9EPP: Jumping Spider Rhodopsin-1

Cryo-EM Structure of Jumping Spider Rhodopsin-1 bound to a Giq heterotrimer. Determined by electron microscopy at 4.06 Å resolution. Released 23 Oct 2024.

Method: Electron microscopy
Resolution: 4.06 Å
Organisms: Hasarius adansoni, Homo sapiens
Chains: 4
Atoms: 7,442
Mol. weight: 121.84 kDa
Ligands: A1H6M
Released: 23 Oct 2024

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

Secondary structure: helices and β-sheets

9EPP contains 29 α-helices and 38 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: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	5-31	27
β-strand	34-39	6	2
α-helix	46-52	7
β-strand	186-191	6	2
β-strand	194-199	6	2
α-helix	211-215	5
β-strand	221-225	5	2
α-helix	227-229	3
β-strand	233	1	3
β-strand	241	1	3
α-helix	242-254	13
β-strand	265-268	4	2
α-helix	273-279	7
α-helix	298-307	10
α-helix	308-310	3
β-strand	323	1	2
α-helix	328-351	24

Chain B: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
β-strand	47-51	5	4
β-strand	58-63	6	5
β-strand	69-74	6	5
β-strand	78-83	6	5
β-strand	89-94	6	5
β-strand	102-104	3	6
β-strand	111-115	5	6
β-strand	121-125	5	6
β-strand	135-139	5	6
β-strand	148-151	4	7
β-strand	156-160	5	7
β-strand	166-170	5	7
β-strand	175-180	6	7
β-strand	187-190	4	8
β-strand	198-203	6	8
β-strand	208-212	5	8
β-strand	217-222	6	8
β-strand	229-234	6	9
β-strand	240-245	6	9
β-strand	250-254	5	9
β-strand	259-264	6	9
β-strand	273-278	6	10
β-strand	284-289	6	10
β-strand	294-298	5	10
β-strand	304-308	5	10
β-strand	315-320	6	4
β-strand	327-331	5	4
β-strand	336-339	4	4

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	6-23	18
α-helix	30-43	14
α-helix	53-55	3
α-helix	60-62	3

Chain R: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	23-26	4
α-helix	29-34	6
α-helix	37-41	5
α-helix	47-77	31
α-helix	84-113	30
α-helix	120-152	33
α-helix	159-161	3
α-helix	163-181	19
α-helix	183-186	4
β-strand	191-193	3	1
β-strand	200-202	3	1
α-helix	209-220	12
α-helix	225-254	30
α-helix	270-301	32
α-helix	310-333	24
α-helix	336-345	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kumopsin1	R	protein	327	Hasarius adansoni	B1B1U5 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	352	Homo sapiens	P63096 (AlphaFold model)
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	60	Homo sapiens	P59768 (AlphaFold model)

Sequence of entity 1 (R), FASTA

>9EPP_1 Kumopsin1 (chains R)
NISIVDLLPEDMLPMIHEHWYKFPPMETSMHYILGMLIIVIGIISVSGNGVVMYLMMTVK
NLRTPGNFLVLNLALSDFGMLFFMMPTMSINCFAETWVIGPFMCELYGMIGSLFGSASIW
SLVMITLDRYNVIVKGMAGKPLTKVGALLRMLFVWIWSLGWTIAPMYGWSRYVPEGSMTS
CTIDYIDTAINPMSYLIAYAIFVYFVPLFIIIYCYAFIVMQVAAHEKSLREQAKKMNIKS
LRSNEDNKKASAEFRLAKVAFMTICCWFMAWTPYLTLSFLGIFSDRTWLTPMTSVWGAIF
AKASACYNPIVYGISHPKYRAALHDKF

Sequence of entity 2 (A), FASTA

>9EPP_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
CTLSAEDKAAVERSKMIDRNLREDGEKARREVKLLLLGAGESGKSTIVKQMKIIHEAGYS
EEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAE
LAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTT
GIVETHFTFKSIHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNR
MHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAY
IQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFCAVKDTILQNNLKECNLV

Sequence of entity 3 (B), FASTA

>9EPP_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
SELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAM
HWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNIC
SIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFT
GHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAF
ATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALK
ADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (G), FASTA

>9EPP_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
NTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREK

Ligands and cofactors

ID	Name	Formula	Copies
A1H6M	11,20-Ethanoretinal	C22 H30 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 B1B1U5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6I9K 2.15 Å, Crystal structure of Jumping Spider Rhodopsin-1 bound to 9-cis retinal
9EPQ 4.15 Å, Cryo-EM Structure of Jumping Spider Rhodopsin-1 bound to a Giq heterotrimer
9EPR 4.9 Å, Cryo-EM Structure of Jumping Spider Rhodopsin-1 bound to a Gi heterotrimer

Browse structure collections

About this viewer

MolViewer shows 9EPP 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.