9U4Y: Xenopus laevis GnRHR

cryo-EM structure of Xenopus laevis GnRHR bound with mammal GnRH. Determined by electron microscopy at 2.67 Å resolution. Released 11 Jun 2025.

Method: Electron microscopy
Resolution: 2.67 Å
Organisms: Homo sapiens, synthetic construct, Ateles
Chains: 6
Atoms: 8,765
Mol. weight: 162.17 kDa
Released: 11 Jun 2025

Explore 9U4Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9U4Y contains 36 α-helices and 61 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: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	10-30	21
α-helix	33	1
β-strand	34-40	7	8
α-helix	47-49	3
β-strand	183-189	7	8
β-strand	192-198	7	8
α-helix	207-210	4
α-helix	211-213	3
β-strand	218-224	7	8
α-helix	231-242	12
α-helix	245-247	3
β-strand	251-257	7	8
α-helix	259-265	7
α-helix	291-292	2
α-helix	297-315	19
β-strand	324-328	5	8
α-helix	336-355	20

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	9-30	22
α-helix	35-38	4
α-helix	43-44	2
β-strand	52-56	5	1
β-strand	63-68	6	2
β-strand	74-79	6	2
β-strand	83-88	6	2
β-strand	93-99	7	2
β-strand	105-110	6	3
β-strand	116-121	6	3
β-strand	126-130	5	3
β-strand	139-144	6	3
β-strand	151-158	8	4
β-strand	161-166	6	4
β-strand	171-175	5	4
β-strand	180-185	6	4
β-strand	192-197	6	5
β-strand	203-208	6	5
β-strand	213-217	5	5
β-strand	223-227	5	5
β-strand	234-239	6	6
β-strand	245-250	6	6
β-strand	254-259	6	6
β-strand	264-269	6	6
β-strand	278-283	6	7
β-strand	289-294	6	7
β-strand	299-303	5	7
β-strand	309-313	5	7
β-strand	320-325	6	1
β-strand	332-336	5	1
β-strand	341-344	4	1

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	7-23	17
α-helix	30-43	14
α-helix	53-55	3

Chain R: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	51-81	31
α-helix	87-115	29
α-helix	123-156	34
α-helix	158-163	6
α-helix	164-181	18
α-helix	185-189	5
β-strand	191-192	2	14
β-strand	204-205	2	14
α-helix	213-224	12
α-helix	225-229	5
α-helix	230-247	18
α-helix	269-303	35
α-helix	306-309	4
α-helix	315-321	7
α-helix	323-337	15

Chain S: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	9
β-strand	9-11	3	10
β-strand	17-24	8	9
α-helix	28-30	3
β-strand	32-38	7	10
β-strand	44-50	7	10
α-helix	52-54	3
β-strand	57-59	3	10
β-strand	64	1	9
β-strand	67-72	6	9
β-strand	77-82	6	9
α-helix	87-89	3
β-strand	91-98	8	10
β-strand	110	1	10
β-strand	114-118	5	10
β-strand	140-142	3	11
β-strand	146-148	3	12
β-strand	155-161	7	11
β-strand	166	1	13
β-strand	172	1	13
β-strand	174-179	6	12
β-strand	186-189	4	12
α-helix	194	1
β-strand	195	1	12
α-helix	196	1
β-strand	203-207	5	11
β-strand	211-216	6	11
α-helix	221-223	3
β-strand	225-231	7	12
β-strand	239	1	12
β-strand	243-246	4	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
Gonadoliberin-1	C	protein	11	synthetic construct	Q28588 (AlphaFold model)
Guanine nucleotide-binding protein G(q) subunit alpha-1	A	protein	246	Homo sapiens
scFv16	S	protein	285	Homo sapiens
Beta-2 adrenergic receptor,Gonadotropin-releasing hormone receptor	R	protein	504	Ateles, Xenopus laevis	P07550 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9U4Y_1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
GSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLA
KIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGG
LDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQ
TTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFP
NGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNV
WDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 2 (G), FASTA

>9U4Y_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 3 (C), FASTA

>9U4Y_3 Gonadoliberin-1 (chains C)
QHWSYGLRPGX

Sequence of entity 4 (A), FASTA

>9U4Y_4 Guanine nucleotide-binding protein G(q) subunit alpha-1 (chains A)
MGSTVSAEDKAAAERSKMIDKNLREDGEKARRTLRLLLLGADNSGKSTIVKQMRILHGGS
GGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWIQCFNDVTAIIFVVDSSDYNRLQE
ALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEP
GEDPRVTRAKYFIRKEFVDISTASGDGRHICYPHFTCAVDTENARRIFNDCKDIILQMNL
REYNLV

Sequence of entity 5 (S), FASTA

>9U4Y_5 scFv16 (chains S)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAVQLVESGGGLVQPGGSRKLSCS
ASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQM
TSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSAGGGGSGGGGSGGGGSADIVMTQ
ATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDR
FSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLEL

Sequence of entity 6 (R), FASTA

>9U4Y_6 Beta-2 adrenergic receptor,Gonadotropin-releasing hormone receptor (chains R)
MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSDYKDDDDVHHHHHHHHDMGQPGNGSAFLLA
PNGSHAPDHDVTQQRDEENLYFQGASMLTMSYQGIMDSQDLCALNRSCFHLKEQEKTYGP
NITVLNDKAFILPTFSTAAKIRVAITCVLFIFSACFNIAALWTITYKYKKKSHIRILIIN
LVAADLFITLVVMPLDAVWNVTLQWYAGDLACRVLMFLKLAAMYSSAFVTVVISLDRQAA
ILNPLGIGDAKKKNKIMLCVAWFLSYLLAIPQLFVFHTVSRSEPIHFVQCATVGSFQAHW
QETIYNMFTFFCLFLLPLLIMVSCYTRILMEISHKMKATCVSSKEIDLRRSSNNIPRARM
RTLKMSLVIVLTFIVCWTPYYLLGIWYWFSPEMLTEEKVPPSLSHILFLFGLLNTCLDPI
IYGLFTIHFRREIRRVCRCAAQGKDHDTASVGTGSFRITTTPAPIKRTVGVLGGSGKFEL
EVTGHGLHSGKCDQCQGRIVESFM

Primary citation

Cryo-EM structures of GnRHR: Foundations for next-generation therapeutics. Shen, S., He, X., Liu, H. et al. Proc Natl Acad Sci U S A (2025) 122:e2500112122-e2500112122. DOI 10.1073/pnas.2500112122 · 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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