9PY4: PDB entry 9PY4

Primed-state loperamide-mu opioid receptor-Gi GDPbS complex (rebound). Determined by electron microscopy at 2.78 Å resolution. Released 12 Nov 2025.

Method: Electron microscopy
Resolution: 2.78 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 4
Atoms: 8,164
Mol. weight: 159.37 kDa
Ligands: VSN, A1CMV, CLR
Released: 12 Nov 2025

Explore 9PY4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PY4 contains 41 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: 19 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	6-31	26
β-strand	34-38	5	1
β-strand	40	1	1
α-helix	46-53	8
α-helix	67-69	3
α-helix	70-87	18
α-helix	100-111	12
α-helix	122-130	9
α-helix	135-142	8
α-helix	152-159	8
α-helix	171-177	7
α-helix	178-181	4
β-strand	185-190	6	1
β-strand	195-200	6	1
α-helix	208-211	4
α-helix	212-214	3
β-strand	220-221	2	1
β-strand	224-225	2	1
α-helix	227-230	4
α-helix	232	1
β-strand	233	1	2
α-helix	234	1
β-strand	241	1	2
α-helix	242-254	13
β-strand	263-268	6	1
α-helix	271-278	8
α-helix	296-308	13
β-strand	319-323	5	1
α-helix	330-350	21

Chain B: 4 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	47-51	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	121-125	5	5
β-strand	134-139	6	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	165-170	6	6
β-strand	176-181	6	6
β-strand	189-192	4	7
β-strand	198-202	5	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	250-254	5	8
β-strand	260-264	5	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	303-308	6	9
β-strand	317-320	4	3
β-strand	327-330	4	3
β-strand	336-339	4	3

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	54-55	2

Chain R: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	68-97	30
α-helix	104-120	17
α-helix	123-132	10
α-helix	138-172	35
α-helix	174-180	7
α-helix	183-207	25
β-strand	208-213	6	10
β-strand	216-221	6	10
α-helix	227-239	13
α-helix	240-244	5
α-helix	245-262	18
α-helix	265-267	3
α-helix	271-307	37
α-helix	314-334	21
α-helix	335-339	5
α-helix	343-350	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
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)
Cytochrome b-562/Mu-type opioid receptor chimera protein,Mu-type opioid receptor	R	protein	622	Escherichia coli, Homo sapiens	P0ABE7 (AlphaFold model), P35372

Sequence of entity 1 (A), FASTA

>9PY4_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>9PY4_2 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 3 (C), FASTA

>9PY4_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (R), FASTA

>9PY4_4 Cytochrome b-562/Mu-type opioid receptor chimera protein,Mu-type opioid receptor (chains R)
MKTIIALSYIFCLVFADYKDHDGDYKDHDIDYKDDDDKLHHHHHHHHHHLEVLFQGPGSG
SADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMK
DFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLGTGSDSSAAPTNA
SNCTDALAYSSCSPAPSPGSWVNLSHLDGNLSDPCGPNRTDLGGRDSLCPPTGSPSMITA
ITIMALYSIVCVVGLFGNFLVMYVIVRYTKMKTATNIYIFNLALADALATSTLPFQSVNY
LMGTWPFGTILCKIVISIDYYNMFTSIFTLCTMSVDRYIAVCHPVKALDFRTPRNAKIIN
VCNWILSSAIGLPVMFMATTKYRQGSIDCTLTFSHPTWYWENLLKICVFIFAFIMPVLII
TVCYGLMILRLKSVRMLSGSKEKDRNLRRITRMVLVVVAVFIVCWTPIHIYVIIKALVTI
PETTFQTVSWHFCIALGYTNSCLNPVLYAFLDENFKRCFREFCIPTSSNIEQQNSTRIRQ
NTRDHPSTANTVDRTNHQLENLEAETAPLPAAALEVLFQGPGSWSHPQFEKGGGSGGGSG
GSSAWSHPQFEKHHHHHHHHHH

Ligands and cofactors

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

Primary citation

Structural snapshots capture nucleotide release at the mu-opioid receptor. Khan, S., Tyson, A.S., Ranjbar, M. et al. Nature (2025) 648:755-763. DOI 10.1038/s41586-025-09677-6 · PubMed

Other PDB entries of the same protein (UniProt P63096 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
3UMR 2.04 Å, Crystal structure of the G202D mutant of human G-alpha-i1
9P7Z 2.1 Å, NTSR1-Gi-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
2OM2 2.2 Å, Crystal Structure Of Human G[alpha]i1 Bound To The Goloco Motif Of Rgs14
8YN9 2.3 Å, Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi
9HYI 2.3 Å, DP81-bound serotonin 5-HT1A receptor - Gi Protein Complex
9O36 2.3 Å, CryoEM structure of mu-opioid receptor - Gi protein complex bound to fluornitrazene (FNZ)
9P80 2.3 Å, NTSR1-Gi-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
8XXV 2.33 Å, Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
3UMS 2.34 Å, Crystal structure of the G202A mutant of human G-alpha-i1
3ONW 2.38 Å, Structure of a G-alpha-i1 mutant with enhanced affinity for the RGS14 GoLoco motif.
20ZG 2.4 Å, Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the…

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