7NYN: SH3 domain of JNK-interacting Protein 1

Mutant Y526A of SH3 domain of JNK-interacting Protein 1 (JIP1). Determined by X-ray diffraction at 1.54 Å resolution. Released 22 Dec 2021.

Method: X-ray diffraction
Resolution: 1.54 Å
Organism: Homo sapiens
Chains: 12
Atoms: 7,091
Mol. weight: 93.6 kDa
Ligands: PO4
Released: 22 Dec 2021

Explore 7NYN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7NYN contains 20 α-helices and 96 β-strands across 12 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.

Chains AAA, DDD, EEE and KKK: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	493-495	3	1
β-strand	499	1	2
β-strand	506	1	1
β-strand	509	1	2
β-strand	514-520	7	1
β-strand	525-530	6	1
β-strand	536-540	5	1
α-helix	541-543	3
β-strand	544-546	3	1

Chains BBB, CCC, GGG, HHH, III, JJJ and LLL: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	493-495	3	3
β-strand	499	1	4
β-strand	506	1	3
α-helix	507-508	2
β-strand	509	1	4
β-strand	514-520	7	3
β-strand	525-530	6	3
β-strand	536-540	5	3
α-helix	541-543	3
β-strand	544-546	3	3

Chain FFF: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	493-495	3	11
β-strand	499	1	12
β-strand	506	1	11
β-strand	509	1	12
β-strand	514-520	7	11
β-strand	525-530	6	11
β-strand	536-540	5	11
α-helix	541-543	3
β-strand	544-546	3	11
α-helix	547-548	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SH3 domain of JNK-interacting Protein 1 (JIP1)	AAA, BBB, CCC, DDD, EEE, FFF, GGG, HHH, III, JJJ, KKK, LLL	protein	63	Homo sapiens	Q9UQF2 (AlphaFold model)

Sequence of entity 1 (AAA, BBB, CCC, DDD, EEE, FFF, GGG, HHH, III, JJJ, KKK, LLL), FASTA

>7NYN_1 SH3 domain of JNK-interacting Protein 1 (JIP1) (chains AAA, BBB, CCC, DDD, EEE, FFF, GGG, HHH, III, JJJ, KKK, LLL)
GHMEQTHRAIFRFVPRHEDELELEVDDPLLVELQAEDYWAEAYNMRTGARGVFPAYYAIE
VTK

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	3

Water and common crystallization additives (1PE, EDO, PG4, SO4, PEG) are not listed.

Primary citation

Visualizing protein breathing motions associated with aromatic ring flipping. Marino Perez, L., Ielasi, F.S., Bessa, L.M. et al. Nature (2022) 602:695-700. DOI 10.1038/s41586-022-04417-6 · PubMed

Other PDB entries of the same protein (UniProt Q9UQF2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7NYO 1.4 Å, Mutant A541L of SH3 domain of JNK-interacting Protein 1 (JIP1)
7NYK 1.45 Å, SH3 domain of JNK-interacting Protein 1 (JIP1)
7NYM 1.61 Å, Mutant V517A - SH3 domain of JNK-interacting Protein 1 (JIP1)
8RPP 1.87 Å, Crystal structure of the JIP1-JIP2-SH3 heterodimer and the JIP2-JIP2-SH3 homodimer
7NYL 1.95 Å, Mutant H493A of SH3 domain of JNK-interacting Protein 1 (JIP1)
7NZB 1.96 Å, Mutant V517L of the SH3 domain of JNK-interacting protein 1 (JIP1)
4H39 1.99 Å, Crystal Structure of JNK3 in Complex with JIP1 Peptide
4HYU 2.15 Å, Crystal structure of JNK1 in complex with JIP1 peptide and…
3OXI 2.2 Å, Design and Synthesis of Disubstituted Thiophene and Thiazole Based Inhibitors of JNK for…
4E73 2.27 Å, Crystal structure of JNK1beta-JIP in complex with an azaquinolone inhbitor
4IZY 2.3 Å, Crystal structure of JNK1 in complex with JIP1 peptide and…
4HYS 2.42 Å, Crystal structure of JNK1 in complex with JIP1 peptide and…

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