8XGM: Human GPR1

Cryo-EM structure of human GPR1 bound to chemerin. Determined by electron microscopy at 3.29 Å resolution. Released 21 Aug 2024.

Method: Electron microscopy
Resolution: 3.29 Å
Organisms: Vicugna pacos, Homo sapiens
Chains: 6
Atoms: 10,319
Mol. weight: 162.36 kDa
Ligands: CLR
Released: 21 Aug 2024

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

Secondary structure: helices and β-sheets

8XGM contains 38 α-helices and 75 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: 17 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	6
α-helix	36-60	25
α-helix	61-65	5
α-helix	71-88	18
α-helix	90-98	9
α-helix	107-140	34
α-helix	142-146	5
α-helix	151-169	19
α-helix	172-175	4
β-strand	176-180	5	7
β-strand	185-189	5	7
α-helix	199-211	13
α-helix	212-216	5
α-helix	217-236	20
α-helix	249-268	20
α-helix	269-272	4
α-helix	280-283	4
α-helix	286-301	16
α-helix	302-306	5
α-helix	309-317	9

Chain B: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-32	3
β-strand	47-51	5	8
β-strand	58-63	6	9
β-strand	69-74	6	9
β-strand	78-83	6	9
β-strand	89-94	6	9
β-strand	100-105	6	10
β-strand	111-116	6	10
β-strand	120-125	6	10
β-strand	135-140	6	10
β-strand	146-151	6	11
β-strand	157-161	5	11
β-strand	165-168	4	11
β-strand	178-181	4	11
β-strand	187	1	12
β-strand	191-192	2	13
β-strand	198-202	5	13
β-strand	203	1	12
β-strand	207-212	6	13
β-strand	218-223	6	13
β-strand	229-234	6	14
β-strand	240-245	6	14
β-strand	250-254	5	14
β-strand	260-264	5	14
β-strand	273-278	6	15
α-helix	280-282	3
β-strand	284-289	6	15
β-strand	294-298	5	15
β-strand	304-308	5	15
β-strand	315-320	6	8
β-strand	327-332	6	8
β-strand	334-339	6	8

Chain C: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-29	23
β-strand	34-40	7	16
α-helix	46-52	7
β-strand	184-191	8	16
β-strand	194-201	8	16
β-strand	220-226	7	16
β-strand	233	1	17
α-helix	234	1
β-strand	241	1	17
α-helix	242-253	12
β-strand	263-269	7	16
α-helix	271-278	8
α-helix	300-308	9
β-strand	319	1	16
β-strand	322-323	2	16
α-helix	330-350	21

Chain D: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	27-40	14	6
β-strand	43-54	12	6
β-strand	55	1	18
α-helix	67-68	2
β-strand	69	1	18
β-strand	75-84	10	6
α-helix	86-88	3
β-strand	90-96	7	6
α-helix	106-119	14
β-strand	121	1	19
β-strand	124	1	19

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	9-22	14
α-helix	30-43	14
α-helix	45-47	3
α-helix	54-55	2

Chain S: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-12	3	2
β-strand	17-24	8	1
β-strand	33-39	7	2
β-strand	45-51	7	2
β-strand	58-60	3	2
β-strand	65	1	1
β-strand	68-73	6	1
β-strand	78-84	7	1
α-helix	88-90	3
β-strand	92-99	8	2
β-strand	110-111	2	2
β-strand	115-119	5	2
α-helix	137-139	3
β-strand	140-141	2	3
β-strand	146-148	3	4
β-strand	155-161	7	3
β-strand	166	1	5
β-strand	172	1	5
β-strand	174-179	6	4
β-strand	186-190	5	4
β-strand	194-195	2	4
α-helix	196	1
β-strand	203-208	6	3
β-strand	211-216	6	3
β-strand	225-231	7	4
β-strand	239	1	4
β-strand	243-246	4	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
scFV16	S	protein	247	Vicugna pacos
G-protein coupled receptor 1	A	protein	306	Homo sapiens	P46091 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	340	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	C	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein subunit gamma	G	protein	55	Homo sapiens	P59768 (AlphaFold model)
Retinoic acid receptor responder protein 2	D	protein	137	Homo sapiens	Q99969

Sequence of entity 1 (S), FASTA

>8XGM_1 scFV16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Sequence of entity 2 (A), FASTA

>8XGM_2 G-protein coupled receptor 1 (chains A)
NYSYDLDYYSLESDLEEKVQLGVVHWVSLVLYCLAFVLGIPGNAIVIWFTGFKWKKTVTT
LWFLNLAIADFIFLLFLPLYISYVAMNFHWPFGIWLCKANSFTAQLNMFASVFFLTVISL
DHYIHLIHPVLSHRHRTLKNSLIVIIFIWLLASLIGGPALYFRDTVEFNNHTLCYNNFQK
HDPDLTLIRHHVLTWVKFIIGYLFPLLTMSICYLCLIFKVKKRSILISSRHFWTILVVVV
AFVVCWTPYHLFSIWELTIHHNSYSHHVMQAGIPLSTGLAFLNSCLNPILYVLISKKFQA
RFRSSV

Sequence of entity 3 (B), FASTA

>8XGM_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (C), FASTA

>8XGM_4 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains C)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 5 (G), FASTA

>8XGM_5 Guanine nucleotide-binding protein subunit gamma (chains G)
SIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFR

Sequence of entity 6 (D), FASTA

>8XGM_6 Retinoic acid receptor responder protein 2 (chains D)
ELTEAQRRGLQVALEEFHKHPPVQWAFQETSVESAVDTPFPAGIFVRLEFKLQQTSCRKR
DWKKPECKVRPNGRKRKCLACIKLGSEDKVLGRLVHCPIETQVLREAEEHQETQCLRVQR
AGEDPHSFYFPGQFAFS

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	1

Primary citation

Structure of G protein-coupled receptor GPR1 bound to full-length chemerin adipokine reveals a chemokine-like reverse binding mode. Liu, A., Liu, Y., Chen, G. et al. PLoS Biol (2024) 22:e3002838-e3002838. DOI 10.1371/journal.pbio.3002838 · PubMed

Other PDB entries of the same protein (UniProt P46091 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8JJP 2.9 Å, G protein-coupled receptor 1
9UYN 2.9 Å, Cryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to beta-arrestin 1 in…
9UYI 3.2 Å, Cryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to chemerin and…
9UYH 3.3 Å, Cryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to chemerin and…
9UYJ 3.3 Å, Cryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to chemerin and…
9UYL 3.3 Å, Cryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to chemerin and…
9UYM 3.5 Å, Composite map of the G protein-coupled receptor 1 (GPR1) bound to chemerin and…
9L3Y 3.6 Å, Cryo-EM structure of the G-protein coupled receptor 1 (GPR1) in complex with chemerin…

Browse structure collections

About this viewer

MolViewer shows 8XGM directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.