7SRR: 5-HT2B receptor

5-HT2B receptor bound to LSD in complex with heterotrimeric mini-Gq protein obtained by cryo-electron microscopy (cryoEM). Determined by electron microscopy at 2.9 Å resolution. Released 21 Sept 2022.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,394
Mol. weight: 145.91 kDa
Ligands: 7LD
Released: 21 Sept 2022

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

Secondary structure: helices and β-sheets

7SRR contains 39 α-helices and 58 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 B: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-29	23
β-strand	33-39	7	1
α-helix	46-48	3
β-strand	69-76	8	1
β-strand	79-86	8	1
β-strand	105-111	7	1
α-helix	118-129	12
α-helix	132-134	3
β-strand	138-144	7	1
α-helix	146-155	10
α-helix	160-163	4
α-helix	165-167	3
α-helix	177-179	3
α-helix	184-203	20
β-strand	211-215	5	1
α-helix	224-242	19

Chain C: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
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	120-125	6	4
α-helix	129-131	3
β-strand	134-140	7	4
β-strand	146-151	6	5
β-strand	156-161	6	5
β-strand	165-170	6	5
β-strand	176-180	5	5
β-strand	187-191	5	6
β-strand	198-203	6	6
β-strand	208-212	5	6
β-strand	220-222	3	6
β-strand	229-232	4	7
β-strand	240-245	6	7
β-strand	249-254	6	7
β-strand	260-264	5	7
β-strand	273-278	6	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 D: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	11-23	13
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3
α-helix	56-58	3

Chain E: 3 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-11	2	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	68-73	6	9
β-strand	78-84	7	9
β-strand	92-99	8	10
β-strand	110-111	2	10
β-strand	115-118	4	10
β-strand	128-129	2	11
β-strand	134-136	3	12
β-strand	143-147	5	13
β-strand	148-149	2	11
β-strand	154	1	14
β-strand	160	1	14
β-strand	162-167	6	12
β-strand	174-178	5	12
β-strand	182-183	2	12
α-helix	184	1
β-strand	191-196	6	13
β-strand	199-204	6	13
β-strand	213-219	7	12
α-helix	225	1
β-strand	231-234	4	12

Chain R: 18 helices, 0 β-strands

Element	Residues	Length
α-helix	57-81	25
α-helix	88-102	15
α-helix	103-107	5
α-helix	108-116	9
α-helix	128-158	31
α-helix	160-163	4
α-helix	169-187	19
α-helix	189-192	4
α-helix	217-220	4
α-helix	227-244	18
α-helix	318-336	19
α-helix	338-349	12
α-helix	355-361	7
α-helix	365-370	6
α-helix	371-374	4
α-helix	376-379	4
α-helix	385-391	7
α-helix	392-394	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
G protein subunit q (Gi2-mini-Gq chimera)	B	protein	246	Homo sapiens
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	340	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	protein	71	Homo sapiens	P59768 (AlphaFold model)
single-chain variable fragment 16 (scFv16)	E	protein	286	Homo sapiens
5-hydroxytryptamine receptor 2B	R	protein	370	Homo sapiens	P41595 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>7SRR_1 G protein subunit q (Gi2-mini-Gq chimera) (chains B)
MGSTVSAEDKAAAERSKMIDKNLREDGEKARRTLRLLLLGADNSGKSTIVKQMRILHGGS
GGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQE
ALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEP
GEDPRVTRAKYFIRKEFVDISTASGDGRHICYPHFTCAVDTENARRIFNDCKDIILQMNL
REYNLV

Sequence of entity 2 (C), FASTA

>7SRR_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (D), FASTA

>7SRR_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (E), FASTA

>7SRR_4 single-chain variable fragment 16 (scFv16) (chains E)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFADVQLVESGGGLVQPGGSRKLSC
SASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQ
MTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSSGGGGSGGGGSGGGGSDIVMTQ
ATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDR
FSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLELK

Sequence of entity 5 (R), FASTA

>7SRR_5 5-hydroxytryptamine receptor 2B (chains R)
TESIPEEMKQIVEEQGNKLHWAALLILMVIIPTIGGNTLVILAVSLEKKLQYATNYFLMS
LAVADLLVGLFVMPIALLTIMFEAMWPLPLVLCPAWLFLDVLFSTASIWHLCAISVDRYI
AIKKPIQANQYNSRATAFIKITVVWLISIGIAIPVPIKGIETDVDNPNNITCVLTKERFG
DFMLFGSLAAFFTPLAIMIVTYFLTIHALQKKAYLVKNKPPQRLTWLTVSTVFQRDETPC
SSPEKVAMLDGSRKDKALPNSGDETLMRRTSTIGKKSVQTISNEQRASKVLGIVFFLFLL
MWCPFFITNITLVLCDSCNQTTLQMLLEIFVWIGYVSSGVNPLVYTLFNKTFRDAFGRYI
TCNYRATKSV

Ligands and cofactors

ID	Name	Formula	Copies
7LD	(8alpha)-N,N-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide	C20 H25 N3 O	1

Primary citation

Signaling snapshots of a serotonin receptor activated by the prototypical psychedelic LSD. Cao, C., Barros-Alvarez, X., Zhang, S. et al. Neuron (2022) 110:3154. DOI 10.1016/j.neuron.2022.08.006 · 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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