7U2L: C5guano-uOR-Gi-scFv16

C5guano-uOR-Gi-scFv16. Determined by electron microscopy at 3.2 Å resolution. Released 4 May 2022.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 8,739
Mol. weight: 154.11 kDa
Ligands: L0X
Released: 4 May 2022

Explore 7U2L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7U2L contains 35 α-helices and 65 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: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-32	24
β-strand	34-40	7	1
α-helix	46-52	7
β-strand	185-190	6	1
β-strand	195-200	6	1
α-helix	208-211	4
β-strand	220-226	7	1
α-helix	242-254	13
α-helix	263	1
β-strand	264-269	6	1
α-helix	271-278	8
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	1
α-helix	330-351	22

Chain B: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	7-24	18
α-helix	30-34	5
α-helix	38-39	2
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	89-94	6	3
α-helix	95	1
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	120-125	6	4
β-strand	134-140	7	4
β-strand	146-151	6	5
β-strand	156-161	6	5
β-strand	166-170	5	5
β-strand	176-180	5	5
β-strand	187	1	6
β-strand	191-192	2	7
β-strand	198-202	5	7
β-strand	203	1	6
β-strand	207-212	6	7
β-strand	218-223	6	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	259-264	6	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	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	10-23	14
α-helix	30-43	14
α-helix	56-58	3

Chain D: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	66-92	27
α-helix	93-97	5
α-helix	102-119	18
α-helix	121-130	10
α-helix	136-170	35
α-helix	172-178	7
α-helix	181-205	25
β-strand	207-210	4	10
β-strand	215-218	4	10
α-helix	225-237	13
α-helix	238-242	5
α-helix	243-259	17
α-helix	263-265	3
α-helix	269-305	37
α-helix	312-332	21
α-helix	333-338	6
α-helix	341-346	6

Chain E: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	11
β-strand	7	1	12
β-strand	11-12	2	13
β-strand	17-23	7	12
β-strand	24	1	11
α-helix	29-31	3
β-strand	33-39	7	14
β-strand	45-51	7	14
β-strand	58-60	3	14
β-strand	68-73	6	12
β-strand	78-84	7	12
α-helix	88-90	3
β-strand	93-99	7	14
β-strand	111	1	14
β-strand	115	1	14
β-strand	118-119	2	13
β-strand	129	1	15
β-strand	134-136	3	16
β-strand	143-147	5	17
β-strand	148	1	15
β-strand	154	1	18
β-strand	160	1	18
β-strand	162-167	6	16
β-strand	174-178	5	16
β-strand	182-183	2	16
α-helix	184	1
β-strand	191-196	6	17
β-strand	199-204	6	17
β-strand	214-219	6	16
α-helix	225	1
β-strand	231-234	4	16

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	344	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)
Mu-type opioid receptor	D	protein	356	Mus musculus	P42866 (AlphaFold model)
scFv16	E	protein	259	Mus musculus

Sequence of entity 1 (A), FASTA

>7U2L_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>7U2L_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
PGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLA
KIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGG
LDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQ
TTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFP
NGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNV
WDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (C), FASTA

>7U2L_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (D), FASTA

>7U2L_4 Mu-type opioid receptor (chains D)
NISDCSDPLAPASCSPAPGSWLNLSHVDGNQSDPCGPNRTGLGENLYFQGSHSLCPQTGS
PSMVTAITIMALYSIVCVVGLFGNFLVMYVIVRYTKMKTATNIYIFNLALADALATSTLP
FQSVNYLMGTWPFGNILCKIVISIDYYNMFTSIFTLCTMSVDRYIAVCHPVKALDFRTPR
NAKIVNVCNWILSSAIGLPVMFMATTKYRQGSIDCTLTFSHPTWYWENLLKICVFIFAFI
MPVLIITVCYGLMILRLKSVRMLSGSKEKDRNLRRITRMVLVVVAVFIVCWTPIHIYVII
KALITIPETTFQTVSWHFCIALGYTNSCLNPVLYAFLDENFKRCFREFCIPTSSTI

Sequence of entity 5 (E), FASTA

>7U2L_5 scFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
L0X	N-(5-carbamimidamidopentyl)-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide	C22 H37 N5 O	1

Primary citation

Structure-based design of bitopic ligands for the μ-opioid receptor. Faouzi, A., Wang, H., Zaidi, S.A. et al. Nature (2023) 613:767-774. DOI 10.1038/s41586-022-05588-y · 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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