6WJG: PDB entry 6WJG

PKA RIIbeta holoenzyme with DnaJB1-PKAc fusion in fibrolamellar hepatoceullar carcinoma. Determined by electron microscopy at 6.2 Å resolution. Released 2 Dec 2020.

Method: Electron microscopy
Resolution: 6.2 Å
Organisms: Homo sapiens, Rattus norvegicus
Chains: 4
Atoms: 7,708
Mol. weight: 187.03 kDa
Released: 2 Dec 2020

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

Secondary structure: helices and β-sheets

6WJG contains 34 α-helices and 42 β-strands across 4 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: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	98-106	9	1
β-strand	111-117	7	1
β-strand	123-129	7	1
α-helix	131-137	7
α-helix	140-149	10
β-strand	164-166	3	1
β-strand	171-175	5	1
β-strand	181-182	2	2
α-helix	183-190	8
α-helix	195-214	20
β-strand	218	1	3
β-strand	228-230	3	2
β-strand	234-236	3	2
β-strand	244	1	3
α-helix	274-285	12
α-helix	298-306	9
α-helix	318-326	9
α-helix	357-361	5
α-helix	370-372	3
α-helix	383-384	2
α-helix	400-402	3

Chain B: 13 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	98-107	10	4
β-strand	110-117	8	4
β-strand	123-128	6	4
α-helix	132-137	6
α-helix	140-150	11
β-strand	164-166	3	4
β-strand	171-176	6	4
α-helix	183-190	8
α-helix	195-214	20
β-strand	218	1	5
β-strand	228-229	2	6
β-strand	235-236	2	6
β-strand	244	1	5
β-strand	256	1	7
β-strand	259	1	7
α-helix	262-265	4
α-helix	273-276	4
α-helix	279-285	7
α-helix	298-306	9
α-helix	318-327	10
α-helix	357-361	5
α-helix	366-367	2
α-helix	370-373	4
α-helix	385-387	3

Chain C: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	114	1	8
α-helix	137-148	12
α-helix	152-154	3
α-helix	158-167	10
β-strand	169-173	5	9
β-strand	185	1	10
α-helix	186	1
β-strand	191-192	2	9
β-strand	199-202	4	11
β-strand	207-211	5	11
β-strand	227	1	8
β-strand	229	1	10
β-strand	234	1	11
β-strand	240-244	5	9
α-helix	247-264	18

Chain D: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	137-147	11
α-helix	151-154	4
α-helix	158-166	9
β-strand	170-173	4	12
β-strand	182	1	13
β-strand	184	1	13
β-strand	185-186	2	14
β-strand	188-191	4	12
β-strand	196-202	7	15
β-strand	207-209	3	15
β-strand	213-214	2	15
α-helix	221-224	4
β-strand	228-229	2	14
β-strand	233-236	4	15
β-strand	240-246	7	12
α-helix	247-264	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DnaJ homolog subfamily B member 1, cAMP-dependent protein kinase catalytic subunit alpha fusion	A, B	protein	405	Homo sapiens	P17612 (AlphaFold model), P25685 (AlphaFold model)
cAMP-dependent protein kinase type II-beta regulatory subunit	C, D	protein	416	Rattus norvegicus	P12369 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6WJG_1 DnaJ homolog subfamily B member 1, cAMP-dependent protein kinase catalytic subunit alpha fusion (chains A, B)
GKDYYQTLGLARGASDEEIKRAYRRQALRYHPDKNKEPGAEEKFKEIAEAYDVLSDPRKR
EIFDRYGEEVKEFLAKAKEDFLKKWESPAQNTAHLDQFERIKTLGTGSFGRVMLVKHKET
GNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPG
GEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDF
GFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKGVDWWALGVLIYEMAAGYPPFFADQPIQ
IYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAI
YQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF

Sequence of entity 2 (C, D), FASTA

>6WJG_2 cAMP-dependent protein kinase type II-beta regulatory subunit (chains C, D)
MSIEIPAGLTELLQGFTVEVLRHQPADLLEFALQHFTRLQQENERKGAARFGHEGRTWGD
AGAAAGGGTPSKGVNFAEEPMRSDSENGEEEEAAEAGAFNAPVINRFTRRASVCAEAYNP
DEEEDDAESRIIHPKTDDQRNRLQEACKDILLFKNLDPEQMSQVLDAMFEKLVKEGEHVI
DQGDDGDNFYVIDRGTFDIYVKCDGVGRCVGNYDNRGSFGELALMYNTPRAATITATSPG
ALWGLDRVTFRRIIVKNNAKKRKMYESFIESLPFLKSLEVSERLKVVDVIGTKVYNDGEQ
IIAQGDSADSFFIVESGEVRITMKRKGKSDIEENGAVEIARCLRGQYFGELALVTNKPRA
ASAHAIGTVKCLAMDVQAFERLLGPCMEIMKRNIATYEEQLVALFGTNMDIVEPTA

Primary citation

Structural analyses of the PKA RII beta holoenzyme containing the oncogenic DnaJB1-PKAc fusion protein reveal protomer asymmetry and fusion-induced allosteric perturbations in fibrolamellar hepatocellular carcinoma. Lu, T.W., Aoto, P.C., Weng, J.H. et al. PLoS Biol (2020) 18:e3001018-e3001018. DOI 10.1371/journal.pbio.3001018 · PubMed

Other PDB entries of the same protein (UniProt P17612 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4WB8 1.55 Å, Crystal structure of human cAMP-dependent protein kinase A (catalytic alpha subunit),…
3OVV 1.58 Å, Human cAMP-dependent protein kinase in complex with an inhibitor
3POO 1.6 Å, human cAMP-dependent protein kinase in complex with an inhibitor
4WB5 1.64 Å, Crystal structure of human cAMP-dependent protein kinase A (catalytic alpha subunit)
6QJ7 1.69 Å, Difluorophenyl diacylhydrazides: Potent inhibitors of Serum- and…
3AMA 1.75 Å, Protein kinase A sixfold mutant model of Aurora B with inhibitor JNJ-7706621
4UJ1 1.77 Å, Protein Kinase A in complex with an Inhibitor
5IZJ 1.85 Å, Complex of PKA with the bisubstrate protein kinase inhibitor ARC-1411
4UJ9 1.87 Å, Protein Kinase A in complex with an Inhibitor
3OWP 1.88 Å, Human cAMP-dependent protein kinase in complex with an inhibitor
6FRX 1.88 Å, PKA variant as Aurora B mimic in complex with a dianilinopyrimidine inhibitor
5BX6 1.89 Å, PKA in complex with a halogenated phthalazinone fragment compound.

Browse structure collections

About this viewer

MolViewer shows 6WJG directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.