9D4Z: PAR1 with endogenous tethered ligand

CryoEM structure of PAR1 with endogenous tethered ligand. Determined by electron microscopy at 2.74 Å resolution. Released 7 May 2025.

Method: Electron microscopy
Resolution: 2.74 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 8,267
Mol. weight: 155.46 kDa
Released: 7 May 2025

Explore 9D4Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D4Z contains 40 α-helices and 64 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, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-37	25
β-strand	40-46	7	15
α-helix	52-54	3
β-strand	189-191	3	15
β-strand	194-196	3	15
β-strand	199-206	8	15
α-helix	216-220	5
β-strand	225-231	7	15
α-helix	235-249	15
α-helix	252-254	3
β-strand	258-264	7	15
α-helix	266-275	10
α-helix	280-283	4
α-helix	285-289	5
α-helix	304-324	21
β-strand	331-332	2	15
β-strand	335	1	15
α-helix	343-362	20

Chain B: 1 helix, 28 β-strands

Element	Residues	Length	Sheet
β-strand	47-51	5	1
β-strand	60-63	4	2
β-strand	69-73	5	2
β-strand	78-83	6	2
β-strand	88-94	7	2
β-strand	100-105	6	3
β-strand	111-116	6	3
β-strand	120-125	6	3
β-strand	134-140	7	3
β-strand	146-151	6	4
β-strand	156-161	6	4
β-strand	166-170	5	4
β-strand	175-180	6	4
β-strand	187-192	6	5
β-strand	198-203	6	5
β-strand	207-212	6	5
β-strand	218-223	6	5
β-strand	229-234	6	6
β-strand	240-245	6	6
β-strand	249-254	6	6
α-helix	255-257	3
β-strand	259-264	6	6
β-strand	273-278	6	7
β-strand	284-289	6	7
β-strand	294-298	5	7
β-strand	304-308	5	7
β-strand	315-320	6	1
β-strand	327-331	5	1
β-strand	336-339	4	1

Chain E: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	10-12	3	12
β-strand	17-25	9	11
α-helix	29-31	3
β-strand	33-39	7	12
β-strand	45-51	7	12
α-helix	53-55	3
β-strand	58-60	3	12
β-strand	68-73	6	11
α-helix	74-76	3
β-strand	78-84	7	11
α-helix	88-90	3
β-strand	92-99	8	12
β-strand	111	1	12
β-strand	115-119	5	12
β-strand	141	1	13
β-strand	146	1	14
β-strand	155-160	6	13
β-strand	174-179	6	14
β-strand	186-190	5	14
β-strand	194-195	2	14
β-strand	203-208	6	13
β-strand	211-216	6	13
β-strand	226-231	6	14
α-helix	237	1
β-strand	239	1	14
β-strand	243-244	2	14

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	36-43	8
α-helix	45-47	3
α-helix	53-55	3

Chain R: 21 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	43-45	3	8
β-strand	46	1	9
β-strand	87	1	9
α-helix	90-96	7
α-helix	99	1
α-helix	100-104	5
α-helix	105-125	21
α-helix	126-130	5
α-helix	136-153	18
α-helix	155-163	9
α-helix	172-205	34
α-helix	207-213	7
α-helix	216-233	18
α-helix	235-239	5
β-strand	244-245	2	10
β-strand	252-253	2	10
β-strand	257-259	3	8
α-helix	260-262	3
α-helix	263-267	5
α-helix	268-275	8
α-helix	276-280	5
α-helix	281-298	18
α-helix	300-303	4
α-helix	309-338	30
α-helix	343-359	17
α-helix	360-362	3
α-helix	363-371	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	339	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	59	Homo sapiens	P59768 (AlphaFold model)
Proteinase-activated receptor 1	R	protein	384	Homo sapiens	P25116 (AlphaFold model)
scFv16	E	protein	251	Mus musculus
Guanine nucleotide-binding protein G(q) subunit alpha chimera	A	protein	360	Homo sapiens

Sequence of entity 1 (B), FASTA

>9D4Z_1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
SELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAM
HWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNIC
SIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFT
GHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAF
ATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALK
ADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 2 (G), FASTA

>9D4Z_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
NTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFRE

Sequence of entity 3 (R), FASTA

>9D4Z_3 Proteinase-activated receptor 1 (chains R)
SFLLRNPNDKYEPFWEDEEKNESGLTEYRLVSINKSSPLQKQLPAFISEDASGYLTSSWL
TLFVPSVYTGVFVVSLPLNIMAIVVFILKMKVKKPAVVYMLHLATADVLFVSVLPFKISY
YFSGSDWQFGSELCRFVTAAFYCNMYASILLMTVISIDRFLAVVYPMQSLSWRTLGRASF
TCLAIWALAIAGVVPLLLKEQTIQVPGLNITTCHDVLNETLLEGYYAYYFSAFSAVFFFV
PLIISTVCYVSIIRCLSSSAVANRSKKSRALFLSAAVFCIFIICFGPTNVLLIAHYSFLS
HTSTTEAAYFAYLLCVCVSSISCCIDPLIYYYASSECQRYVYSILCCKESSDPSSYNSSG
QLMASKMDTCSSNLNNSIYKKLLT

Sequence of entity 4 (E), FASTA

>9D4Z_4 scFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAA

Sequence of entity 5 (A), FASTA

>9D4Z_5 Guanine nucleotide-binding protein G(q) subunit alpha chimera (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKARRELKLLLLGTGESGKSTFIKQMRIIHGSG
YSDEDKRGFTKLVYQNIFTAMQAMIRAMDTLKIPYKYEHNKAHAQLVREVDVEKVSAFEN
PYVDAIKSLWNDPGIQECYDRRREYQLSDSTKYYLNDLDRVADPAYLPTQQDVLRVRVPT
TGIIEYPFDLQKVNFHMFDVGGQRSERRKWIQCFNDVTAIIFVVDSSDYNRLQEALNDFK
SIWNNRWLRTISVILFLNKQDLLAEKVLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRV
TRAKYFIRKEFVDISTASGDGRHICYPHFTCAVDTENARRIFNDCKDIILQMNLREYNLV

Primary citation

Structural basis for the activation of proteinase-activated receptors PAR1 and PAR2. Lyu, Z., Lyu, X., Malyutin, A.G. et al. Nat Commun (2025) 16:3931-3931. DOI 10.1038/s41467-025-59138-x · 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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