6WJF: PDB entry 6WJF

PKA RIIbeta holoenzyme with DnaJB1-PKAc fusion in fibrolamellar hepatoceullar carcinoma. Determined by electron microscopy at 7.5 Å resolution. Released 2 Dec 2020.

Method: Electron microscopy
Resolution: 7.5 Å
Organisms: Homo sapiens, Rattus norvegicus
Chains: 4
Atoms: 9,527
Mol. weight: 187.03 kDa
Released: 2 Dec 2020

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

Secondary structure: helices and β-sheets

6WJF contains 42 α-helices and 54 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: 15 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
α-helix	18-29	12
α-helix	40-54	15
α-helix	57-85	29
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: 9 helices, 22 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	247-270	24
α-helix	280-289	10
β-strand	293-295	3	12
β-strand	300	1	13
β-strand	312	1	14
β-strand	314-316	3	12
β-strand	319	1	15
β-strand	322	1	16
β-strand	342	1	15
β-strand	348	1	14
β-strand	362	1	16
β-strand	364	1	13
β-strand	365	1	15
β-strand	369-371	3	12
α-helix	376-379	4
α-helix	386-390	5
α-helix	394-397	4

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	17
β-strand	182	1	18
β-strand	184	1	18
β-strand	185-186	2	19
β-strand	188-191	4	17
β-strand	196-202	7	20
β-strand	207-209	3	20
β-strand	213-214	2	20
α-helix	221-224	4
β-strand	228-229	2	19
β-strand	233-236	4	20
β-strand	240-246	7	17
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

>6WJF_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

>6WJF_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.

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