8K9L: PDB entry 8K9L

Full agonist- and positive allosteric modulator-bound mu-type opioid receptor-G protein complex. Determined by electron microscopy at 3.05 Å resolution. Released 29 May 2024.

Method: Electron microscopy
Resolution: 3.05 Å
Organisms: Escherichia coli, Homo sapiens, synthetic construct
Chains: 6
Atoms: 8,919
Mol. weight: 166.73 kDa
Ligands: VV9
Released: 29 May 2024

Explore 8K9L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8K9L contains 42 α-helices and 62 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: 12 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-31	23
β-strand	34-39	6	2
α-helix	46-52	7
β-strand	185-191	7	2
β-strand	194-200	7	2
α-helix	208-211	4
α-helix	212-215	4
β-strand	220-226	7	2
α-helix	227-231	5
α-helix	232-234	3
α-helix	242-254	13
α-helix	257-259	3
β-strand	263-269	7	2
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-322	4	2
α-helix	331-350	20

Chain B: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	3-24	22
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	89-94	6	4
α-helix	95	1
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	146-153	8	6
β-strand	156-161	6	6
β-strand	166-170	5	6
β-strand	175-180	6	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	208-212	5	7
β-strand	217-222	6	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	249-250	2	8
β-strand	253-254	2	8
β-strand	259-260	2	8
β-strand	264	1	8
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	304-308	5	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain G: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	6-23	18
α-helix	30-44	15
α-helix	45-47	3
α-helix	53-55	3
α-helix	56-58	3
α-helix	60-62	3

Chain H: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-12	3	11
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	34-39	6	11
β-strand	45-51	7	11
β-strand	58-60	3	11
β-strand	68-73	6	10
α-helix	74-76	3
β-strand	78-83	6	10
α-helix	88-90	3
β-strand	92-98	7	11
β-strand	110-111	2	11
β-strand	115-119	5	11
α-helix	138-139	2
β-strand	140-141	2	12
β-strand	146-149	4	13
β-strand	155-161	7	12
β-strand	166	1	14
β-strand	172	1	14
β-strand	174-179	6	13
β-strand	186-190	5	13
β-strand	194-195	2	13
α-helix	196	1
β-strand	203-208	6	12
β-strand	211-216	6	12
β-strand	226-231	6	13
α-helix	237	1
β-strand	238-239	2	13
β-strand	243-247	5	13

Chain R: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	67-94	28
α-helix	95-99	5
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	208-211	4	1
β-strand	218-221	4	1
α-helix	227-239	13
α-helix	240-244	5
α-helix	245-261	17
α-helix	271-307	37
α-helix	310-312	3
α-helix	314-335	22
α-helix	336-340	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble cytochrome b562,Mu-type opioid receptor,Mu-type opioid receptor	R	protein	453	Escherichia coli, Homo sapiens	P0ABE7 (AlphaFold model), P35372 (AlphaFold model)
Damgo	S	protein	5	synthetic construct
G protein subunit alpha i3	A	protein	354	Macaca mulatta	P08754 (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	72	Homo sapiens	P59768
scFv16	H	protein	257	synthetic construct

Sequence of entity 1 (R), FASTA

>8K9L_1 Soluble cytochrome b562,Mu-type opioid receptor,Mu-type opioid receptor (chains R)
CLVFADYKDDDDALEVLFQGPMADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAAL
DAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTR
NAYIQKYLGGSPGARSASSPSMITAITIMALYSIVCVVGLFGNFLVMYVIVRYTKMKTAT
NIYIFNLALADALATSTLPFQSVNYLMGTWPFGTILCKIVISIDYYNMFTSIWTLCTMSV
DRYIAVCHPVKALDFRTPRNAKIINVCNWILSSAIGLPVMFMATTKYRQGSIDCTLTFSH
PTWYWENLLKICVFIFAFIMPVLIITVCYGLMILRLKSVRMLSGSKEKDRNLRRITRMVL
VVVAVFIVCWTPIHIYVIIKALVTIPETTFQTVSWHFCIALGYTNSCLNPVLYAFLDENF
KRCFREFCIPTSSNIEQLEVLFQGPHHHHHHHH

Sequence of entity 2 (S), FASTA

>8K9L_2 DAMGO (chains S)
YAGFX

Sequence of entity 3 (A), FASTA

>8K9L_3 G protein subunit alpha i3 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAKEVKLLLLGAGESGKSTIVKQMKIIHEDG
YSEDECKQYKVVVYSNTIQSIIAIIRAMGRLKIDFGEAARADDARQLFVLAGSAEEGVMT
PELAGVIKRLWRDGGVQACFSRSREYQLNDSASYYLNDLDRISQSNYIPTQQDVLRTRVK
TTGIVETHFTFKDLYFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTETSIILFLNKKDLFEEKIKRSPLTICYPEYTGSNTYEEAA
AYIQCQFEDLNRRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKECGLY

Sequence of entity 4 (B), FASTA

>8K9L_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHHHSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLR
GHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYV
ACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIE
TGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAI
CFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDF
NCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 5 (G), FASTA

>8K9L_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MAASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASEN
PFREKKFFCAIL

Sequence of entity 6 (H), FASTA

>8K9L_6 scFv16 (chains H)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAALEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
VV9	(2~{S})-2-(3-bromanyl-4-methoxy-phenyl)-3-(4-chlorophenyl)sulfonyl-1,3-thiazoli…	C16 H15 Br Cl N O3 S2	1

Primary citation

Structural and dynamic insights into the activation of the mu-opioid receptor by an allosteric modulator. Kaneko, S., Imai, S., Uchikubo-Kamo, T. et al. Nat Commun (2024) 15:3544-3544. DOI 10.1038/s41467-024-47792-6 · 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

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