9CBM: PDB entry 9CBM

Cryo-EM structure of dexmedetomidine-bound alpha-2A-adrenergic receptor in complex with heterotrimeric Gi-protein. Determined by electron microscopy at 3.2 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Rattus norvegicus, Bos taurus, Enterobacteria phage T4
Chains: 4
Atoms: 6,338
Mol. weight: 143.19 kDa
Ligands: CZX
Released: 11 Sept 2024

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

Secondary structure: helices and β-sheets

9CBM contains 34 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: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-31	20
β-strand	34-40	7	1
α-helix	46-52	7
β-strand	185-189	5	1
β-strand	196-200	5	1
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	227-231	5
β-strand	233	1	2
β-strand	241	1	2
α-helix	242-254	13
β-strand	264-269	6	1
α-helix	271-277	7
α-helix	283-286	4
α-helix	296-308	13
β-strand	319-322	4	1
α-helix	331-350	20

Chain B: 6 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	4-22	19
α-helix	23-25	3
α-helix	30-33	4
α-helix	34-36	3
α-helix	38-39	2
β-strand	43	1	3
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	91-94	4	5
β-strand	104-105	2	6
β-strand	111-113	3	6
β-strand	121-125	5	6
β-strand	134-139	6	6
β-strand	146-151	6	7
β-strand	157-161	5	7
β-strand	165-168	4	7
β-strand	178-181	4	7
β-strand	189-192	4	8
β-strand	198-202	5	8
β-strand	207-212	6	8
β-strand	218-223	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
α-helix	272-273	2
β-strand	276-277	2	10
β-strand	286-287	2	10
β-strand	295	1	10
β-strand	306	1	3
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	9-23	15
α-helix	30-43	14
α-helix	54-55	2
α-helix	56-58	3

Chain R: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	49-74	26
α-helix	84-99	16
α-helix	102-110	9
α-helix	133-138	6
α-helix	141-151	11
α-helix	153-157	5
α-helix	162-180	19
α-helix	212-219	8
α-helix	233-240	8
α-helix	386-401	16
α-helix	403-411	9
α-helix	412-414	3
α-helix	420-426	7
α-helix	429-440	12
α-helix	446-456	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	379	Rattus norvegicus	P10824 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	339	Bos taurus	P62871 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Bos taurus	P63212 (AlphaFold model)
Endolysin,Alpha-2A adrenergic receptor	R	protein	484	Enterobacteria phage T4, Homo sapiens	P00720, P08913

Sequence of entity 1 (A), FASTA

>9CBM_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGSSHHHHHHSSGLEVLFQGPHMASMGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVK
LLLLGAGESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDF
GDAARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYY
LNDLDRIAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCF
EGVTAIIFCVALSDYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFE
EKIKKSPLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFV
FDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>9CBM_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
SELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAM
HWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNIC
SIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFT
GHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAF
ATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALK
ADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>9CBM_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFSAIL

Sequence of entity 4 (R), FASTA

>9CBM_4 Endolysin,Alpha-2A adrenergic receptor (chains R)
MKTIIALSYIFCLVFADYKDDDDKNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSP
SLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRA
ALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGT
WDAYAAAGGGARATPYSLQVTLTLVCLAGLLMLLTVFGNVLVIIAVFTSRALKAPQNLFL
VSLASADILVATLVIPFSLANEVMGYWYFGKAWCEIYLALDVLFCTSSIVHLCAISLDRY
WSITQAIEYNLKRTPRRIKAIIITVWVISAVISFPPLISIEKKGGGGGPQPAEPRCEIND
QKWYVISSCIGSFFAPCLIMILVYVRIYQIAKRRTRQNREKRFTFVLAVVIGVFVVCWFP
FFFTYTLTAVGCSVPRTLFKFFFWFGYCNSSLNPVIYTIFNHDFRRAFKKILCRGDASLE
VLFQ

Ligands and cofactors

ID	Name	Formula	Copies
CZX	4-[(1~{S})-1-(2,3-dimethylphenyl)ethyl]-1~{H}-imidazole	C13 H16 N2	1

Primary citation

Distinct binding conformations of epinephrine with alpha- and beta-adrenergic receptors. Lou, J.S., Su, M., Wang, J. et al. Exp Mol Med (2024) 56:1952-1966. DOI 10.1038/s12276-024-01296-x · PubMed

Other PDB entries of the same protein (UniProt P10824 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1CIP 1.5 Å, Gi-alpha-1 subunit of guanine nucleotide-binding protein complexed with a GTP analogue
1SVS 1.5 Å, Structure of the K180P mutant of Gi alpha subunit bound to GppNHp.
4N0D 1.55 Å, Crystal structure of the K345L variant of the Gi alpha1 subunit bound to GTPgammaS
5KDO 1.9 Å, Heterotrimeric complex of the 4 alanine insertion variant of the Gi alpha1 subunit and…
1AS0 2.0 Å, GTP-gamma-S bound G42V GIA1
1GIA 2.0 Å, Structure of active conformations of GIA1 and the mechanism of GTP hydrolysis
1SVK 2.0 Å, Structure of the K180P mutant of Gi alpha subunit bound to AlF4 and GDP
4PAQ 2.0 Å, A conserved phenylalanine as relay between the 5 helix and the GDP binding region of…
4PAO 2.0 Å, A conserved phenylalanine as relay between the 5 helix and the GDP binding region of…
1FQJ 2.02 Å, Crystal structure of the heterotrimeric complex of the rgs domain of RGS9, the gamma…
6M8H 2.07 Å, Crystal Structure of the R208Q mutant of G(i) subunit alpha-1
1BH2 2.1 Å, A326S mutant of an inhibitory alpha subunit

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