8P13: Rhodopsin-Gi

Cryo-EM structure of Rhodopsin-Gi bound with antibody fragments scFv16 and Fab79, conformation 1. Determined by electron microscopy at 5.2 Å resolution. Released 20 Nov 2024.

Method: Electron microscopy
Resolution: 5.2 Å
Organisms: Bos taurus, Homo sapiens, Mus musculus
Chains: 7
Atoms: 12,902
Mol. weight: 210.33 kDa
Released: 20 Nov 2024

Explore 8P13 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8P13 contains 57 α-helices and 103 β-strands across 7 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: 18 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-29	18
β-strand	34-38	5	3
α-helix	46-57	12
α-helix	63-67	5
α-helix	70-91	22
α-helix	100-110	11
α-helix	121-132	12
α-helix	134-140	7
α-helix	143-145	3
α-helix	152-157	6
α-helix	159-163	5
α-helix	171-176	6
β-strand	186-187	2	3
β-strand	190-191	2	4
β-strand	194-195	2	4
β-strand	196-200	5	3
α-helix	208-211	4
β-strand	220-222	3	3
β-strand	223-226	4	5
α-helix	243-254	12
α-helix	257-259	3
β-strand	266-269	4	5
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-308	13
α-helix	332-348	17

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	30-34	5
α-helix	38-39	2
β-strand	47-50	4	6
β-strand	58-63	6	7
β-strand	69-74	6	7
β-strand	78-83	6	7
β-strand	88-94	7	7
α-helix	95	1
β-strand	103-105	3	8
β-strand	111-114	4	8
β-strand	121-125	5	8
β-strand	137-139	3	8
β-strand	146-151	6	9
β-strand	156-161	6	9
β-strand	166-170	5	9
β-strand	175-180	6	9
β-strand	187-192	6	10
β-strand	198-203	6	10
β-strand	207-212	6	10
β-strand	217-222	6	10
β-strand	229-234	6	11
β-strand	240-245	6	11
β-strand	250-254	5	11
β-strand	259-264	6	11
β-strand	273-278	6	12
β-strand	284-289	6	12
β-strand	294-298	5	12
β-strand	304-308	5	12
β-strand	315-320	6	6
β-strand	327-331	5	6
β-strand	336-339	4	6

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	33-45	13
α-helix	59-61	3

Chain H: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	18
β-strand	30-31	2	19
β-strand	37-44	8	18
β-strand	53-58	6	20
β-strand	64-70	7	20
β-strand	77-78	2	20
β-strand	88-92	5	18
β-strand	97-102	6	18
α-helix	107-109	3
β-strand	111-117	7	20
α-helix	120-122	3
β-strand	130-132	3	20
β-strand	133-134	2	19
β-strand	140	1	21
α-helix	141-142	2
β-strand	143-147	5	22
β-strand	160-168	9	22
β-strand	169	1	21
α-helix	172	1
β-strand	174-177	4	23
β-strand	182	1	23
β-strand	186-188	3	22
α-helix	189-191	3
β-strand	192-194	3	22
β-strand	197-205	9	22
β-strand	217-222	6	23
β-strand	227-232	6	23

Chain L: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	25-27	3	24
β-strand	39-44	6	24
β-strand	58-63	6	25
α-helix	64	1
β-strand	70-74	5	25
β-strand	78-79	2	25
β-strand	88-92	5	24
β-strand	95-100	6	24
α-helix	105-107	3
β-strand	109-115	7	25
β-strand	127-129	3	25
β-strand	139-143	5	26
α-helix	144-146	3
α-helix	147-151	5
β-strand	154-164	11	26
β-strand	169-175	7	27
β-strand	178-180	3	27
β-strand	184-188	5	26
β-strand	198-207	10	26
α-helix	208-213	6
β-strand	217-223	7	27
β-strand	230-234	5	27

Chain R: 17 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	10-11	2	1
α-helix	34-64	31
α-helix	66-68	3
α-helix	71-73	3
α-helix	74-85	12
α-helix	86-92	7
α-helix	93-98	6
α-helix	106-140	35
α-helix	150-168	19
α-helix	170-172	3
β-strand	178-181	4	2
β-strand	186-189	4	2
α-helix	200-208	9
α-helix	209-213	5
α-helix	214-236	23
α-helix	241-277	37
α-helix	285-288	4
α-helix	290-296	7
α-helix	298-303	6
α-helix	304-308	5

Chain S: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	13
β-strand	10-12	3	14
β-strand	18-25	8	13
α-helix	29-31	3
β-strand	33-39	7	14
β-strand	45-51	7	14
β-strand	58-60	3	14
α-helix	62-64	3
β-strand	69-73	5	13
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	92-99	8	14
β-strand	110-111	2	14
β-strand	115-119	5	14
α-helix	138-139	2
β-strand	140-141	2	15
β-strand	146-149	4	16
β-strand	155-161	7	15
β-strand	166	1	17
β-strand	172	1	17
β-strand	174-179	6	16
β-strand	186-190	5	16
β-strand	194-195	2	16
α-helix	196	1
β-strand	203-208	6	15
β-strand	211-216	6	15
α-helix	221-223	3
β-strand	225-231	7	16
α-helix	237	1
β-strand	238-239	2	16
β-strand	243-247	5	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rhodopsin	R	protein	348	Bos taurus	P02699 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	376	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)
single-chain Fv 16	S	protein	259	Mus musculus
Immunoglobin G heavy chain FAB fragment	H	protein	262	Mus musculus
Immunoglobin G light chain	L	protein	239	Mus musculus

Sequence of entity 1 (R), FASTA

>8P13_1 Rhodopsin (chains R)
MCGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLY
VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG
GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP
EGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQES
ATTQKAEKEVTRMVIIYVIAFLICWLPYAGVAFYIFTHQGSCFGPIFMTIPAFFAKTSAV
YNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA

Sequence of entity 2 (A), FASTA

>8P13_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MKKHHHHHHHHHHENLYFQGGSMGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLL
LGAGESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDS
ARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLND
LDRIAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGV
TAIIFCVALSDYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKI
KKSPLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDA
VTDVIIKNNLKDCGLF

Sequence of entity 3 (B), FASTA

>8P13_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 (G), FASTA

>8P13_4 Guanine nucleotide-binding protein G(T) subunit gamma-T1 (chains G)
MPVINIEDLTEKDKLKMEVDQLKKEVTLERMLVSKCCEEFRDYVEERSGEDPLVKGIPED
KNPFKELKGGCVIS

Sequence of entity 5 (S), FASTA

>8P13_5 single-chain Fv 16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAHHHHHHHH

Sequence of entity 6 (H), FASTA

>8P13_6 Immunoglobin G heavy chain FAB fragment (chains H)
MNFVLSLIFLALILKGVQCEVQLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQTP
EKRLEWVATISSRGLYTYFPDSMKGRFTISRDNAKNTLSLQMSSLRSEDTAMYYCLRGGG
YDADYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSG
SLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPTI
KPCPPCKCPAPNLLGGPSVFIF

Sequence of entity 7 (L), FASTA

>8P13_7 Immunoglobin G light chain (chains L)
MMSPAQFLFLLVLWIRETNGDVVMTQTPLTLSVTIGQPASISCKSSQSLLDSDGETSLNW
LLQRPGQSPKRLIYLVSKLDSGVPDRFTGSGSGTDFTLKISRVEAADLGVYYCWQGTHFP
LTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSER
QNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Primary citation

Tool antibody fragments reveal multiple conformations of the rhodopsin-Gi signaling complex. Pamula, F., Tejero, O., Muhle, J. et al. Biophys J (2025). DOI 10.1016/j.bpj.2025.09.044 · PubMed

Other PDB entries of the same protein (UniProt P02699 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7ZBC 1.8 Å, Dark state crystal structure of bovine rhodopsin in Lipidic Cubic Phase (SACLA)
7ZBE 1.8 Å, Dark state crystal structure of bovine rhodopsin in Lipidic Cubic Phase (SwissFEL)
8A6C 1.8 Å, 1 picosecond light activated crystal structure of bovine rhodopsin in Lipidic Cubic Phase
8A6D 1.8 Å, 10 picosecond light activated crystal structure of bovine rhodopsin in Lipidic Cubic Phase
8A6E 1.8 Å, 100 picosecond light activated crystal structure of bovine rhodopsin in Lipidic Cubic…
1U19 2.2 Å, Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution
4X1H 2.29 Å, Opsin/G(alpha) peptide complex stabilized by nonyl-glucoside
5DYS 2.3 Å, Crystal Structure of T94I rhodopsin mutant
6FK6 2.36 Å, Crystal structure of N2C/D282C stabilized opsin bound to RS01
6FKC 2.46 Å, Crystal structure of N2C/D282C stabilized opsin bound to RS15
6FKD 2.49 Å, Crystal structure of N2C/D282C stabilized opsin bound to RS16
1L9H 2.6 Å, Crystal structure of bovine rhodopsin at 2.6 angstroms RESOLUTION

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