6B20: PDB entry 6B20

Crystal structure of a complex between G protein beta gamma dimer and an inhibitory Nanobody regulator. Determined by X-ray diffraction at 2.34 Å resolution. Released 30 May 2018.

Method: X-ray diffraction
Resolution: 2.34 Å
Organisms: Bos taurus, Lama glama
Chains: 6
Atoms: 8,301
Mol. weight: 113.23 kDa
Released: 30 May 2018

Explore 6B20 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6B20 contains 27 α-helices and 80 β-strands across 6 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, 29 β-strands

Element	Residues	Length	Sheet
α-helix	4-23	20
α-helix	30-33	4
α-helix	38-42	5
β-strand	43	1	1
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	89-94	6	3
α-helix	95	1
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	120-125	6	4
β-strand	134-140	7	4
β-strand	146-151	6	5
β-strand	156-161	6	5
β-strand	166-170	5	5
β-strand	175-180	6	5
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	208-212	5	6
β-strand	217-222	6	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	250-254	5	7
β-strand	259-264	6	7
α-helix	272	1
β-strand	273-278	6	1
β-strand	284-289	6	1
β-strand	293-298	6	1
β-strand	304-309	6	1
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	336-339	4	2

Chain B: 5 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	4-23	20
α-helix	30-33	4
α-helix	38-40	3
β-strand	43	1	8
β-strand	47-51	5	9
β-strand	58-63	6	10
β-strand	69-74	6	10
β-strand	78-83	6	10
β-strand	89-94	6	10
α-helix	95	1
β-strand	100-105	6	11
β-strand	111-116	6	11
β-strand	121-125	5	11
β-strand	134-139	6	11
β-strand	146-151	6	12
β-strand	156-161	6	12
β-strand	166-170	5	12
β-strand	175-180	6	12
β-strand	187-192	6	13
β-strand	198-203	6	13
β-strand	208-212	5	13
β-strand	217-222	6	13
β-strand	229-234	6	14
β-strand	240-245	6	14
β-strand	250-254	5	14
β-strand	259-264	6	14
α-helix	272	1
β-strand	273-278	6	8
β-strand	284-289	6	8
β-strand	294-298	5	8
β-strand	304-308	5	8
β-strand	315-320	6	9
β-strand	327-331	5	9
β-strand	336-339	4	9

Chain C: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	12-26	15
α-helix	30-32	3
α-helix	33-47	15
α-helix	48-50	3
α-helix	52-55	4

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	11-25	15
α-helix	30-32	3
α-helix	33-47	15
α-helix	52-55	4

Chains E and F: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	15
β-strand	10-13	4	16
β-strand	18-24	7	15
α-helix	28-30	3
β-strand	34-39	6	16
β-strand	46-51	6	16
β-strand	57-59	3	16
β-strand	67-72	6	15
α-helix	73-75	3
β-strand	77-82	6	15
α-helix	87-89	3
β-strand	91-97	7	16
α-helix	99-101	3
β-strand	103-104	2	16
β-strand	108-113	6	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	A, B	protein	338	Bos taurus	P62871 (AlphaFold model)
Guanine nucleotide-binding protein G(T) subunit gamma-T1	C, D	protein	60	Bos taurus	P02698 (AlphaFold model)
Nanobody against G protein beta gamma dimer	E, F	protein	114	Lama glama

Sequence of entity 1 (A, B), FASTA

>6B20_1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains A, B)
ELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMH
WGTDSRLLLSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICS
IYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTG
HTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFA
TGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKA
DRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 2 (C, D), FASTA

>6B20_2 Guanine nucleotide-binding protein G(T) subunit gamma-T1 (chains C, D)
EDLTEKDKLKMEVDQLKKEVTLERMLVSKCCEEFRDYVEERSGEDPLVKGIPEDKNPFKE

Sequence of entity 3 (E, F), FASTA

>6B20_3 Nanobody against G protein beta gamma dimer (chains E, F)
QVQLVESGGGLVQAGGSLRLSCAASGSIFSINAMGWYRQAPGKQRELVAAITRGGRTNYA
DSVKGRFTLSRDNAKNTVYLQMNSLKPEDTAVYYCNVGRSRGYWGQGTQVTVSS

Primary citation

Targeting G protein-coupled receptor signaling at the G protein level with a selective nanobody inhibitor. Gulati, S., Jin, H., Masuho, I. et al. Nat Commun (2018) 9:1996-1996. DOI 10.1038/s41467-018-04432-0 · PubMed

Other PDB entries of the same protein (UniProt P62871 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5KDO 1.9 Å, Heterotrimeric complex of the 4 alanine insertion variant of the Gi alpha1 subunit and…
1GOT 2.0 Å, Heterotrimeric complex of a gt-alpha/gi-alpha chimera and the gt-beta-gamma subunits
3V5W 2.07 Å, Human G Protein-Coupled Receptor Kinase 2 in Complex with Soluble Gbetagamma Subunits…
1TBG 2.1 Å, Beta-gamma dimer of the heterotrimeric G-protein transducin
1GP2 2.3 Å, G protein heterotrimer GI_ALPHA_1 BETA_1 GAMMA_2 with GDP bound
5WG4 2.31 Å, Human GRK2 in complex with Gbetagamma subunits and CCG257284
1GG2 2.4 Å, G protein heterotrimer mutant GI_ALPHA_1(G203A) BETA_1 GAMMA_2 with GDP bound
2TRC 2.4 Å, Phosducin/transducin beta-gamma complex
4MK0 2.4 Å, Crystal structure of G protein-coupled receptor kinase 2 in complex with a a rationally…
6U7C 2.44 Å, Human GRK2 in complex with Gbetagamma subunits and CCG258747
3PVU 2.48 Å, Bovine GRK2 in complex with Gbetagamma subunits and a selective kinase inhibitor (CMPD101)
3PVW 2.49 Å, Bovine GRK2 in complex with Gbetagamma subunits and a selective kinase inhibitor…

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