9PXY: PDB entry 9PXY

Primed-state naloxone-mu opioid receptor-Gi GDPbS complex (rebound). Determined by electron microscopy at 3.0 Å resolution. Released 12 Nov 2025.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,160
Mol. weight: 159.22 kDa
Ligands: CLR, A1APV, VSN
Released: 12 Nov 2025

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

Secondary structure: helices and β-sheets

9PXY contains 39 α-helices and 42 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: 17 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	6-31	26
β-strand	33-38	6	2
β-strand	40	1	3
α-helix	46-51	6
α-helix	62-66	5
α-helix	70-88	19
α-helix	101-114	14
α-helix	122-129	8
α-helix	136-142	7
α-helix	143-145	3
α-helix	152-159	8
α-helix	172-177	6
α-helix	179-181	3
β-strand	185-190	6	2
β-strand	195-200	6	2
α-helix	208-210	3
β-strand	220-221	2	2
β-strand	224-225	2	3
α-helix	227-230	4
β-strand	233	1	4
β-strand	241	1	4
α-helix	242-254	13
β-strand	263-264	2	2
β-strand	267-268	2	3
α-helix	271-280	10
α-helix	296-308	13
β-strand	319	1	2
β-strand	322-323	2	3
α-helix	329-350	22

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	47-50	4	5
β-strand	60-62	3	6
β-strand	71-73	3	6
β-strand	78-81	4	6
β-strand	91-94	4	6
β-strand	100-105	6	7
β-strand	111-116	6	7
β-strand	121-125	5	7
β-strand	134-139	6	7
β-strand	148-151	4	8
β-strand	156-160	5	8
β-strand	166-170	5	8
β-strand	176-180	5	8
β-strand	187-192	6	9
β-strand	198-203	6	9
β-strand	208-212	5	9
β-strand	218-222	5	9
β-strand	231-234	4	10
β-strand	240-244	5	10
β-strand	249-254	6	10
β-strand	260-265	6	10
β-strand	273-278	6	11
β-strand	284-289	6	11
β-strand	294-298	5	11
β-strand	304-308	5	11
β-strand	315-320	6	5
β-strand	327-331	5	5
β-strand	336-339	4	5

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	11-23	13
α-helix	30-41	12
α-helix	53-55	3

Chain R: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	69-93	25
α-helix	94-98	5
α-helix	104-119	16
α-helix	120-122	3
α-helix	123-132	10
α-helix	138-172	35
α-helix	174-178	5
α-helix	183-205	23
β-strand	211-213	3	1
β-strand	216-218	3	1
α-helix	227-239	13
α-helix	240-244	5
α-helix	245-263	19
α-helix	265-267	3
α-helix	271-307	37
α-helix	314-335	22
α-helix	336-340	5
α-helix	343-350	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble cytochrome b562,Mu-type opioid receptor,Soluble cytochrome b562,Mu-type opioid receptor,Mu…	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 (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

Sequence of entity 1 (R), FASTA

>9PXY_1 Soluble cytochrome b562,Mu-type opioid receptor,Soluble cytochrome b562,Mu-type opioid receptor,Mu opioid receptor (chains R)
MKTIIALSYIFCLVFADYKDHDGDYKDHDIDYKDDDDKLHHHHHHHHHHLEVLFQGPGSG
SADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMK
DFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLGTGSDSSAAPTNA
SNCTDALAYSSCSPAPSPGSWVNLSHLDGNLSDPCGPNRTDLGGRDSLCPPTGSPSMITA
ITIMALYSIVCVVGLFGNFLVMYVIVRYTKMKTATNIYIFNLALADALATSTLPFQSVNY
LMGTWPFGTILCKIVISIDYYNMFTSIFTLCTMSVDRYIAVCHPVKALDFRTPRNAKIIN
VCNWILSSAIGLPVMFMATTKYRQGSIDCTLTFSHPTWYWENLLKICVFIFAFIMPVLII
TVCYGLMILRLKSVRMLSGSKEKDRNLRRITRMVLVVVAVFIVCWTPIHIYVIIKALVTI
PETTFQTVSWHFCIALGYTNSCLNPVLYAFLDENFKRCFREFCIPTSSNIEQQNSTRIRQ
NTRDHPSTANTVDRTNHQLENLEAETAPLPAAALEVLFQGPGSWSHPQFEKGGGSGGGSG
GSSAWSHPQFEKHHHHHHHHHH

Sequence of entity 2 (A), FASTA

>9PXY_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (B), FASTA

>9PXY_3 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 4 (C), FASTA

>9PXY_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	2
A1APV	Naloxone	C19 H21 N O4	1
VSN	5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]guanosine	C10 H15 N5 O10 P2 S	1

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 P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

Browse structure collections

About this viewer

MolViewer shows 9PXY 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.