9EPR: Jumping Spider Rhodopsin-1

Cryo-EM Structure of Jumping Spider Rhodopsin-1 bound to a Gi heterotrimer. Determined by electron microscopy at 4.9 Å resolution. Released 30 Oct 2024.

Method: Electron microscopy
Resolution: 4.9 Å
Organisms: Homo sapiens, Bos taurus, Hasarius adansoni
Chains: 4
Atoms: 7,046
Mol. weight: 129.47 kDa
Ligands: RET
Released: 30 Oct 2024

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

Secondary structure: helices and β-sheets

9EPR contains 28 α-helices and 37 β-strands across 4 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, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	33-40	8	1
α-helix	46-53	8
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	205-207	3
β-strand	221-226	6	1
α-helix	242-254	13
β-strand	264-269	6	1
α-helix	271-277	7
α-helix	300-308	9
α-helix	314-316	3
α-helix	332-348	17

Chain B: 2 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	30-33	4
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	89-93	5	3
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	120-125	6	4
β-strand	137-140	4	4
β-strand	148-149	2	5
β-strand	156-160	5	5
β-strand	166-170	5	5
β-strand	176-180	5	5
β-strand	189	1	6
β-strand	198-202	5	6
β-strand	207-212	6	6
β-strand	218-223	6	6
β-strand	229	1	7
β-strand	234	1	8
β-strand	240-244	5	8
β-strand	245	1	7
β-strand	250-254	5	8
β-strand	260-263	4	8
α-helix	272-273	2
β-strand	276-278	3	9
β-strand	284-288	5	9
β-strand	294-298	5	9
β-strand	304-308	5	9
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	34-47	14
α-helix	48-50	3

Chain R: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	23-26	4
α-helix	52-77	26
α-helix	84-100	17
α-helix	103-106	4
α-helix	121-154	34
α-helix	163-182	20
α-helix	183-186	4
β-strand	191-193	3	10
β-strand	200-202	3	10
α-helix	209-219	11
α-helix	220-224	5
α-helix	225-254	30
α-helix	265-268	4
α-helix	271-301	31
α-helix	313-323	11
α-helix	326-333	8
α-helix	336-342	7
α-helix	345-348	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	357	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	340	Bos taurus	P62871 (AlphaFold model)
Guanine nucleotide-binding protein G(T) subunit gamma-T1	G	protein	74	Bos taurus	P02698 (AlphaFold model)
Kumopsin1	R	protein	380	Hasarius adansoni	B1B1U5 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9EPR_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
GGSMGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIH
EAGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEG
FMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRT
RVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAED
EEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYE
EAAAYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>9EPR_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 (G), FASTA

>9EPR_3 Guanine nucleotide-binding protein G(T) subunit gamma-T1 (chains G)
MPVINIEDLTEKDKLKMEVDQLKKEVTLERMLVSKCCEEFRDYVEERSGEDPLVKGIPED
KNPFKELKGGCVIS

Sequence of entity 4 (R), FASTA

>9EPR_4 Kumopsin1 (chains R)
MLPHAAKMAARVAGDHDGRNISIVDLLPEDMLPMIHEHWYKFPPMETSMHYILGMLIIVI
GIISVSGNGVVMYLMMTVKNLRTPGNFLVLNLALSDFGMLFFMMPTMSINCFAETWVIGP
FMCELYGMIGSLFGSASIWSLVMITLDRYNVIVKGMAGKPLTKVGALLRMLFVWIWSLGW
TIAPMYGWSRYVPEGSMTSCTIDYIDTAINPMSYLIAYAIFVYFVPLFIIIYCYAFIVMQ
VAAHEKSLREQAKKMNIKSLRSNEDNKKASAEFRLAKVAFMTICCWFMAWTPYLTLSFLG
IFSDRTWLTPMTSVWGAIFAKASACYNPIVYGISHPKYRAALHDKFPCLKCGSDSPKGDS
ASTVAESEKAGEETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
RET	Retinal	C20 H28 O	1

Primary citation

Active state structures of a bistable visual opsin bound to G proteins. Tejero, O., Pamula, F., Koyanagi, M. et al. Nat Commun (2024) 15:8928-8928. DOI 10.1038/s41467-024-53208-2 · 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…

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