6DW1: Gamma-aminobutyric acid receptor subunit gamma-2

Cryo-EM structure of the benzodiazepine-sensitive alpha1beta1gamma2S tri-heteromeric GABAA receptor in complex with GABA (ECD map). Determined by electron microscopy at 3.1 Å resolution. Released 8 Aug 2018.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Rattus norvegicus
Chains: 5
Atoms: 8,595
Mol. weight: 242.41 kDa
Ligands: ABU
Released: 8 Aug 2018

Explore 6DW1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6DW1 contains 23 α-helices and 84 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: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	14-22	9
α-helix	37	1
β-strand	38-43	6	12
β-strand	46-53	8	13
β-strand	58-63	6	13
β-strand	64-70	7	12
α-helix	72-74	3
β-strand	83-85	3	12
α-helix	87-90	4
β-strand	98-100	3	14
β-strand	103-106	4	13
β-strand	110	1	15
β-strand	114	1	15
β-strand	116-120	5	12
β-strand	125-131	7	12
β-strand	134-137	4	13
α-helix	142-144	3
β-strand	149-153	5	14
β-strand	156-158	3	14
β-strand	166-170	5	12
β-strand	180	1	13
β-strand	190-203	14	14
β-strand	208-220	13	14

Chain B: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
α-helix	35	1
β-strand	36-47	12	18
β-strand	51	1	18
β-strand	56-68	13	18
β-strand	82-83	2	18
α-helix	85-87	3
β-strand	96-98	3	19
β-strand	101-106	6	18
β-strand	114-117	4	18
β-strand	123-135	13	18
β-strand	150-156	7	19
β-strand	164-168	5	18
β-strand	175-176	2	18
α-helix	178-180	3
β-strand	190-199	10	19
β-strand	204-213	10	19

Chain C: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	13-18	6
α-helix	37	1
β-strand	38-49	12	6
α-helix	51-52	2
β-strand	53	1	6
β-strand	58-68	11	6
β-strand	70	1	7
β-strand	82-85	4	8
α-helix	90-92	3
β-strand	99-100	2	9
β-strand	103	1	6
α-helix	106	1
β-strand	107-108	2	6
α-helix	109	1
β-strand	110	1	10
β-strand	114	1	10
β-strand	116	1	6
β-strand	118-121	4	8
β-strand	125	1	7
β-strand	130-137	8	6
β-strand	149-157	9	9
β-strand	166-170	5	6
α-helix	174-176	3
β-strand	179-180	2	6
β-strand	185	1	6
β-strand	190-198	9	9
β-strand	201-203	3	11
β-strand	208-210	3	11
β-strand	211-220	10	9

Chain D: 2 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	26-32	7
β-strand	52-65	14	1
β-strand	71-83	13	1
α-helix	85-87	3
β-strand	95-98	4	1
β-strand	112-113	2	2
β-strand	120-121	2	1
β-strand	129-134	6	1
β-strand	138-150	13	1
β-strand	163	1	3
β-strand	166-167	2	4
β-strand	169-170	2	2
β-strand	180-183	4	1
β-strand	190-191	2	1
β-strand	205-208	4	4
β-strand	211-214	4	5
β-strand	219-222	4	5
β-strand	225-228	4	4
β-strand	229	1	3

Chain E: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	11-19	9
α-helix	35	1
β-strand	36-46	11	16
β-strand	51	1	16
β-strand	56-68	13	16
α-helix	70-72	3
β-strand	82-83	2	16
α-helix	85-87	3
β-strand	96-98	3	17
β-strand	101-106	6	16
β-strand	114-117	4	16
β-strand	123-135	13	16
β-strand	150	1	17
β-strand	153-156	4	17
β-strand	164-168	5	16
α-helix	171-174	4
β-strand	175-176	2	16
β-strand	188-199	12	17
β-strand	204-214	11	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gamma-aminobutyric acid receptor subunit gamma-2	D	protein	490	Rattus norvegicus	P18508 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit alpha-1,Gamma-aminobutyric acid receptor subunit alpha-1	A, C	protein	402	Rattus norvegicus	P62813 (AlphaFold model)
Gamma-aminobutyric acid receptor subunit beta-1,Gamma-aminobutyric acid receptor subunit beta-1	B, E	protein	384	Rattus norvegicus	P15431 (AlphaFold model)

Sequence of entity 1 (D), FASTA

>6DW1_1 Gamma-aminobutyric acid receptor subunit gamma-2 (chains D)
MSSPNTWSTGSTVYSPVFSQKMTLWILLLLSLYPGFTSQKSDDDYEDYASNKTWVLTPKV
PEGDVTVILNNLLEGYDNKLRPDIGVKPTLIHTDMYVNSIGPVNAINMEYTIDIFFAQTW
YDRRLKFNSTIKVLRLNSNMVGKIWIPDTFFRNSKKADAHWITTPNRMLRIWNDGRVLYT
LRLTIDAECQLQLHNFPMDEHSCPLEFSSYGYPREEIVYQWKRSSVEVGDTRSWRLYQFS
FVGLRNTTEVVKTTSGDYVVMSVYFDLSRRMGYFTIQTYIPCTLIVVLSWVSFWINKDAV
PARTSLGITTVLTMTTLSTIARKSLPKVSYVTAMDLFVSVCFIFVFSALVEYGTLHYFVS
NRKPSKDKDKKKKNPAPTIDIRPRSATIQMNNATHLQERDEEYGYECLDGKDCASFFCCF
EDCRTGAWRHGRIHIRIAKMDSYARIFFPTAFCLFNLVYWVSYLYLLVPRGSRHHHHHHH
HTETSQVAPA

Sequence of entity 2 (A, C), FASTA

>6DW1_2 Gamma-aminobutyric acid receptor subunit alpha-1,Gamma-aminobutyric acid receptor subunit alpha-1 (chains A, C)
MKKSRGLSDYLWAWTLILSTLSGRSYGQPSQDELKDNTTVFTRILDRLLDGYDNRLRPGL
GERVTEVKTDIFVTSFGPVSDHDMEYTIDVFFRQSWKDERLKFKGPMTVLRLNNLMASKI
WTPDTFFHNGKKSVAHNMTMPNKLLRITEDGTLLYTMRLTVRAECPMHLEDFPMDAHACP
LKFGSYAYTRAEVVYEWTREPARSVVVAEDGSRLNQYDLLGQTVDSGIVQSSTGEYVVMT
THFHLKRKIGYFVIQTYLPCIMTVILSQVSFWLNRESVPARTVFGVTTVLTMTTLSISAR
NSLPKVAYATAMDWFIAVCYAFVFSALIEFATVNYFTKRGTKKTFNSVSKIDRLSRIAFP
LLFGIFNLVYWATYLNREPQLKAPTPHQLVPRGSHHHHHHHH

Sequence of entity 3 (B, E), FASTA

>6DW1_3 Gamma-aminobutyric acid receptor subunit beta-1,Gamma-aminobutyric acid receptor subunit beta-1 (chains B, E)
MWTVQNRESLGLLSFPVMVAMVCCAHSSNEPSNMSYVKETVDRLLKGYDIRLRPDFGGPP
VDVGMRIDVASIDMVSEVNMDYTLTMYFQQSWKDKRLSYSGIPLNLTLDNRVADQLWVPD
TYFLNDKKSFVHGVTVKNRMIRLHPDGTVLYGLRITTTAACMMDLRRYPLDEQNCTLEIE
SYGYTTDDIEFYWNGGEGAVTGVNKIELPQFSIVDYKMVSKKVEFTTGAYPRLSLSFRLK
RNIGYFILQTYMPSTLITILSWVSFWINYDASAARVALGITTVLTMTTISTHLRETLPKI
PYVKAIDIYLMGCFVFVFLALLEYAFVNYIFFGGTIPDLTDVNSIDKWSRMFFPITFSLF
NVVYWLYYVHLVPRGSHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ABU	Gamma-amino-butanoic acid	C4 H9 N O2	3

Primary citation

Cryo-EM structure of the benzodiazepine-sensitive alpha 1 beta 1 gamma 2S tri-heteromeric GABAAreceptor in complex with GABA. Phulera, S., Zhu, H., Yu, J. et al. Elife (2018) 7. DOI 10.7554/eLife.39383 · PubMed

Other PDB entries of the same protein (UniProt P18508 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2PR9 2.51 Å, Mu2 adaptin subunit (AP50) of AP2 adaptor (second domain), complexed with GABAA…
9OUN 2.74 Å, Native GABA-A receptor from rat cerebella, beta2-alpha1-beta2-alpha1-gamma2 subtype, in…
9OUP 2.82 Å, Native GABA-A receptor from rat cerebella, beta2-alpha1-beta1-alpha6-gamma2 subtype, in…
9OUR 2.84 Å, Native GABA-A receptor from rat cerebella, beta2-alpha1-beta2-alpha1-gamma2 subtype, in…
9OUQ 2.89 Å, Native GABA-A receptor from rat cerebella, beta1-alpha1-beta2-alpha1-gamma2 subtype, in…
9OUM 2.9 Å, Native GABA-A receptor from rat cerebella, beta2-alpha1-beta1-alpha6-gamma2 subtype, in…
9OUO 2.92 Å, Native GABA-A receptor from rat cerebella, beta1-alpha1-beta1-alpha1-gamma2 subtype, in…
9OV4 2.93 Å, Native GABA-A receptor from rat cerebella, beta1-alpha1-beta2-alpha1-gamma2 subtype, in…
6DW0 3.8 Å, Cryo-EM structure of the benzodiazepine-sensitive alpha1beta1gamma2S tri-heteromeric…

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