5OJM: Chimaeric beta3-alpha5 GABAA receptor

Structure of a chimaeric beta3-alpha5 GABAA receptor in complex with nanobody Nb25. Determined by X-ray diffraction at 3.3 Å resolution. Released 4 Oct 2017.

Method: X-ray diffraction
Resolution: 3.3 Å
Organisms: synthetic construct, Homo sapiens, Lama glama
Chains: 10
Atoms: 18,538
Mol. weight: 296.52 kDa
Ligands: NAG
Released: 4 Oct 2017

Explore 5OJM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5OJM contains 90 α-helices and 117 β-strands across 10 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: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	12-20	9
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	114-118	5	1
β-strand	123-135	13	1
α-helix	140-142	3
β-strand	147-156	10	2
β-strand	164-168	5	1
α-helix	171-174	4
β-strand	175-176	2	1
α-helix	178-180	3
β-strand	186-200	15	2
β-strand	203-216	14	2
α-helix	217	1
α-helix	227-229	3
α-helix	230-234	5
α-helix	235-246	12
α-helix	247-249	3
α-helix	255-277	23
α-helix	288-313	26
α-helix	318-416	29

Chain B: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
α-helix	35	1
β-strand	36-51	16	3
β-strand	56-68	13	3
α-helix	70-72	3
β-strand	81-83	3	3
α-helix	85-90	6
β-strand	96-98	3	4
β-strand	101-106	6	3
β-strand	110	1	2
β-strand	114-118	5	3
β-strand	123-135	13	3
α-helix	140-142	3
β-strand	147-156	10	4
β-strand	164-168	5	3
α-helix	171-173	3
β-strand	175-176	2	3
α-helix	178-180	3
β-strand	186-200	15	4
β-strand	203-216	14	4
α-helix	217	1
α-helix	227-229	3
α-helix	230-234	5
α-helix	235-246	12
α-helix	247-249	3
α-helix	255-277	23
α-helix	288-313	26
α-helix	318-416	29

Chain C: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	12-20	9
α-helix	35	1
β-strand	36-51	16	5
β-strand	56-68	13	5
α-helix	70-72	3
β-strand	81-83	3	5
α-helix	85-90	6
β-strand	96-98	3	6
β-strand	101-106	6	5
β-strand	114-118	5	5
β-strand	123-135	13	5
α-helix	140-142	3
β-strand	147-156	10	6
β-strand	164-168	5	5
α-helix	171-173	3
β-strand	175-176	2	5
α-helix	178-180	3
β-strand	186-200	15	6
β-strand	203-216	14	6
α-helix	217	1
α-helix	227-229	3
α-helix	230-234	5
α-helix	235-246	12
α-helix	247-249	3
α-helix	255-277	23
α-helix	288-313	26
α-helix	318-416	29

Chain D: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	11
α-helix	35	1
β-strand	36-51	16	7
β-strand	56-68	13	7
α-helix	70-72	3
β-strand	81-83	3	7
α-helix	85-90	6
β-strand	96-98	3	8
β-strand	101-106	6	7
β-strand	114-118	5	7
β-strand	123-135	13	7
α-helix	140-142	3
β-strand	147-156	10	8
β-strand	164-168	5	7
α-helix	171-174	4
β-strand	175-176	2	7
α-helix	178-180	3
β-strand	186-200	15	8
β-strand	203-216	14	8
α-helix	217	1
α-helix	227-229	3
α-helix	230-234	5
α-helix	235-246	12
α-helix	247-249	3
α-helix	255-277	23
α-helix	288-313	26
α-helix	318-416	29

Chain E: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	12-20	9
β-strand	36-51	16	9
β-strand	56-68	13	9
α-helix	70-72	3
β-strand	81-83	3	9
α-helix	85-90	6
β-strand	96-98	3	10
β-strand	101-106	6	9
β-strand	114-118	5	9
β-strand	123-135	13	9
α-helix	140-142	3
β-strand	147-156	10	10
β-strand	164-168	5	9
α-helix	171-174	4
β-strand	175-176	2	9
α-helix	178-180	3
β-strand	186-200	15	10
β-strand	203-216	14	10
α-helix	217	1
α-helix	227-229	3
α-helix	230-234	5
α-helix	235-246	12
α-helix	247-249	3
α-helix	255-277	23
α-helix	286-287	2
α-helix	288-313	26
α-helix	318-416	29

Chains K, L, M and O: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	11
β-strand	11	1	12
β-strand	18-26	9	11
β-strand	33-39	7	13
α-helix	44-45	2
β-strand	46-51	6	13
β-strand	58-60	3	13
β-strand	68-73	6	11
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-99	8	13
α-helix	109-111	3
β-strand	112-121	10	13
β-strand	122	1	12

Chain N: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	20
β-strand	11	1	21
β-strand	18-26	9	20
β-strand	33-39	7	22
α-helix	44-45	2
β-strand	46-51	6	22
β-strand	58-60	3	22
β-strand	68-73	6	20
β-strand	78-83	6	20
α-helix	88-90	3
β-strand	92-99	8	22
β-strand	104	1	8
α-helix	109-111	3
β-strand	112-121	10	22
β-strand	122	1	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Human GABAA receptor chimera beta3-alpha5,Gamma-aminobutyric acid receptor subunit…	A, B, C, D, E	protein	395	synthetic construct, Homo sapiens	P28472 (AlphaFold model), P31644 (AlphaFold model)
Nanobody Nb25	K, L, M, N, O	protein	125	Lama glama

Sequence of entity 1 (A, B, C, D, E), FASTA

>5OJM_1 Human GABAA receptor chimera beta3-alpha5,Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit alpha-5 (chains A, B, C, D, E)
MGILPSPGMPALLSLVSLLSVLLMGCVAETGQSVNDPGNMSFVKETVDKLLKGYDIRLRP
DFGGPPVCVGMNIDIASIDMVSEVNMDYTLTMYFQQYWRDKRLAYSGIPLNLTLDNRVAD
QLWVPDTYFLNDKKSFVHGVTVKNRMIRLHPDGTVLYGLRITTTAACMMDLRRYPLDEQN
CTLEIESYGYTTDDIEFYWRGGDKAVTGVERIELPQFSIVEHRLVSRNVVFATGAYPRLS
LSFRLKRNIGYFVIQTYLPCIMTVILSQVSFWLNRESVPARTVFGVTTVLTMTTLSISAR
NSLPKVAYATAMDWFIAVCYAFVFSALIEFATVNYFTKSQPARAAKIDKMSRIVFPILFG
TFNLVYWATYLNREPVIKGATSPKGTTETSQVAPA

Sequence of entity 2 (K, L, M, N, O), FASTA

>5OJM_2 Nanobody Nb25 (chains K, L, M, N, O)
QVQLQESGGGLVQAGGSLRLSCAASGHTFNYPIMGWFRQAPGKEREFVGAISWSGGSTSY
ADSVKDRFTISRDNAKNTVYLEMNNLKPEDTAVYYCAAKGRYSGGLYYPTNYDYWGQGTQ
VTVSS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Primary citation

Structural basis for GABAA receptor potentiation by neurosteroids. Miller, P.S., Scott, S., Masiulis, S. et al. Nat Struct Mol Biol (2017) 24:986-992. DOI 10.1038/nsmb.3484 · PubMed

Other PDB entries of the same protein (UniProt P28472 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7A5V 1.7 Å, CryoEM structure of a human gamma-aminobutyric acid receptor, the GABA(A)R-beta3…
9RGD 2.0 Å, CryoEM structure of human alpha1beta3gamma2L GABA(A)R in CL47a
9EQG 2.4 Å, CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with GABA…
6QFA 2.49 Å, CryoEM structure of a beta3K279T GABA(A)R homomer in complex with histamine and megabody…
7QN5 2.5 Å, Cryo-EM structure of human full-length extrasynaptic alpha4beta3delta GABA(A)R in…
9FAS 2.5 Å, CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with…
9FEU 2.5 Å, Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the…
9FFU 2.5 Å, Cryo-EM structure of the alpha1beta3 GABA(A) receptor in complex with GABA and Mb25 in…
9G2E 2.5 Å, Cryo-EM structure of the beta3 homomeric GABA(A) receptor in the long-lived desensitised…
9QJS 2.52 Å, GABA-A receptor a2b3 (1:4) + a2NB16(silent) + b3Mb125 + GABA
8PET 2.6 Å, Cryo-EM structure of the full-length human alpha1beta3 GABA(A) receptor (babba…
9FAJ 2.6 Å, CryoEM structure of human full-length alpha1beta3gamma2 GABA(A) receptor in complex with…

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