6K42: Alpha2BAR-Gi1 complex

cryo-EM structure of alpha2BAR-Gi1 complex. Determined by electron microscopy at 4.1 Å resolution. Released 15 Apr 2020.

Method: Electron microscopy
Resolution: 4.1 Å
Organisms: Bos taurus, Mus musculus, Homo sapiens
Chains: 5
Atoms: 8,816
Mol. weight: 178.06 kDa
Ligands: CZX
Released: 15 Apr 2020

Explore 6K42 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6K42 contains 24 α-helices and 58 β-strands across 5 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: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	9-32	24
β-strand	36-39	4	1
β-strand	186-190	5	1
β-strand	195-199	5	1
α-helix	212-215	4
β-strand	220-225	6	1
α-helix	242-254	13
β-strand	263-268	6	1
α-helix	271-275	5
α-helix	296-308	13
β-strand	320-323	4	1
α-helix	333-350	18

Chain B: 2 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	4-14	11
α-helix	15-19	5
β-strand	49-51	3	2
β-strand	61-62	2	3
β-strand	69-73	5	3
β-strand	78-83	6	3
β-strand	89-94	6	3
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	121-125	5	4
β-strand	134-139	6	4
β-strand	146-151	6	5
β-strand	157-161	5	5
β-strand	166-169	4	5
β-strand	176-179	4	5
β-strand	190-192	3	6
β-strand	199-201	3	6
β-strand	209-211	3	6
β-strand	218-220	3	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	249-254	6	7
β-strand	262-265	4	7
β-strand	273-277	5	8
β-strand	285-289	5	8
β-strand	294-297	4	8
β-strand	304	1	8
β-strand	315-317	3	9
β-strand	320	1	10
β-strand	327	1	10
β-strand	328-329	2	2
β-strand	330-331	2	9
β-strand	336-338	3	2

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	10-21	12
α-helix	30-43	14
α-helix	56-58	3

Chain H: 0 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	11
β-strand	17-25	9	11
β-strand	33-39	7	12
β-strand	45-51	7	12
β-strand	58-60	3	12
β-strand	68-73	6	11
β-strand	78-84	7	11
β-strand	93-99	7	12
β-strand	116	1	12
β-strand	128-130	3	13
β-strand	135-136	2	14
β-strand	144	1	15
β-strand	147-149	3	13
β-strand	162-167	6	16
β-strand	174-177	4	16
β-strand	191-196	6	15
β-strand	199-204	6	15
β-strand	214-219	6	16
β-strand	226	1	16
β-strand	231-232	2	16
β-strand	233-234	2	14

Chain R: 13 helices, 0 β-strands

Element	Residues	Length
α-helix	13-28	16
α-helix	30-38	9
α-helix	49-73	25
α-helix	84-115	32
α-helix	118-121	4
α-helix	126-144	19
α-helix	170-177	8
α-helix	178-182	5
α-helix	183-201	19
α-helix	360-396	37
α-helix	407-416	10
α-helix	418-428	11
α-helix	431-441	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Bos taurus	P63097 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	350	Mus musculus	P62874 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
Alpha-2A adrenergic receptor,Endolysin,Alpha-2B adrenergic receptor,Alpha-2B adrenergic receptor	R	protein	512	Homo sapiens, Enterobacteria phage RB59	P08913 (AlphaFold model), P18089
scFv	H	protein	307	Mus musculus

Sequence of entity 1 (A), FASTA

>6K42_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>6K42_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
HHHHHHGSSGQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRT
LRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGN
YVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWD
IETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDIN
AICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYD
DFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>6K42_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (R), FASTA

>6K42_4 Alpha-2A adrenergic receptor,Endolysin,Alpha-2B adrenergic receptor,Alpha-2B adrenergic receptor (chains R)
DDDDAHHHHHHMGSLQPDAGNASWNGTEAPGGGARATPENLYFQGNIFEMLRIDEGLRLK
IYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVR
GILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKS
RWYNQTPNRAKRVITTFRTGTWDAYYSVQATAAIAAAITFLILFTIFGNALVILAVLTSR
SLRAPQNLFLVSLAAADILVATLIIPFSLANELLGYWYFRRTWCEVYLALDVLFCTSSIV
HLCAISLDRYWAVSRALEYNSKRTPRRIKCIILTVWLIAAVISLPPLIYKGDQGPQPRGR
PQCKLNQEAWYILASSIGSFFAPCLIMILVYLRIYLIAKRSNRRGPRAKGGPGQGEQWWR
RRAQLTREKRFTFVLAVVIGVFVLCWFPFFFSYSLGAICPKHCKVPHGLFQFFFWIGYCN
SSLNPVIYTIFNQDFRRAFRRILCRPWTQTAW

Sequence of entity 5 (H), FASTA

>6K42_5 scFv (chains H)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFADVQLVESGGGLVQPGGSRKLSC
SASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQ
MTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSSGGGGSGGGGSGGGGSDIVMTQ
ATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDR
FSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLELKGSLEVLFQGPAAAH
HHHHHHH

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

Activation of the alpha2Badrenoceptor by the sedative sympatholytic dexmedetomidine. Yuan, D., Liu, Z., Kaindl, J. et al. Nat Chem Biol (2020) 16:507-512. DOI 10.1038/s41589-020-0492-2 · PubMed

Other PDB entries of the same protein (UniProt P63097 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9XDR 2.58 Å, Cryo-EM structure of asimadoline-BMS-986187-bound KOR-Gi1 complex
9J5V 2.86 Å, Human Lysophosphatidic Acid Receptor 1-Gi complex bound to CpY
6NBF 3.0 Å, Cryo-EM structure of parathyroid hormone receptor type 1 in complex with a long-acting…
7D68 3.0 Å, Cryo-EM structure of the human glucagon-like peptide-2 receptor-Gs protein complex
9XHH 3.0 Å, Structure of the CCL19-CCR7-Gi-scFv16 complex
9XC6 3.04 Å, Cryo-EM structure of BMS-986187-bound MOR-Gi1 complex
8X17 3.19 Å, Cryo-EM structure of adenosine receptor A3AR bound to CF102
9XHI 3.2 Å, Structure of the CCL21-CCR7-Gi-scFv16 complex
9M54 3.24 Å, Cryo-EM structure of neuropeptide FF receptor 2 complex with NPVF
8X16 3.29 Å, Cryo-EM structure of adenosine receptor A3AR bound to CF101
7EQ1 3.3 Å, GPR114-Gs-scFv16 complex
6NBH 3.5 Å, Cryo-EM structure of parathyroid hormone receptor type 1 in complex with a long-acting…

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