7L1V: Orexin Receptor 2

Orexin Receptor 2 (OX2R) in Complex with G Protein and Small-Molecule Agonist Compound 1. Determined by electron microscopy at 3.0 Å resolution. Released 10 Feb 2021.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Homo sapiens, Mus musculus, Lama glama
Chains: 6
Atoms: 9,606
Mol. weight: 157.96 kDa
Ligands: XGD
Released: 10 Feb 2021

Explore 7L1V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7L1V contains 33 α-helices and 72 β-strands across 6 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: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	14-38	25
β-strand	40-47	8	1
α-helix	53-58	6
β-strand	209-213	5	1
β-strand	218-223	6	1
β-strand	243-249	7	1
α-helix	266-277	12
β-strand	286-292	7	1
α-helix	294-303	10
α-helix	313-317	5
α-helix	326-327	2
α-helix	332-349	18
β-strand	359-363	5	1
α-helix	371-390	20

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3-24	22
α-helix	30-33	4
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	88-94	7	3
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	121-125	5	4
β-strand	134-139	6	4
β-strand	146-151	6	5
β-strand	156-161	6	5
β-strand	165-170	6	5
β-strand	176-181	6	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	208-212	5	6
β-strand	218-222	5	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	250-254	5	7
β-strand	260-264	5	7
α-helix	272	1
β-strand	273-277	5	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	304-308	5	8
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	6-23	18
α-helix	30-42	13
α-helix	45-47	3
α-helix	54-55	2

Chain H: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	17-25	9	9
α-helix	29-31	3
β-strand	33-39	7	10
β-strand	45-51	7	10
β-strand	58-60	3	10
β-strand	65	1	9
β-strand	68-73	6	9
β-strand	78-84	7	9
β-strand	92-99	8	10
β-strand	111	1	10
β-strand	115-119	5	10
β-strand	141	1	11
β-strand	146-148	3	12
β-strand	155-160	6	11
β-strand	166	1	13
β-strand	172	1	13
β-strand	174-179	6	12
β-strand	186-190	5	12
β-strand	194-195	2	12
α-helix	196	1
β-strand	203-208	6	11
β-strand	211-216	6	11
β-strand	226-231	6	12
α-helix	237-238	2
β-strand	244-246	3	12

Chain R: 14 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	56-81	26
α-helix	83-85	3
α-helix	91-106	16
α-helix	108-117	10
α-helix	123-156	34
α-helix	166-183	18
α-helix	186-189	4
β-strand	191-196	6	14
β-strand	207-212	6	14
β-strand	213-214	2	15
α-helix	219-228	10
α-helix	229-233	5
α-helix	234-249	16
α-helix	293-316	24
α-helix	318-328	11
α-helix	342-364	23
α-helix	369-375	7

Chain S: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	16
β-strand	10-11	2	15
β-strand	17-25	9	16
β-strand	33-38	6	15
β-strand	44-50	7	15
β-strand	57-59	3	15
β-strand	67-72	6	16
β-strand	77-83	7	16
α-helix	87-89	3
β-strand	91-98	8	15
β-strand	102-103	2	15
β-strand	108-111	4	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Engineered Guanine nucleotide-binding protein subunit alpha	A	protein	244	Homo sapiens
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	349	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)
single-chain antibody Fv fragment (svFv16)	H	protein	250	Mus musculus
Hypocretin receptor type 2	R	protein	374	Homo sapiens	O43614 (AlphaFold model)
Synthetic nanobody 51 (Sb51)	S	protein	118	Lama glama

Sequence of entity 1 (A), FASTA

>7L1V_1 Engineered Guanine nucleotide-binding protein subunit alpha (chains A)
GTLSAEDKAAVERSKMIEKQLQKDKQVYRRTLRLLLLGADNSGKSTIVKQMRILHGGSGG
SGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEAL
NDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGE
DPRVTRAKYFIRKEFVDISTASGDGRHICYPHFTCAVDTENARRIFNDCKDIILQMNLRE
YNLV

Sequence of entity 2 (B), FASTA

>7L1V_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MGHHHHHHHHSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTL
RGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNY
VACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDI
ETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINA
ICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDD
FNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (C), FASTA

>7L1V_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFSAIL

Sequence of entity 4 (H), FASTA

>7L1V_4 single-chain antibody Fv fragment (svFv16) (chains H)
GSDVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTI
YYADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLT
VSSGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFL
QRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLT
FGAGTKLELK

Sequence of entity 5 (R), FASTA

>7L1V_5 Hypocretin receptor type 2 (chains R)
DYKDDDAMGTKLEDSPPCRNWSSASELNETQEPFLNPTDYDDEEFLRYLWREYLHPKEYE
WVLIAGYIIVFVVALIGNVLVCVAVWKNHHMRTVTNYFIVNLSLADVLVTITCLPATLVV
DITETWFFGQSLCKVIPYLQTVSVSVSVLTLSCIALDRWYAICHPLMFKSTAKRARNSIV
IIWIVSCIIMIPQAIVMECSTVFPGLANKTTLFTVCDERWGGEIYPKMYHICFFLVTYMA
PLCLMVLAYLQIFRKLWCRQIPGTSSEIKQIRARRKTARMLMVVLLVFAICYLPISILNV
LKRVFGMFAHTEDRETVYAWFTFSHWLVYANSAANPIIYNFLSGKFREEFKAAFSCCCLG
VHHRHHHHHHHHHH

Sequence of entity 6 (S), FASTA

>7L1V_6 Synthetic nanobody 51 (Sb51) (chains S)
GSSSQVQLVESGGGLVQAGGSLRLSCAASGFPVGRVMYWYRQAPGKEREWVAAISSHGDM
TAYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCEVYVGYFYHGQGTQVTVSA

Ligands and cofactors

ID	Name	Formula	Copies
XGD	4'-methoxy-N,N-dimethyl-3'-{[3-(2-{[2-(2H-1,2,3-triazol-2-yl)benzene-1-carbonyl…	C33 H32 N6 O5 S	1

Primary citation

Structures of active-state orexin receptor 2 rationalize peptide and small-molecule agonist recognition and receptor activation. Hong, C., Byrne, N.J., Zamlynny, B. et al. Nat Commun (2021) 12:815-815. DOI 10.1038/s41467-021-21087-6 · PubMed

Other PDB entries of the same protein (UniProt P62873 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QEH 1.43 Å, Crystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor
8QEG 1.7 Å, Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
9YDQ 1.94 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE and allosteric…
9YDP 1.95 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE
6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
8F0J 2.0 Å, Calcitonin Receptor in complex with Gs and Pramlintide analogue peptide San45
8F2B 2.0 Å, Amylin 3 Receptor in complex with Gs and Pramlintide analogue peptide San45
9XXT 2.0 Å, Cryo-EM structure of lysophosphatidylserine (18:0)-bound GPR174-Gs complex
6X18 2.1 Å, GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor
6X19 2.1 Å, Non peptide agonist CHU-128, bound to Glucagon-Like peptide-1 (GLP-1) Receptor
9NTU 2.1 Å, Cryo-EM structure of BETP-GLP-1(9-36)-GLP-1R-Gs complex

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