6ZR5: JNK1

Name: PDB 6ZR5: Crystal structure of JNK1 in complex with ATF2(19-58)
Published: 2020-11-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transcription

Crystal structure of JNK1 in complex with ATF2(19-58). Determined by X-ray diffraction at 2.7 Å resolution. Released 18 Nov 2020.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,152
Mol. weight: 94.48 kDa
Ligands: ZN, ANP, MG
Released: 18 Nov 2020

Explore 6ZR5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZR5 contains 47 α-helices and 26 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: 22 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
β-strand	10-15	6	1
β-strand	18-23	6	1
β-strand	26-35	10	2
β-strand	38-45	8	2
β-strand	50-58	9	2
α-helix	64-79	16
β-strand	85	1	3
β-strand	88-92	5	2
β-strand	103-108	6	2
β-strand	113-114	2	3
α-helix	116-119	4
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	232-241	10
α-helix	243-245	3
α-helix	246-248	3
α-helix	253-257	5
α-helix	264-265	2
α-helix	271-274	4
α-helix	285-301	17
α-helix	306-308	3
α-helix	310-311	2
α-helix	312-316	5
α-helix	322-324	3
α-helix	327-330	4
α-helix	332-335	4
α-helix	341-343	3
α-helix	349-360	12

Chain B: 23 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	10-15	6	5
β-strand	18-23	6	5
β-strand	26-35	10	6
β-strand	38-45	8	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	103-108	6	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	248-250	3
α-helix	254-261	8
α-helix	264-265	2
α-helix	271-274	4
α-helix	281-282	2
α-helix	285-301	17
α-helix	306-308	3
α-helix	310-311	2
α-helix	312-316	5
α-helix	322-324	3
α-helix	327-330	4
α-helix	341-343	3
α-helix	349-360	12

Chain C: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	4
β-strand	35-36	2	4
α-helix	39-49	11

Chain D: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	26	1	8
β-strand	35	1	8
α-helix	39-49	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitogen-activated protein kinase 8	A, B	protein	366	Homo sapiens	P45983 (AlphaFold model)
Cyclic AMP-dependent transcription factor ATF-2	C, D	protein	40	Homo sapiens	P15336 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6ZR5_1 Mitogen-activated protein kinase 8 (chains A, B)
GSMSRSKRDNNFYSVEIGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAILERNVAIKKLS
RPFQNQTHAKRAYRELVLMKCVNHKNIIGLLNVFTPQKSLEEFQDVYIVMELMDANLCQV
IQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGT
SFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMIKGGVLFPGTDHIDQWNKVI
EQLGTPCPEFMKKLQPTVRTYVENRPKYAGYSFEKLFPDVLFPADSEHNKLKASQARDLL
SKMLVIDASKRISVDEALQHPYINVWYDPSEAEAPPPKIPDKQLDEREHTIEEWKELIYK
EVMDLE

Sequence of entity 2 (C, D), FASTA

>6ZR5_2 Cyclic AMP-dependent transcription factor ATF-2 (chains C, D)
YSDDKPFLCTAPGCGRRFTNEDHLAVHKRKHEMTLKFGPA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	2
MG	Magnesium ion	Mg	4

Primary citation

Co-regulation of the transcription controlling ATF2 phosphoswitch by JNK and p38. Kirsch, K., Zeke, A., Toke, O. et al. Nat Commun (2020) 11:5769-5769. DOI 10.1038/s41467-020-19582-3 · 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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