4YR8: JNK

Crystal structure of JNK in complex with a regulator protein. Determined by X-ray diffraction at 2.4 Å resolution. Released 16 Mar 2016.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 8
Atoms: 14,988
Mol. weight: 247.14 kDa
Released: 16 Mar 2016

Explore 4YR8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4YR8 contains 119 α-helices and 62 β-strands across 8 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: 20 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	10-15	6	5
β-strand	18-23	6	5
β-strand	26-31	6	6
β-strand	39-45	7	6
β-strand	50-58	9	6
α-helix	64-79	16
β-strand	85	1	7
α-helix	86-87	2
β-strand	88-92	5	6
β-strand	103-109	7	6
β-strand	113-114	2	7
α-helix	115-119	5
α-helix	125-144	20
α-helix	154-156	3
β-strand	157-159	3	7
β-strand	165-167	3	7
α-helix	194-197	4
α-helix	206-220	15
α-helix	230-241	12
α-helix	243-245	3
α-helix	246-249	4
α-helix	254-261	8
α-helix	264-265	2
α-helix	271-274	4
α-helix	277-279	3
α-helix	287-301	15
α-helix	306-308	3
α-helix	310-311	2
α-helix	312-316	5
α-helix	322-324	3
α-helix	351-360	10

Chain B: 10 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	159	1
β-strand	160-163	4	8
β-strand	166-170	5	8
α-helix	171-174	4
α-helix	177-182	6
β-strand	187-190	4	8
α-helix	195-197	3
α-helix	203-205	3
β-strand	206-208	3	8
α-helix	220-222	3
α-helix	223-235	13
β-strand	240-244	5	8
α-helix	250-263	14
α-helix	267-277	11
α-helix	285-297	13

Chain C: 21 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	26-31	6	9
β-strand	40-45	6	9
β-strand	50-57	8	9
α-helix	64-79	16
β-strand	85	1	10
α-helix	86-87	2
β-strand	88-92	5	9
β-strand	104-109	6	9
β-strand	113-114	2	10
α-helix	115-119	5
α-helix	125-144	20
α-helix	154-156	3
β-strand	157-159	3	10
β-strand	165-167	3	10
α-helix	194-197	4
α-helix	206-220	15
α-helix	230-241	12
α-helix	243-245	3
α-helix	246-249	4
α-helix	254-261	8
α-helix	264-265	2
α-helix	271-274	4
α-helix	277-279	3
α-helix	288-301	14
α-helix	306-308	3
α-helix	310-311	2
α-helix	312-316	5
α-helix	319-322	4
α-helix	327-330	4
α-helix	352-360	9

Chain D: 9 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	159	1
β-strand	160-163	4	11
β-strand	166-169	4	11
α-helix	171-174	4
α-helix	177-182	6
β-strand	185-190	6	11
α-helix	203-205	3
β-strand	206-208	3	11
α-helix	220-222	3
α-helix	223-235	13
β-strand	239-243	5	11
α-helix	250-263	14
α-helix	267-277	11
α-helix	285-297	13

Chain E: 18 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	10-15	6	1
β-strand	18-23	6	1
β-strand	26-31	6	2
β-strand	39-45	7	2
β-strand	50-58	9	2
α-helix	64-79	16
β-strand	85	1	3
α-helix	86-87	2
β-strand	88-92	5	2
β-strand	103-109	7	2
β-strand	113-114	2	3
α-helix	115-119	5
α-helix	125-144	20
α-helix	154-156	3
β-strand	157-159	3	3
β-strand	165-167	3	3
α-helix	194-197	4
α-helix	206-220	15
α-helix	230-241	12
α-helix	243-245	3
α-helix	246-249	4
α-helix	254-261	8
α-helix	271-274	4
α-helix	277-279	3
α-helix	287-301	15
α-helix	310-311	2
α-helix	312-316	5
α-helix	322-324	3
α-helix	354-360	7

Chain F: 22 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	12-14	3	12
β-strand	19-21	3	12
β-strand	27-31	5	13
β-strand	40-44	5	13
β-strand	51-56	6	13
α-helix	66-79	14
β-strand	85	1	14
α-helix	86-87	2
β-strand	88-92	5	13
β-strand	105-109	5	13
β-strand	113-114	2	14
α-helix	115-119	5
α-helix	125-144	20
α-helix	154-156	3
β-strand	157-159	3	14
β-strand	165-167	3	14
α-helix	194-197	4
α-helix	206-220	15
α-helix	230-241	12
α-helix	243-245	3
α-helix	246-249	4
α-helix	254-261	8
α-helix	264-265	2
α-helix	271-274	4
α-helix	277-279	3
α-helix	288-301	14
α-helix	306-308	3
α-helix	310-311	2
α-helix	312-316	5
α-helix	319-322	4
α-helix	327-330	4
α-helix	332-335	4
α-helix	356-359	4

Chain G: 9 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	159	1
β-strand	160-163	4	4
β-strand	166-170	5	4
α-helix	171-175	5
α-helix	177-183	7
β-strand	187-190	4	4
α-helix	195-198	4
α-helix	203-205	3
β-strand	206-208	3	4
α-helix	223-235	13
β-strand	240-244	5	4
α-helix	250-262	13
α-helix	267-277	11
α-helix	285-297	13

Chain H: 10 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	159	1
β-strand	160-163	4	15
β-strand	166-169	4	15
α-helix	171-174	4
α-helix	177-182	6
β-strand	185-190	6	15
α-helix	196-198	3
α-helix	203-205	3
β-strand	206-208	3	15
α-helix	220-222	3
α-helix	223-233	11
β-strand	239-243	5	15
α-helix	250-262	13
α-helix	267-277	11
α-helix	285-299	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitogen-activated protein kinase 8	A, C, E, F	protein	371	Homo sapiens	P45983 (AlphaFold model)
Dual specificity protein phosphatase 16	B, D, G, H	protein	167	Homo sapiens	Q9BY84 (AlphaFold model)

Sequence of entity 1 (A, C, E, F), FASTA

>4YR8_1 Mitogen-activated protein kinase 8 (chains A, C, E, F)
MSRSKRDNNFYSVEIGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAILERNVAIKKLSRP
FQNQTHAKRAYRELVLMKCVNHKNIIGLLNVFTPQKSLEEFQDVYIVMELMDANLCQVIQ
MELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGTSF
MMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMIKGGVLFPGTDHIDQWNKVIEQ
LGTPCPEFMKKLQPTVRTYVENRPKYAGYSFEKLFPDVLFPADSEHNKLKASQARDLLSK
MLVIDASKRISVDEALQHPYINVWYDPSEAEAPPPKIPDKQLDEREHTIEEWKELIYKEV
MDLLEHHHHHH

Sequence of entity 2 (B, D, G, H), FASTA

>4YR8_2 Dual specificity protein phosphatase 16 (chains B, D, G, H)
MGSSHHHHHHSSGLVPRGSHMNIGPTRILPNLYLGCQRDVLNKELMQQNGIGYVLNASNT
CPKPDFIPESHFLRVPVNDSFCEKILPWLDKSVDFIEKAKASNGCVLVHCLAGISRSATI
AIAYIMKRMDMSLDEAYRFVKEKRPTISPNFNFLGQLLDYEKKIKNQ

Primary citation

A conserved motif in JNK/p38-specific MAPK phosphatases as a determinant for JNK1 recognition and inactivation. Liu, X., Zhang, C.S., Lu, C. et al. Nat Commun (2016) 7:10879-10879. DOI 10.1038/ncomms10879 · PubMed

Other PDB entries of the same protein (UniProt P45983 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2XRW 1.33 Å, Linear binding motifs for JNK and for calcineurin antagonistically control the nuclear…
12CV 1.5 Å, Crystal Structure of human JNK1 Kinase Domain in complex with inhibitor CCD-2728
4QTD 1.5 Å, Structure of human JNK1 in complex with SCH772984 and the AMPPNP-hydrolysed triphosphate…
11ZL 1.55 Å, Crystal Structure of human JNK1 Kinase Domain in complex with inhibitor CCD-3013
8R5E 1.7 Å, JNK1 covalently bound to RU77 cyclohexenone based inhibitor
3ELJ 1.8 Å, Jnk1 complexed with a bis-anilino-pyrrolopyrimidine inhibitor.
4AWI 1.91 Å, Human Jnk1alpha kinase with 4-phenyl-7-azaindole IKK2 inhibitor.
4L7F 1.95 Å, Co-crystal Structure of JNK1 and AX13587
3PZE 2.0 Å, JNK1 in complex with inhibitor
8X5M 2.0 Å, The Crystal Structure of JNK1 from Biortus.
4HYU 2.15 Å, Crystal structure of JNK1 in complex with JIP1 peptide and…
4E73 2.27 Å, Crystal structure of JNK1beta-JIP in complex with an azaquinolone inhbitor

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