9BJK: Inactive mu opioid receptor

Inactive mu opioid receptor bound to Nb6, naloxone and NAM. Determined by electron microscopy at 3.26 Å resolution. Released 17 Jul 2024.

Method: Electron microscopy
Resolution: 3.26 Å
Organisms: Lama glama, Mus musculus
Chains: 2
Atoms: 2,525
Mol. weight: 63.58 kDa
Ligands: A1APU, A1APV
Released: 17 Jul 2024

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

Secondary structure: helices and β-sheets

9BJK contains 13 α-helices and 5 β-strands across 2 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 N: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	32-37	6	1
β-strand	98-102	5	1
α-helix	108-109	2
β-strand	110-113	4	1

Chain R: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	66-95	30
α-helix	105-118	14
α-helix	121-130	10
α-helix	138-170	33
α-helix	172-177	6
α-helix	181-204	24
β-strand	206-208	3	2
β-strand	217-219	3	2
α-helix	227-237	11
α-helix	238-242	5
α-helix	244-261	18
α-helix	269-305	37
α-helix	312-339	28
α-helix	341-349	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
kappa opioid receptor Nanobody 6	N	protein	133	Lama glama
Mu-type opioid receptor	R	protein	426	Mus musculus	P42866 (AlphaFold model)

Sequence of entity 1 (N), FASTA

>9BJK_1 kappa opioid receptor Nanobody 6 (chains N)
MAQVQLQESGGGLVQAGESLRLSCAASGTIFRLYDMGWYRRVSGNQRELVASITSGGSTK
YGDSVKGRFTISRDNAKNTVYLQMSSLKPEDTAVYYCNAEYRTGIWEELLDGWGQGTQVT
VSSHHHHHHEPEA

Sequence of entity 2 (R), FASTA

>9BJK_2 Mu-type opioid receptor (chains R)
MKTIIALSYIFCLVFADYKDDDDAMGPGNISDCSDPLAPASCSPAPGSWLNLSHVDGNQS
DPCGPNRTGLGGSHSLCPQTGSPSMVTAITIMALYSIVCVVGLFGNFLVMYVIVRYTKMK
TATNIYIFNLALADALATSTLPFQSVNYLMGTWPFGNILCKIVISIDYYNMFTSIFTLCT
MSVDRYIAVCHPVKALDFRTPRNAKIVNVCNWILSSAIGLPVMFMATTKYRQGSIDCTLT
FSHPTWYWENLLKICVFIFAFIMPVLIITVCYGLMILRLKSVRLLSGSREKDRNLRRITR
MVLVVVAVFIVCWTPIHIYVIIKALITIPETTFQTVSWHFCIALGYTNSCLNPVLYAFLD
ENFKRCFREFCIPTSSTIEQQNSARIRQNTREHPSTANTVDRTNHQLENLEAETAPLPDI
HHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
A1APU	Nalpha-[({(1M)-1-[5-(benzyloxy)pyridin-3-yl]naphthalen-2-yl}sulfanyl)acetyl]-3-…	C36 H35 N3 O4 S	1
A1APV	Naloxone	C19 H21 N O4	1

Primary citation

A mu-opioid receptor modulator that works cooperatively with naloxone. O'Brien, E.S., Rangari, V.A., El Daibani, A. et al. Nature (2024) 631:686-693. DOI 10.1038/s41586-024-07587-7 · PubMed

Other PDB entries of the same protein (UniProt P42866 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5C1M 2.07 Å, Crystal structure of active mu-opioid receptor bound to the agonist BU72
8E0G 2.1 Å, Re-refined model of active mu-opioid receptor (PDB 5c1m) as an adduct with BU72
9O36 2.3 Å, CryoEM structure of mu-opioid receptor - Gi protein complex bound to fluornitrazene (FNZ)
9ODF 2.4 Å, Structure of the MOR/Gi/Lofentanil Complex, GTP-bound G-Primed
9ODN 2.4 Å, Structure of the MOR/Gi/DAMGO Complex, GTP-Bound, G-Primed
7T2G 2.5 Å, CryoEM structure of mu-opioid receptor - Gi protein complex bound to mitragynine…
9ODE 2.5 Å, Structure of the MOR/Gi/Lofentanil Complex, Nucleotide Free
4DKL 2.8 Å, Crystal structure of the mu-opioid receptor bound to a morphinan antagonist
7UL4 2.8 Å, CryoEM Structure of Inactive MOR Bound to Alvimopan and Mb6
9ODM 2.8 Å, Structure of the MOR/Gi/DAMGO Complex, Nucleotide Free, Baseline
9WSV 2.8 Å, Cryo-EM structure of DAMGO-muOR-arrestin-1-Fab30 complex
9WSW 2.8 Å, Cryo-EM structure of endomorphin-1-muOR-Gz-scFv16 complex

Browse structure collections

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