8DD2: Human GABAA receptor alpha1-beta2-gamma2 subtype

Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus Zolpidem. Determined by electron microscopy at 2.9 Å resolution. Released 17 Aug 2022.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Homo sapiens, Mus musculus
Chains: 9
Atoms: 17,459
Mol. weight: 365.53 kDa
Ligands: NAG, R5R, ABU
Released: 17 Aug 2022

Explore 8DD2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DD2 contains 67 α-helices and 118 β-strands across 9 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: 12 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	11
α-helix	28	1
α-helix	35	1
β-strand	36-51	16	1
β-strand	56-68	13	1
α-helix	70-72	3
β-strand	81-83	3	1
α-helix	85-90	6
β-strand	96-98	3	2
β-strand	101-106	6	1
β-strand	110	1	3
β-strand	114-118	5	1
β-strand	123-135	13	1
β-strand	147-148	2	2
β-strand	151-156	6	2
β-strand	164-168	5	1
β-strand	175-176	2	1
β-strand	186-200	15	2
β-strand	203-216	14	2
α-helix	218-221	4
α-helix	222-226	5
α-helix	227-235	9
α-helix	238-241	4
α-helix	247-271	25
α-helix	280-308	29
α-helix	310-339	30

Chain B: 12 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	13-22	10
β-strand	39-54	16	4
β-strand	59-71	13	4
α-helix	73-75	3
β-strand	83-86	4	4
α-helix	89-93	5
β-strand	99-101	3	5
β-strand	104-109	6	4
β-strand	113	1	2
β-strand	117-122	6	4
β-strand	126-138	13	4
β-strand	150-159	10	5
β-strand	167-171	5	4
α-helix	175-177	3
β-strand	179-181	3	4
β-strand	186	1	4
β-strand	191-204	14	5
β-strand	209-221	13	5
α-helix	224-226	3
α-helix	227-231	5
α-helix	232-242	11
α-helix	243-246	4
α-helix	252-274	23
α-helix	283-284	2
α-helix	285-309	25
α-helix	315-346	32

Chain C: 12 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	11
α-helix	35	1
β-strand	36-51	16	6
β-strand	56-68	13	6
α-helix	70-72	3
α-helix	80	1
β-strand	81-83	3	6
α-helix	85-89	5
β-strand	96-98	3	7
β-strand	101-106	6	6
β-strand	110	1	5
β-strand	114-118	5	6
β-strand	123-135	13	6
α-helix	140-142	3
β-strand	147-156	10	7
β-strand	164-168	5	6
β-strand	175-176	2	6
β-strand	183	1	7
β-strand	186-200	15	7
β-strand	203-216	14	7
α-helix	218-221	4
α-helix	222-226	5
α-helix	227-241	15
α-helix	247-271	25
α-helix	280-304	25
α-helix	310-338	29

Chain D: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	13-23	11
β-strand	39-54	16	8
β-strand	59-71	13	8
α-helix	73-75	3
β-strand	83-86	4	8
α-helix	88-93	6
β-strand	99-101	3	9
β-strand	104	1	8
β-strand	108-109	2	8
β-strand	117-122	6	8
β-strand	126-138	13	8
β-strand	150-154	5	9
β-strand	157-159	3	9
β-strand	167-171	5	8
α-helix	175-177	3
β-strand	179-181	3	8
β-strand	186	1	8
β-strand	191-205	15	9
β-strand	208-221	14	9
α-helix	224-226	3
α-helix	227-231	5
α-helix	232-242	11
α-helix	243-246	4
α-helix	252-276	25
α-helix	285-310	26
α-helix	315-345	31

Chain E: 11 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	26-35	10
α-helix	43	1
α-helix	50	1
β-strand	51-62	12	10
β-strand	71-83	13	10
α-helix	85-87	3
β-strand	95-98	4	10
α-helix	100-102	3
β-strand	111-113	3	3
β-strand	116-121	6	10
β-strand	125	1	9
β-strand	129-134	6	10
β-strand	138-150	13	10
β-strand	162-166	5	3
β-strand	169-171	3	3
β-strand	179-182	4	10
β-strand	188-190	3	10
β-strand	201-215	15	3
β-strand	218-231	14	3
α-helix	234-236	3
α-helix	237-241	5
α-helix	242-252	11
α-helix	262-285	24
α-helix	295-323	29
α-helix	325-356	32

Chain I: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-12	3	12
β-strand	19-25	7	11
β-strand	33-38	6	12
β-strand	45-49	5	12
β-strand	53-54	2	12
α-helix	55	1
β-strand	62-66	5	11
β-strand	70-75	6	11
β-strand	85-90	6	12
β-strand	96-97	2	12
β-strand	101-104	4	12

Chain J: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	13
α-helix	7-9	3
β-strand	10-12	3	14
β-strand	18-25	8	13
α-helix	29-31	3
β-strand	34-39	6	14
β-strand	45-52	8	14
β-strand	57-60	4	14
β-strand	65	1	13
β-strand	68-73	6	13
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	92-98	7	14
β-strand	107-108	2	14
β-strand	112-116	5	14

Chain K: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	17
β-strand	10-12	3	18
β-strand	18-25	8	17
β-strand	34-39	6	18
β-strand	45-52	8	18
β-strand	57-60	4	18
α-helix	62-64	3
β-strand	65	1	19
β-strand	68	1	19
β-strand	69-73	5	17
β-strand	78-83	6	17
α-helix	88-90	3
β-strand	92-99	8	18
β-strand	105-108	4	18
β-strand	112-116	5	18

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gamma-aminobutyric acid receptor subunit beta-2	A, C	protein	364	Homo sapiens	P47870 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit alpha-1	B, D	protein	358	Homo sapiens	P14867 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit gamma-2	E	protein	417	Homo sapiens	P18507 (AlphaFold model)
Kappa Fab Light Chain	I, L	protein	213	Mus musculus
IgG2b Fab Heavy Chain	J, K	protein	454	Mus musculus

Sequence of entity 1 (A, C), FASTA

>8DD2_1 Gamma-aminobutyric acid receptor subunit beta-2 (chains A, C)
QSVNDPSNMSLVKETVDRLLKGYDIRLRPDFGGPPVAVGMNIDIASIDMVSEVNMDYTLT
MYFQQAWRDKRLSYNVIPLNLTLDNRVADQLWVPDTYFLNDKKSFVHGVTVKNRMIRLHP
DGTVLYGLRITTTAACMMDLRRYPLDEQNCTLEIESYGYTTDDIEFYWRGDDNAVTGVTK
IELPQFSIVDYKLITKKVVFSTGSYPRLSLSFKLKRNIGYFILQTYMPSILITILSWVSF
WINYDASAARVALGITTVLTMTTINTHLRETLPKIPYVKAIDMYLMGCFVFVFMALLEYA
LVNYIFFSQPARAAAIDRWSRIFFPVVFSFFNIVYWLYYVNVDGSGATNFSLLKQAGDVE
ENPG

Sequence of entity 2 (B, D), FASTA

>8DD2_2 Gamma-aminobutyric acid receptor subunit alpha-1 (chains B, D)
QPSLQDELKDNTTVFTRILDRLLDGYDNRLRPGLGERVTEVKTDIFVTSFGPVSDHDMEY
TIDVFFRQSWKDERLKFKGPMTVLRLNNLMASKIWTPDTFFHNGKKSVAHNMTMPNKLLR
ITEDGTLLYTMRLTVRAECPMHLEDFPMDAHACPLKFGSYAYTRAEVVYEWTREPARSVV
VAEDGSRLNQYDLLGQTVDSGIVQSSTGEYVVMTTHFHLKRKIGYFVIQTYLPCIMTVIL
SQVSFWLNRESVPARTVFGVTTVLTMTTLSISARNSLPKVAYATAMDWFIAVCYAFVFSA
LIEFATVNYFTKSQPARAAKIDRLSRIAFPLLFGIFNLVYWATYLNREPQLKAPTPHQ

Sequence of entity 3 (E), FASTA

>8DD2_3 Gamma-aminobutyric acid receptor subunit gamma-2 (chains E)
WSHPQFEKGGGSGGGSGGSSAWSHPQFEKLEVLFQGPQKSDDDYEDYASNKTWVLTPKVP
EGDVTVILNNLLEGYDNKLRPDIGVKPTLIHTDMYVNSIGPVNAINMEYTIDIFFAQTWY
DRRLKFNSTIKVLRLNSNMVGKIWIPDTFFRNSKKADAHWITTPNRMLRIWNDGRVLYTL
RLTIDAECQLQLHNFPMDEHSCPLEFSSYGYPREEIVYQWKRSSVEVGDTRSWRLYQFSF
VGLRNTTEVVKTTSGDYVVMSVYFDLSRRMGYFTIQTYIPCTLIVVLSWVSFWINKDAVP
ARTSLGITTVLTMTTLSTIARKSLPKVSYVTAMDLFVSVCFIFVFSALVEYGTLHYFVSS
QPARAAKMDSYARIFFPTAFCLFNLVYWVSYLYLSRGSGATNFSLLKQAGDVEENPG

Sequence of entity 4 (I, L), FASTA

>8DD2_4 Kappa Fab Light Chain (chains I, L)
NIVMTQSPKSMSMSVGERVTLSCKASEYVGTYVSWYQQKPEQSPKLLIYGASNRYTGVPD
RFTGSGSATDFTLTIGSVQAEDLADYHCGQSYSYPTFGAGTKLELKRADAAPTVSIFPPS
SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTL
TKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 5 (J, K), FASTA

>8DD2_5 IgG2b Fab Heavy Chain (chains J, K)
EVQLQQSGAELVKPGASVKLSCTASGFNIKDTYMYWVKQRPEQGLEWIGRIDPANGDTKY
DPKFQGKATITTDTFSNTAYLQLSSLTSEDTAVYYCARKGLRWAMDYWGQGTSVTVSTAK
TTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLY
TMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTINPCPPCKECHKCPAPN
LEGGPSVFIFPPNIKDVLMISLTPKVTCVVVDVSEDDPDVQISWFVNNVEVHTAQTQTHR
EDYNSTIRVVSTLPIQHQDWMSGKEFKCKVNNKDLPSPIERTISKIKGLVRAPQVYILPP
PAEQLSRKDVSLTCLVVGFNPGDISVEWTSNGHTEENYKDTAPVLDSDGSYFIYSKLNMK
TSKWEKTDSFSCNVRHEGLKNYYLKKTISRSPGK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
R5R	Zolpidem	C19 H21 N3 O	3
ABU	Gamma-amino-butanoic acid	C4 H9 N O2	2

Primary citation

Structural and dynamic mechanisms of GABA A receptor modulators with opposing activities. Zhu, S., Sridhar, A., Teng, J. et al. Nat Commun (2022) 13:4582-4582. DOI 10.1038/s41467-022-32212-4 · PubMed

Other PDB entries of the same protein (UniProt P47870 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6X3T 2.55 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus propofol
8VRN 2.57 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus PPTQ
8SGO 2.65 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus pregnenolone…
8SID 2.71 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus…
8VQY 2.82 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus methaqualone
6X40 2.86 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus picrotoxin
8DD3 2.9 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus DMCM
9CRS 2.9 Å, Native human GABAA receptor of beta2-alpha1-beta2-alpha1-gamma2 assembly
6X3X 2.92 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus diazepam
9DRX 2.95 Å, Human GABAA receptor of beta2-alpha1-beta2-alpha1-gamma2 subtype in complex with GABA…
8SI9 2.98 Å, Human GABAA receptor alpha1-beta2-gamma2 subtype in complex with GABA plus…
7T0W 3.0 Å, Complex of GABA-A synaptic receptor with autoimmune antibody Fab115

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