8ZQE: GPR15L(C11)-bound GPR15 complex

Cryo-EM structure of the GPR15L(C11)-bound GPR15 complex. Determined by electron microscopy at 2.9 Å resolution. Released 10 Jul 2024.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,767
Mol. weight: 217.87 kDa
Released: 10 Jul 2024

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

Secondary structure: helices and β-sheets

8ZQE contains 32 α-helices and 62 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: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-32	26
β-strand	34-40	7	1
α-helix	46-53	8
β-strand	185-190	6	1
β-strand	195-200	6	1
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	271-280	10
α-helix	296-309	14
β-strand	319	1	1
β-strand	323	1	1
α-helix	331-350	20

Chain B: 5 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-34	5
α-helix	38-39	2
β-strand	47-52	6	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
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	120-125	6	4
β-strand	134-135	2	4
β-strand	139-140	2	4
β-strand	146-151	6	5
β-strand	156-161	6	5
β-strand	165-170	6	5
β-strand	178-181	4	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	207-212	6	6
β-strand	218-222	5	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	249-254	6	7
β-strand	262-265	4	7
α-helix	272	1
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	304-307	4	8
α-helix	308-310	3
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	335-339	5	2

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-23	16
α-helix	30-43	14

Chain R: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	36-60	25
α-helix	67-84	18
α-helix	86-94	9
α-helix	103-136	34
α-helix	147-171	25
β-strand	175-177	3	15
β-strand	180-182	3	15
α-helix	190-200	11
α-helix	201-205	5
α-helix	206-228	23
α-helix	236-269	34
α-helix	278-287	10
α-helix	289-292	4
α-helix	293-304	12
α-helix	308-314	7

Chain S: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-12	3	10
β-strand	17-25	9	9
α-helix	29-31	3
β-strand	33-39	7	11
β-strand	45-51	7	11
β-strand	60	1	11
α-helix	62-64	3
β-strand	70-73	4	9
β-strand	78-84	7	9
α-helix	88-90	3
β-strand	92-94	3	10
β-strand	95-99	5	11
β-strand	111	1	11
β-strand	115-119	5	10
β-strand	128-130	3	12
β-strand	134-135	2	13
β-strand	144-149	6	12
β-strand	154	1	14
β-strand	160	1	14
β-strand	162-167	6	13
β-strand	173-177	5	13
β-strand	183	1	13
β-strand	192-195	4	12
β-strand	199-203	5	12
α-helix	209-211	3
β-strand	214-219	6	13
β-strand	231-233	3	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (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)/G(S)/G(O) subunit gamma-2	C	protein	97	Homo sapiens	P59768 (AlphaFold model)
scFv16	S	protein	279	Homo sapiens
GPR15	R	protein	881	Homo sapiens	P0ABE7 (AlphaFold model), P0AEX9, P49685
Protein GPR15LG	L	protein	10	Homo sapiens	Q6UWK7

Sequence of entity 1 (A), FASTA

>8ZQE_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVLIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>8ZQE_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (C), FASTA

>8ZQE_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MHHHHHHGGGSDSLEFIASKLAGGGSMASNNTASIAQARKLVEQLKMEANIDRIKVSKAA
ADLMAYCEAHAKEDPLLTPVPASENPFREKKFFCAIL

Sequence of entity 4 (S), FASTA

>8ZQE_4 scFv16 (chains S)
MVSAIVLYVLLAAAAHSAFADVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQA
PEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSI
YYYGSSPFDFWGQGTTLTVSSGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCR
SSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLE
AEDVGVYYCMQHLEYPLTFGAGTKLELKAAAHHHHHHHH

Sequence of entity 5 (R), FASTA

>8ZQE_5 GPR15 (chains R)
MKTIIALSYIFCLVFADYKDDDDAGRAADLEDNWETLNDNLKVIEKADNAAQVKDALTKM
RAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQ
LKTTRNAYIQKYLMDPEETSVYLDYYYATSPNSDIRETHSHVPYTSVFLPVFYTAVFLTG
VLGNLVLMGALHFKPGSRRLIDIFIINLAASDFIFLVTLPLWVDKEASLGLWRTGSFLCK
GSSYMISVNMHCSVLLLTCMSVDRYLAIVWPVVSRKFRRTDCAYVVCASIWFISCLLGLP
TLLSRELTLIDDKPYCAEKKATPIKLIWSLVALIFTFFVPLLSIVTCYCCIARKLCAHYQ
QSGKHNKKLKKSIKIIFIVVAAFLVSWLPFNTFKFLAIVSGLRQEHYLPSAILQLGMEVS
GPLAFANSCVNPFIYYIFDSYIRRAIVHCLCPCLKNYDFGSSTETSDSHLTKALSTFIHA
EDFARRRKRSVSLEFLEVLFQGPMAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKV
TVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWD
AVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPY
FTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEA
AFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKEL
AKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQ
MSAFWYAVRTAVINAASGRQTVDEALKDAQTHHHHHHHHHH

Sequence of entity 6 (L), FASTA

>8ZQE_6 Protein GPR15LG (chains L)
WVVPGALPQV

Primary citation

Molecular recognition of the atypical chemokine-like peptide GPR15L by its cognate receptor GPR15. Zhang, Z., Zheng, Y., Xu, L. et al. Cell Discov (2024) 10:69-69. DOI 10.1038/s41421-024-00698-5 · PubMed

Other PDB entries of the same protein (UniProt P63096 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
3UMR 2.04 Å, Crystal structure of the G202D mutant of human G-alpha-i1
9P7Z 2.1 Å, NTSR1-Gi-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
2OM2 2.2 Å, Crystal Structure Of Human G[alpha]i1 Bound To The Goloco Motif Of Rgs14
8YN9 2.3 Å, Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi
9HYI 2.3 Å, DP81-bound serotonin 5-HT1A receptor - Gi Protein Complex
9O36 2.3 Å, CryoEM structure of mu-opioid receptor - Gi protein complex bound to fluornitrazene (FNZ)
9P80 2.3 Å, NTSR1-Gi-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
8XXV 2.33 Å, Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
3UMS 2.34 Å, Crystal structure of the G202A mutant of human G-alpha-i1
3ONW 2.38 Å, Structure of a G-alpha-i1 mutant with enhanced affinity for the RGS14 GoLoco motif.
20ZG 2.4 Å, Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the…

Browse structure collections

About this viewer

MolViewer shows 8ZQE 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.