8IOD: PDB entry 8IOD

Cryo-EM structure of the PG-901-bound human melanocortin receptor 5 (MC5R)-Gs complex. Determined by electron microscopy at 2.59 Å resolution. Released 20 Sept 2023.

Method: Electron microscopy
Resolution: 2.59 Å
Organisms: Homo sapiens, Bos taurus, synthetic construct
Chains: 6
Atoms: 8,061
Mol. weight: 165.32 kDa
Ligands: CA
Released: 20 Sept 2023

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

Secondary structure: helices and β-sheets

8IOD contains 31 α-helices and 47 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	34-39	6	1
α-helix	46-50	5
β-strand	185-189	5	1
β-strand	196-200	5	1
α-helix	213-215	3
β-strand	220-226	7	1
α-helix	233-244	12
β-strand	253-259	7	1
α-helix	261-269	9
α-helix	275-278	4
α-helix	280-282	3
α-helix	293-294	2
α-helix	299-316	18
β-strand	326-330	5	1
α-helix	339-357	19

Chain B: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	6-24	19
α-helix	38-39	2
β-strand	45-51	7	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	157-161	5	5
β-strand	166-170	5	5
β-strand	175-180	6	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	207-212	6	6
β-strand	218-223	6	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	249-254	6	7
β-strand	259-264	6	7
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	303-308	6	8
β-strand	315	1	9
β-strand	319-320	2	2
β-strand	327-328	2	2
β-strand	331	1	9
β-strand	336-341	6	2

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	12-23	12
α-helix	30-42	13
α-helix	53-55	3
α-helix	56-58	3

Chain N: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	10
β-strand	10-12	3	11
β-strand	17-25	9	10
α-helix	29-31	3
β-strand	34-39	6	11
β-strand	45-51	7	11
β-strand	58-60	3	11
α-helix	62-64	3
β-strand	69-71	3	10
β-strand	78-84	7	10
α-helix	88-90	3
β-strand	92-98	7	11
β-strand	118	1	11
β-strand	122-126	5	11

Chain R: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	40-43	4
α-helix	45-59	15
α-helix	70-100	31
α-helix	108-145	38
α-helix	156-179	24
α-helix	184-219	36
α-helix	234-246	13
α-helix	253-260	8
α-helix	268-274	7
α-helix	277-295	19
α-helix	300-311	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s)…	A	protein	361	Homo sapiens	P63092 (AlphaFold model), P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,HiBiT	B	protein	371	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Bos taurus	P63212 (AlphaFold model)
PG-901	L	protein	9	synthetic construct
Nanobody-35	N	protein	160	Homo sapiens
HA signal peptide,Melanocortin receptor 5,LgBiT subunit	R	protein	513	Influenza A virus (strain A/Victoria/3/1975 H3N2), Homo sapiens	P03435, P33032

Sequence of entity 1 (A), FASTA

>8IOD_1 Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
MGCTLSAEDKAAVERSKMIEKQLQKDKQVYRATHRLLLLGADNSGKSTIVKQMRIYHVNG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDF
KSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPR
VTRAKYFIRDEFLRISTASGDGRHYCYPHFTCSVDTENARRIFNDCRDIIQRMHLRQYEL
L

Sequence of entity 2 (B), FASTA

>8IOD_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,HiBiT (chains B)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGGGSGGGGSSG
VSGWRLFKKIS

Sequence of entity 3 (G), FASTA

>8IOD_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (L), FASTA

>8IOD_4 PG-901 (chains L)
XLDPXRWKX

Sequence of entity 5 (N), FASTA

>8IOD_5 Nanobody-35 (chains N)
MKYLLPTAAAGLLLLAAQPAMAQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVR
QAPGKGLEWVSDISQSGASISYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCAR
CPAPFTRDCFDVTSTTYAYRGQGTQVTVSSHHHHHHEPEA

Sequence of entity 6 (R), FASTA

>8IOD_6 HA signal peptide,Melanocortin receptor 5,LgBiT subunit (chains R)
MKTIIALSYIFCLVFANSSFHLHFLDLNLNATEGNLSGPNVKNKSSPCEDMGIAVEVFLT
LGVISLLENILVIGAIVKNKNLHSPMYFFVCSLAVADMLVSMSSAWETITIYLLNNKHLV
IADAFVRHIDNVFDSMICISVVASMCSLLAIAVDRYVTIFYALRYHHIMTARRSGAIIAG
IWAFCTGCGIVFILYSESTYVILCLISMFFAMLFLLVSLYIHMFLLARTHVKRIAALPGA
SSARQRTSMQGAVTVTMLLGVFTVCWAPFFLHLTLMLSCPQNLYCSRFMSHFNMYLILIM
CNSVMDPLIYAFRSQEMRKTFKEIICCRGFRIACSFPRRDGSSGGGGSGGGGSSGVFTLE
DFVGDWEQTAAYNLDQVLEQGGVSSLLQNLAVSVTPIQRIVRSGENALKIDIHVIIPYEG
LSADQMAQIEEVFKVVYPVDDHHFKVILPYGTLVIDGVTPNMLNYFGRPYEGIAVFDGKK
ITVTGTLWNGNKIIDERLITPDGSMLFRVTINS

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Primary citation

Structural insights into ligand recognition and subtype selectivity of the human melanocortin-3 and melanocortin-5 receptors. Feng, W., Zhou, Q., Chen, X. et al. Cell Discov (2023) 9:81. DOI 10.1107/S0907444909042073 · PubMed

Other PDB entries of the same protein (UniProt P63092 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7BPH 1.57 Å, Crystal structure of GppNHp-bound GNAS in complex with the cyclic peptide inhibitor GN13
6AU6 1.7 Å, Crystal structure of GDP-bound human GNAS R201C mutant
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
7E5E 1.95 Å, Crystal structure of GDP-bound GNAS in complex with the cyclic peptide inhibitor GD20
7MBX 1.95 Å, Human Cholecystokinin 1 receptor (CCK1R) Gs complex
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
7RTB 2.14 Å, Peptide-19 bound to the Glucagon-Like Peptide-1 Receptor (GLP-1R)

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