9PY3: PDB entry 9PY3

Unlatched-state loperamide-mu opioid receptor-Gi GDPbS complex (rebound). Determined by electron microscopy at 3.2 Å resolution. Released 12 Nov 2025.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,227
Mol. weight: 159.37 kDa
Ligands: CLR, A1CMV, VSN
Released: 12 Nov 2025

Explore 9PY3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PY3 contains 31 α-helices and 40 β-strands across 4 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: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-29	24
α-helix	30-32	3
β-strand	34-38	5	10
α-helix	46-49	4
β-strand	185-190	6	10
β-strand	195-200	6	10
α-helix	209-212	4
β-strand	220-222	3	10
β-strand	224-225	2	11
α-helix	228-230	3
α-helix	242-254	13
β-strand	263-266	4	10
β-strand	267-268	2	11
α-helix	272-278	7
α-helix	296-308	13
β-strand	319-321	3	10
α-helix	330-350	21

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	7-25	19
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-52	6	1
β-strand	58-62	5	2
β-strand	69-74	6	2
β-strand	78-83	6	2
β-strand	88-94	7	2
β-strand	102-105	4	3
β-strand	111-115	5	3
β-strand	120-125	6	3
β-strand	134-140	7	3
β-strand	148-151	4	4
β-strand	156-160	5	4
β-strand	166-170	5	4
β-strand	175-180	6	4
β-strand	187-192	6	5
β-strand	198-203	6	5
β-strand	208-212	5	5
β-strand	218-222	5	5
β-strand	232-234	3	6
β-strand	240-243	4	6
β-strand	250-254	5	6
β-strand	260-264	5	6
β-strand	273-278	6	7
β-strand	284-289	6	7
β-strand	294-298	5	7
β-strand	304-308	5	7
β-strand	318-320	3	1
β-strand	327-330	4	1
β-strand	335-339	5	1

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	11-23	13
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3

Chain R: 15 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	68-93	26
α-helix	94-98	5
α-helix	104-119	16
α-helix	120-122	3
α-helix	123-129	7
α-helix	140-172	33
α-helix	174-180	7
α-helix	183-207	25
β-strand	208	1	8
β-strand	211-213	3	9
β-strand	216-218	3	9
β-strand	221	1	8
α-helix	227-239	13
α-helix	240-244	5
α-helix	245-262	18
α-helix	271-307	37
α-helix	310-312	3
α-helix	314-338	25
α-helix	343-350	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	361	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	71	Homo sapiens	P59768 (AlphaFold model)
Soluble cytochrome b562,Mu-type opioid receptor	R	protein	622	Homo sapiens	P0ABE7 (AlphaFold model), P35372 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096

Sequence of entity 1 (B), FASTA

>9PY3_1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
HHHHHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDP
VGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSW
VMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVT
SSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCR
QTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFS
KSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIW
N

Sequence of entity 2 (C), FASTA

>9PY3_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 3 (R), FASTA

>9PY3_3 Soluble cytochrome b562,Mu-type opioid receptor (chains R)
MKTIIALSYIFCLVFADYKDHDGDYKDHDIDYKDDDDKLHHHHHHHHHHLEVLFQGPGSG
SADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMK
DFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLGTGSDSSAAPTNA
SNCTDALAYSSCSPAPSPGSWVNLSHLDGNLSDPCGPNRTDLGGRDSLCPPTGSPSMITA
ITIMALYSIVCVVGLFGNFLVMYVIVRYTKMKTATNIYIFNLALADALATSTLPFQSVNY
LMGTWPFGTILCKIVISIDYYNMFTSIFTLCTMSVDRYIAVCHPVKALDFRTPRNAKIIN
VCNWILSSAIGLPVMFMATTKYRQGSIDCTLTFSHPTWYWENLLKICVFIFAFIMPVLII
TVCYGLMILRLKSVRMLSGSKEKDRNLRRITRMVLVVVAVFIVCWTPIHIYVIIKALVTI
PETTFQTVSWHFCIALGYTNSCLNPVLYAFLDENFKRCFREFCIPTSSNIEQQNSTRIRQ
NTRDHPSTANTVDRTNHQLENLEAETAPLPAAALEVLFQGPGSWSHPQFEKGGGSGGGSG
GSSAWSHPQFEKHHHHHHHHHH

Sequence of entity 4 (A), FASTA

>9PY3_4 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	2
A1CMV	4-[4-(4-chlorophenyl)-4-hydroxypiperidin-1-yl]-N,N-dimethyl-2,2-diphenylbutanam…	C29 H33 Cl N2 O2	1
VSN	5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]guanosine	C10 H15 N5 O10 P2 S	1

Primary citation

Ligand efficacy is driven by conformational control of nucleotide exchange at the mu opioid receptor. Khan, S., Han, G.W., Gati, C. To be published.

Other PDB entries of the same protein (UniProt P62873 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QEH 1.43 Å, Crystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor
8QEG 1.7 Å, Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
9YDQ 1.94 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE and allosteric…
9YDP 1.95 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE
6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
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

Browse structure collections

About this viewer

MolViewer shows 9PY3 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.