7CKZ: PDB entry 7CKZ

Cryo-EM structure of Dopamine and LY3154207 bound dopamine receptor DRD1-Gs signaling complex. Determined by electron microscopy at 3.1 Å resolution. Released 3 Mar 2021.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Homo sapiens, Lama glama
Chains: 5
Atoms: 8,133
Mol. weight: 159.14 kDa
Ligands: G4C, LDP, CLR
Released: 3 Mar 2021

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

Secondary structure: helices and β-sheets

7CKZ contains 33 α-helices and 47 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: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	16-39	24
β-strand	41-47	7	1
α-helix	53-58	6
β-strand	210-214	5	1
β-strand	217-223	7	1
α-helix	234-237	4
β-strand	243-249	7	1
α-helix	265-277	13
α-helix	282-284	3
β-strand	286-292	7	1
α-helix	294-303	10
α-helix	313-315	3
α-helix	326-327	2
α-helix	332-349	18
β-strand	359	1	1
β-strand	362	1	1
α-helix	371-390	20

Chain B: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3-24	22
α-helix	30-32	3
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	88-94	7	3
β-strand	102-105	4	4
β-strand	111-115	5	4
β-strand	121-125	5	4
β-strand	134-139	6	4
β-strand	146-151	6	5
β-strand	157-161	5	5
β-strand	165-168	4	5
β-strand	178-181	4	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	208-212	5	6
β-strand	218-222	5	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	249-254	6	7
β-strand	259-265	7	7
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	303-308	6	8
β-strand	317-320	4	2
β-strand	327-330	4	2
β-strand	336-339	4	2

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	6-23	18
α-helix	30-44	15
α-helix	45-47	3

Chain N: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	9
β-strand	10-12	3	10
β-strand	17-25	9	9
α-helix	29-31	3
β-strand	34	1	11
β-strand	35-39	5	10
β-strand	45-50	6	10
β-strand	59-60	2	10
β-strand	68-73	6	9
β-strand	78-84	7	9
α-helix	88-90	3
β-strand	92-95	4	10
β-strand	98	1	11
β-strand	122-126	5	10

Chain R: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	23-50	28
α-helix	58-75	18
α-helix	78-87	10
α-helix	93-95	3
α-helix	96-126	31
α-helix	128-134	7
α-helix	137-160	24
α-helix	192-199	8
α-helix	200-204	5
α-helix	205-236	32
α-helix	264-274	11
α-helix	275-279	5
α-helix	280-292	13
α-helix	295-297	3
α-helix	310-330	21
α-helix	335-343	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	A	protein	394	Homo sapiens	P63092 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	348	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)
Nanobody 35	N	protein	156	Lama glama
D(1A) dopamine receptor	R	protein	446	Homo sapiens	P21728 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7CKZ_1 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
MGCLGNSKTEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGAGESGKSTIVKQM
RILHVNGFNGEGGEEDPQAARSNSDGEKATKVQDIKNNLKEAIETIVAAMSNLVPPVELA
NPENQFRVDYILSVMNVPDFDFPPEFYEHAKALWEDEGVRACYERSNEYQLIDCAQYFLD
KIDVIKQADYVPSDQDLLRCRVLTTGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFND
VTAIIFVVASSSYNMVIREDNQTNRLQEALNLFKSIWNNRWLRTISVILFLNKQDLLAEK
VLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCY
PHFTCSVDTENIRRVFNDCRDIIQRMHLRQYELL

Sequence of entity 2 (B), FASTA

>7CKZ_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLR
GHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYV
ACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIE
TGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAI
CFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDF
NCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>7CKZ_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (N), FASTA

>7CKZ_4 Nanobody 35 (chains N)
MKYLLPTAAAGLLLLAAQPAMAQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVR
QAPGKGLEWVSDISQSGASISYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCAR
CPAPFTRDCFDVTSTTYAYRGQGTQVTVSSHHHHHH

Sequence of entity 5 (R), FASTA

>7CKZ_5 D(1A) dopamine receptor (chains R)
MRTLNTSAMDGTGLVVERDFSVRILTACFLSLLILSTLLGNTLVCAAVIRFRHLRSKVTN
FFVISLAVSDLLVAVLVMPWKAVAEIAGFWPFGSFCNIWVAFDIMCSTASILNLCVISVD
RYWAISSPFRYERKMTPKAAFILISVAWTLSVLISFIPVQLSWHKAKPTSPSDGNATSLA
ETIDNCDSSLSRTYAISSSVISFYIPVAIMIVTYTRIYRIAQKQIRRIAALERAAVHAKN
CQTTTGNGKPVECSQPESSFKMSFKRETKVLKTLSVIMGVFVCCWLPFFILNCILPFCGS
GETQPFCIDSNTFDVFVWFGWANSSLNPIIYAFNADFRKAFSTLLGCYRLCPATNNAIET
VSINNNGAAMFSSHHEPRGSISKECNLVYLIPHAVGSSEDLKKEEAAGIARPLEKLSPAL
SVILDYDTDVSLEKIQPITQNGQHPT

Ligands and cofactors

ID	Name	Formula	Copies
G4C	2-[2,6-bis(chloranyl)phenyl]-1-[(1S,3R)-3-(hydroxymethyl)-1-methyl-5-(3-methyl-…	C24 H29 Cl2 N O3	1
LDP	L-dopamine	C8 H11 N O2	1
CLR	Cholesterol	C27 H46 O	1

Primary citation

Ligand recognition and allosteric regulation of DRD1-Gs signaling complexes. Xiao, P., Yan, W., Gou, L. et al. Cell (2021) 184:943-956.e18. DOI 10.1016/j.cell.2021.01.028 · PubMed

Other PDB entries of the same protein (UniProt P63092 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7BPH 1.57 Å, Crystal structure of GppNHp-bound GNAS in complex with the cyclic peptide inhibitor GN13
6AU6 1.7 Å, Crystal structure of GDP-bound human GNAS R201C mutant
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
7E5E 1.95 Å, Crystal structure of GDP-bound GNAS in complex with the cyclic peptide inhibitor GD20
7MBX 1.95 Å, Human Cholecystokinin 1 receptor (CCK1R) Gs complex
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
7RTB 2.14 Å, Peptide-19 bound to the Glucagon-Like Peptide-1 Receptor (GLP-1R)

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