6VJM: PDB entry 6VJM

Human metabotropic GABA(B) receptor in its apo state. Determined by electron microscopy at 3.97 Å resolution. Released 10 Jun 2020.

Method: Electron microscopy
Resolution: 3.97 Å
Organism: Homo sapiens
Chains: 2
Atoms: 10,629
Mol. weight: 176.94 kDa
Ligands: NAG
Released: 10 Jun 2020

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

Secondary structure: helices and β-sheets

6VJM contains 52 α-helices and 47 β-strands across 2 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: 25 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	168-175	8	1
α-helix	185-200	16
β-strand	209-216	8	1
α-helix	222-233	12
β-strand	241-242	2	2
α-helix	248-256	9
α-helix	257-259	3
β-strand	263-266	4	2
α-helix	272-275	4
β-strand	283-285	3	2
α-helix	290-293	4
α-helix	294-304	11
β-strand	308-314	7	3
α-helix	317-330	14
α-helix	331-333	3
β-strand	336-343	8	3
α-helix	348-356	9
β-strand	361-365	5	3
α-helix	368-380	13
β-strand	389-393	5	3
α-helix	412-418	7
β-strand	422-425	4	3
α-helix	443-453	11
α-helix	468-484	17
α-helix	504-514	11
β-strand	517-520	4	4
β-strand	523-526	4	4
β-strand	527	1	5
β-strand	532	1	2
β-strand	533	1	5
α-helix	534	1
β-strand	536	1	6
β-strand	539-542	4	3
β-strand	547-551	5	3
β-strand	554	1	6
α-helix	573-574	2
β-strand	578-583	6	7
α-helix	590-614	25
α-helix	628-643	16
α-helix	659-692	34
α-helix	709-731	23
β-strand	735-736	2	8
β-strand	739	1	9
β-strand	752-757	6	7
β-strand	758	1	9
β-strand	761-762	2	8
α-helix	767-790	24
α-helix	802-824	23
α-helix	833-852	20
α-helix	854-860	7

Chain B: 27 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	55-62	8	10
α-helix	70-90	21
β-strand	98-105	8	10
α-helix	110-123	14
β-strand	130-132	3	10
α-helix	136-145	10
β-strand	153-155	3	10
α-helix	161-164	4
β-strand	172-174	3	10
α-helix	179-182	4
α-helix	183-192	10
β-strand	197-202	6	11
α-helix	206-219	14
β-strand	225-230	6	11
α-helix	236-245	10
β-strand	250-254	5	11
α-helix	257-268	12
β-strand	278-281	4	11
α-helix	286	1
α-helix	289-291	3
α-helix	305-308	4
β-strand	314-319	6	11
α-helix	335-345	11
α-helix	350-352	3
α-helix	355-377	23
α-helix	394-404	11
β-strand	408-410	3	12
β-strand	413-415	3	12
β-strand	425	1	13
β-strand	426-431	6	11
β-strand	436-440	5	11
β-strand	442-443	2	13
β-strand	448-449	2	13
β-strand	469	1	14
β-strand	472-474	3	15
α-helix	475-476	2
α-helix	479-508	30
α-helix	519-541	23
α-helix	547-549	3
α-helix	552-582	31
α-helix	592-618	27
β-strand	624-627	4	15
β-strand	639	1	14
β-strand	642-647	6	15
α-helix	654-677	24
α-helix	678-680	3
α-helix	692-711	20
α-helix	719-740	22
α-helix	743-747	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gamma-aminobutyric acid type B receptor subunit 1	A	protein	762	Homo sapiens	Q9UBS5 (AlphaFold model)
Gamma-aminobutyric acid type B receptor subunit 2	B	protein	779	Homo sapiens	O75899 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6VJM_1 Gamma-aminobutyric acid type B receptor subunit 1 (chains A)
GSERRAVYIGALFPMSGGWPGGQACQPAVEMALEDVNSRRDILPDYELKLIHHDSKCDPG
QATKYLYELLYNDPIKIILMPGCSSVSTLVAEAARMWNLIVLSYGSSSPALSNRQRFPTF
FRTHPSATLHNPTRVKLFEKWGWKKIATIQQTTEVFTSTLDDLEERVKEAGIEITFRQSF
FSDPAVPVKNLKRQDARIIVGLFYETEARKVFCEVYKERLFGKKYVWFLIGWYADNWFKI
YDPSINCTVDEMTEAVEGHITTEIVMLNPANTRSISNMTSQEFVEKLTKRLKRHPEETGG
FQEAPLAYDAIWALALALNKTSGGGGRSGVRLEDFNYNNQTITDQIYRAMNSSSFEGVSG
HVVFDASGSRMAWTLIEQLQGGSYKKIGYYDSTKDDLSWSKTDKWIGGSPPADQTLVIKT
FRFLSQKLFISVSVLSSLGIVLAVVCLSFNIYNSHVRYIQNSQPNLNNLTAVGCSLALAA
VFPLGLDGYHIGRNQFPFVCQARLWLLGLGFSLGYGSMFTKIWWVHTVFTKKEEKKEWRK
TLEPWKLYATVGLLVGMDVLTLAIWQIVDPLHRTIETFAKEEPKEDIDVSILPQLEHCSS
RKMNTWLGIFYGYKGLLLLLGIFLAYETKSVSTEKINDHRAVGMAIYNVAVLCLITAPVT
MILSSQQDAAFAFASLAIVFSSYITLVVLFVPKMRRLITRGEWQSEAQDTMKTGSSTNNN
EEEKSRLLEKENRELEKIIAEKEERVSELRHQLQSRLEVLFQ

Sequence of entity 2 (B), FASTA

>6VJM_2 Gamma-aminobutyric acid type B receptor subunit 2 (chains B)
GWARGAPRPPPSSPPLSIMGLMPLTKEVAKGSIGRGVLPAVELAIEQIRNESLLRPYFLD
LRLYDTECDNAKGLKAFYDAIKYGPNHLMVFGGVCPSVTSIIAESLQGWNLVQLSFAATT
PVLADKKKYPYFFRTVPSDNAVNPAILKLLKHYQWKRVGTLTQDVQRFSEVRNDLTGVLY
GEDIEISDTESFSNDPCTSVKKLKGNDVRIILGQFDQNMAAKVFCCAYEENMYGSKYQWI
IPGWYEPSWWEQVHTEANSSRCLRKNLLAAMEGYIGVDFEPLSSKQIKTISGKTPQQYER
EYNNKRSGVGPSKFHGYAYDGIWVIAKTLQRAMETLHASSRHQRIQDFNYTDHTLGRIIL
NAMNETNFFGVTGQVVFRNGERMGTIKFTQFQDSREVKVGEYNAVADTLEIINDTIRFQG
SEPPKDKTIILEQLRKISLPLYSILSALTILGMIMASAFLFFNIKNRNQKLIKMSSPYMN
NLIILGGMLSYASIFLFGLDGSFVSEKTFETLCTVRTWILTVGYTTAFGAMFAKTWRVHA
IFKNVKMKKKIIKDQKLLVIVGGMLLIDLCILICWQAVDPLRRTVEKYSMEPDPAGRDIS
IRPLLEHCENTHMTIWLGIVYAYKGLLMLFGCFLAWETRNVSIPALNDSKYIGMSVYNVG
IMCIIGAAVSFLTRDQPNVQFCIVALVIIFCSTITLCLVFVPKLITLRTNPDAATQNRRF
QFTQNQKKEDSKTSTSVTSVNQASTSRLEGLQSENHRLRMKITELDKDLEEVTMQLQDT

Ligands and cofactors

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

Primary citation

Structural basis of the activation of a metabotropic GABA receptor. Shaye, H., Ishchenko, A., Lam, J.H. et al. Nature (2020) 584:298-303. DOI 10.1038/s41586-020-2408-4 · PubMed

Other PDB entries of the same protein (UniProt Q9UBS5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4PAS 1.62 Å, Heterodimeric coiled-coil structure of human GABA(B) receptor
4MS4 1.9 Å, Crystal structure of the extracellular domain of human GABA(B) receptor bound to the…
4MR7 2.15 Å, Crystal structure of the extracellular domain of human GABA(B) receptor bound to the…
4MR8 2.15 Å, Crystal structure of the extracellular domain of human GABA(B) receptor bound to the…
4MQF 2.22 Å, Crystal structure of the extracellular domain of human GABA(B) receptor bound to the…
4MS1 2.25 Å, Crystal structure of the extracellular domain of human GABA(B) receptor bound to the…
4MQE 2.35 Å, Crystal structure of the extracellular domain of human GABA(B) receptor in the apo form
4MR9 2.35 Å, Crystal structure of the extracellular domain of human GABA(B) receptor bound to the…
4MS3 2.5 Å, Crystal structure of the extracellular domain of human GABA(B) receptor bound to the…
4MRM 2.86 Å, Crystal structure of the extracellular domain of human GABA(B) receptor bound to the…
7C7S 2.9 Å, Cryo-EM structure of the CGP54626-bound human GABA(B) receptor in inactive state.
7C7Q 3.0 Å, Cryo-EM structure of the baclofen/BHFF-bound human GABA(B) receptor in active state

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