-205	4
β-strand	207-211	5	8
β-strand	222-226	5	8
α-helix	230-241	12
α-helix	242-246	5
α-helix	247-270	24
α-helix	294-327	34
α-helix	336-367	32
α-helix	369-377	9

Molecules and chains

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

Sequence of entity 1 (G), FASTA

>8JPB_1 Beta-adrenergic receptor kinase 1 (chains G)
ADLEAVLADVSYLMAMEKSKATPAARASKKILLPEPSIRSVMQKYLEDRGEVTFEKIFSQ
KLGYLLFRDFCLKHLEEAKPLVEFYEEIKKYEKLETEEERLVCSREIFDTYIMKELLACS
HPFSKSAIEHVQGHLVKKQVPPDLFQPYIEEICQNLRGDVFQKFIESDKFTRFCQWKNVE
LNIHLTMNDFSVHRIIGRGGFGEVYGCRKADTGKMYAMKCLDKKRIKMKQGETLALNERI
MLSLVSTGDCPFIVCMSYAFHTPDKLSFILDLMNGGDLHYHLSQHGVFSEPDMIFYAAEI
ILGLEHMHNRFVVYRDLKPANILLDEHGHVRISDLGLACDFSKKKPHASVGTHGYMAPEV
LQKGVAYDSSADWFSLGCMLFKLLRGHSPFRQHKTKDKHEIDRMTLTMAVELPDSFSPEL
RSLLEGLLQRDVNRRLGCLGRGAQEVKESPFFRDLDWQMVFLQKYPPPLIPPRGEVNAAD
AFDIGSFDEEDTKGIKLLDSDQELYRNFPLTISERWQQEVAETVFDTINAETDRLEARKK
TKNKQLGHEEDYALGKDCIMHGYMSKMGNPFLTQWQRRYFYLFPNRLEWRGEGEAPQSLL
TMEEIQSVEETQIKERKCLLLKIRGGKQFVLQCDSDPELVQWKKELRDAYREAQQLVQRV
PKMKNKPRSPVVELSKVPLIQRGSANGL

Sequence of entity 2 (L), FASTA

>8JPB_2 NTS(8-13) (chains L)
RRPYIL

Sequence of entity 3 (Q), FASTA

>8JPB_3 Guanine nucleotide-binding protein G(q) subunit alpha (chains Q)
MGCTLSAEDKAAVERSKMIDRNLREDGERSRRELKLLLLGTGESGKSTFIKQMRIIHGSG
YSDEDKRGFTKLVYQNIFTAMQAMIRAMDTLKIPYKYEHNKAHAQLVREVDVEKVSAFEN
PYVDAIKSLWNDPGIQECYDRRREYQLSDSTKYYLNDLDRVADPAYLPTQQDVLRVRVPT
TGIIEYPFDLQSVIFRMVDVGGQRSERRKWIHCFENVTSIMFLVALSEYDQVLVESDNEN
RMEESKALFRTIITYPWFQNSSVILFLNKKDLLEEKIMYSHLVDYFPEYDGPQRDAQAAR
EFILKMFVDLNPDSDKIIYSHFTCATDTENIRFVFAAVKDTILQLNLKEYNLV

Sequence of entity 4 (R), FASTA

>8JPB_4 Neurotensin receptor type 1 (chains R)
MRLNSSAPGTPGTPAADPFQRAQAGLEEALLAPGFGNASGNASERVLAAPSSELDVNTDI
YSKVLVTAVYLALFVVGTVGNTVTAFTLARKKSLQSLQSTVHYHLGSLALSDLLTLLLAM
PVELYNFIWVHHPWAFGDAGCRGYYFLRDACTYATALNVASLSVERYLAICHPFKAKTLM
SRSRTKKFISAIWLASALLAVPMLFTMGEQNRSADGQHAGGLVCTPTIHTATVKVVIQVN
TFMSFIFPMVVISVLNTIIANKLTVMVRQAAEQGQVCTVGGEHSTFSMAIEPGRVQALRH
GVRVLRAVVIAFVVCWLPYHVRRLMFCYISDEQWTPFLYDFYHYFYMVTNALFYVSSTIN
PILYNLVSANFRHIFLATLACLCPVWRRRRKRPAFSRKADSVSSNHTLSSNATRETLY

Ligands and cofactors

ID	Name	Formula	Copies
SRW	2-[{2-(1-fluorocyclopropyl)-4-[4-(2-methoxyphenyl)piperidin-1-yl]quinazolin-6-y…	C26 H31 F N4 O2	1
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

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 P21146 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3PVU 2.48 Å, Bovine GRK2 in complex with Gbetagamma subunits and a selective kinase inhibitor (CMPD101)
3PVW 2.49 Å, Bovine GRK2 in complex with Gbetagamma subunits and a selective kinase inhibitor…
1OMW 2.5 Å, Crystal Structure of the complex between G Protein-Coupled Receptor Kinase 2 and…
5HE0 2.56 Å, Bovine GRK2 in complex with Gbetagamma subunits and CCG215022
3PSC 2.67 Å, Bovine GRK2 in complex with Gbetagamma subunits
5HE3 2.74 Å, Bovine GRK2 in complex with Gbetagamma subunits and CCG224411
5HE2 2.79 Å, Bovine GRK2 in complex with Gbetagamma subunits and CCG224406
8JPD 2.81 Å, Focused refinement structure of GRK2 in NTSR1-GRK2-Galpha(q) complexes
5UKM 3.03 Å, bovine GRK2 in complex with human Gbetagamma subunits and CCG258208 (14as)
2BCJ 3.06 Å, Crystal Structure of G Protein-Coupled Receptor Kinase 2 in Complex with Galpha-q and…
8JPC 3.07 Å, cryo-EM structure of NTSR1-GRK2-Galpha(q) complexes 2
3UZT 3.51 Å, Structure of the C13.18 RNA Aptamer in Complex with G Protein-Coupled Receptor Kinase 2

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