8P12: Rhodopsin-Gi

Cryo-EM structure of Rhodopsin-Gi bound to antibody fragment Fab13. Determined by electron microscopy at 3.21 Å resolution. Released 20 Nov 2024.

Method: Electron microscopy
Resolution: 3.21 Å
Organisms: Bos taurus, Homo sapiens, Mus musculus
Chains: 6
Atoms: 10,266
Mol. weight: 181.99 kDa
Released: 20 Nov 2024

Explore 8P12 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8P12 contains 45 α-helices and 86 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: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-32	28
β-strand	34-40	7	3
α-helix	46-57	12
β-strand	185-191	7	3
β-strand	194-200	7	3
α-helix	208-211	4
α-helix	212-215	4
β-strand	220-226	7	3
α-helix	227-229	3
α-helix	243-254	12
α-helix	257-260	4
β-strand	263-269	7	3
α-helix	271-278	8
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	3
α-helix	328-350	23

Chain B: 1 helix, 28 β-strands

Element	Residues	Length	Sheet
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	102-105	4	6
β-strand	111-115	5	6
β-strand	120-125	6	6
β-strand	134-140	7	6
β-strand	146-151	6	7
β-strand	156-161	6	7
β-strand	166-170	5	7
β-strand	176-180	5	7
β-strand	189-192	4	8
β-strand	198-202	5	8
β-strand	208-212	5	8
β-strand	221-222	2	8
β-strand	231-234	4	9
β-strand	240-244	5	9
β-strand	249-254	6	9
β-strand	260-265	6	9
β-strand	273-278	6	10
β-strand	284-289	6	10
β-strand	293-298	6	10
β-strand	303-309	7	10
β-strand	315-320	6	4
β-strand	327-331	5	4
β-strand	336-339	4	4

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	33-47	15
α-helix	48-50	3
α-helix	52-55	4

Chain H: 2 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	16
β-strand	30-31	2	17
β-strand	37-44	8	16
β-strand	52-58	7	18
β-strand	65-70	6	18
β-strand	76-78	3	18
β-strand	86-91	6	16
β-strand	96-101	6	16
α-helix	106-108	3
β-strand	110-117	8	18
β-strand	118	1	19
β-strand	124	1	19
β-strand	128	1	18
β-strand	132-134	3	18
β-strand	135-136	2	17
α-helix	139-141	3
β-strand	142	1	20
β-strand	146-149	4	21
β-strand	160-163	4	22
β-strand	164-170	7	21
β-strand	171	1	20
β-strand	176-179	4	23
β-strand	189-196	8	21
β-strand	199-205	7	21
β-strand	206-209	4	22
β-strand	219-224	6	23
β-strand	229-234	6	23

Chain L: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	11
β-strand	29-32	4	12
β-strand	39-44	6	11
β-strand	57-62	6	12
β-strand	69-73	5	12
β-strand	77-78	2	12
α-helix	79	1
β-strand	86-91	6	11
β-strand	94-99	6	11
α-helix	104-106	3
β-strand	108-114	7	12
α-helix	120	1
β-strand	121-122	2	12
β-strand	123	1	11
β-strand	126-130	5	12
β-strand	135	1	13
α-helix	136-137	2
β-strand	138-142	5	14
α-helix	143-145	3
α-helix	146-151	6
β-strand	154-163	10	14
β-strand	164	1	13
β-strand	169-174	6	15
β-strand	177-179	3	15
β-strand	183-184	2	14
β-strand	187	1	14
α-helix	189-191	3
β-strand	197-205	9	14
α-helix	207-211	5
β-strand	215-221	7	15
α-helix	228	1
β-strand	229-234	6	15

Chain R: 19 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	106-135	30
α-helix	136-140	5
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	285-289	5
α-helix	291-296	6
α-helix	298-303	6
α-helix	304-308	5
α-helix	311-316	6

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)
Immunoglobin G light chain	L	protein	238	Mus musculus
Immunoglobin G heavy chain FAB fragment	H	protein	258	Mus musculus

Sequence of entity 1 (R), FASTA

>8P12_1 Rhodopsin (chains R)
MCGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLY
VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG
GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP
EGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQES
ATTQKAEKEVTRMVIIYVIAFLICWLPYAGVAFYIFTHQGSCFGPIFMTIPAFFAKTSAV
YNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA

Sequence of entity 2 (A), FASTA

>8P12_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

>8P12_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

>8P12_4 Guanine nucleotide-binding protein G(T) subunit gamma-T1 (chains G)
MPVINIEDLTEKDKLKMEVDQLKKEVTLERMLVSKCCEEFRDYVEERSGEDPLVKGIPED
KNPFKELKGGCVIS

Sequence of entity 5 (L), FASTA

>8P12_5 Immunoglobin G light chain (chains L)
MKLPVRLLVLMFWIPASSSDVLMTQTPLSLPVSLGDQASISCRSSQIIVNRNGNTYLEWY
LQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISGVEAEDLGVYYCFQGSHVPW
TFGGGTQLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQ
NGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 6 (H), FASTA

>8P12_6 Immunoglobin G heavy chain FAB fragment (chains H)
MAVLVLFLCLVAFPSCVLSQVQLKESGPGLVAPSQSLSITCTVSGFSLTNYGVHWVRQPP
GKGLEWLGIIWAGGGTSYDSALMSRLSISKDNSKSQVFLKMNSLQSTDTAMYYCASENYS
YDRGFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWN
SGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC
GCKPCICTVPEVSSVFIF

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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