5QU4: Cytoplasmic protein NCK1

Crystal Structure of swapped human Nck SH3.1 domain, 1.05A, orthorhombic form I. Determined by X-ray diffraction at 1.05 Å resolution. Released 12 Feb 2020.

Method: X-ray diffraction
Resolution: 1.05 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,425
Mol. weight: 41.2 kDa
Released: 12 Feb 2020

Explore 5QU4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5QU4 contains 5 α-helices and 32 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: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	14	1	2
β-strand	21	1	1
β-strand	24	1	2
β-strand	29-44	16	1
β-strand	49-53	5	1
α-helix	54-56	3
β-strand	57-59	3	1

Chain B: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	6-10	5	3
β-strand	14	1	4
β-strand	21	1	3
β-strand	24	1	4
β-strand	29-32	4	3
β-strand	39-43	5	3
β-strand	49-53	5	3
α-helix	54-56	3
β-strand	57-60	4	5

Chain C: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	1
β-strand	14	1	6
β-strand	21	1	1
β-strand	24	1	6
β-strand	29-32	4	1
β-strand	39-43	5	1
β-strand	49-53	5	1
α-helix	54-56	3
β-strand	57-58	2	1

Chain D: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	5
β-strand	14	1	7
β-strand	21	1	3
β-strand	24	1	7
β-strand	29	1	5
β-strand	31-32	2	3
β-strand	39-43	5	3
β-strand	49-53	5	3
α-helix	54-56	3
β-strand	57-58	2	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytoplasmic protein NCK1	A, B, C, D	protein	87	Homo sapiens	P16333 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5QU4_1 Cytoplasmic protein NCK1 (chains A, B, C, D)
SGGLNDIFEAQKIEWHEGSENLYFQSMAEEVVVVAKFDYVAQQEQELDIKKNERLWLLDD
SKSWWRVRNSMNKTGFVPSNYVERKNS

Primary citation

Small molecule AX-024 reduces T cell proliferation independently of CD3ε/Nck1 interaction, which is governed by a domain swap in the Nck1-SH3.1 domain. Richter, K., Rufer, A.C., Muller, M. et al. J Biol Chem (2020) 295:7849-7864. DOI 10.1074/jbc.RA120.012788 · PubMed

Other PDB entries of the same protein (UniProt P16333 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5QU8 0.93 Å, Crystal Structure of symmetric swapped human Nck SH3.1 domain, 0.93A, orthorhombic form IV
5QU3 1.02 Å, Crystal Structure of domain swapped human Nck SH3.1, 1.01A, monoclinic
5QU2 1.04 Å, Crystal Structure of human Nck SH3.1 in complex with peptide PPPVPNPDY
5QU1 1.08 Å, Crystal Structure of the monomeric human Nck SH3.1 domain, triclinic, 1.08A
5QU5 1.11 Å, Domain Swap in the first SH3 domain of human Nck1
5QU7 1.27 Å, Crystal Structure of swapped human Nck SH3.1 domain, 1.3A, orthorhombic form III
2CI9 1.5 Å, Nck1 SH2-domain in complex with a dodecaphosphopeptide from EPEC protein Tir
5QUA 1.51 Å, Crystal Structure of swapped human Nck SH3.1 domain, 1.5A, C2221
2CI8 1.8 Å, sh2 domain of human nck1 adaptor protein - uncomplexed
5QU6 1.82 Å, Crystal Structure of swapped human Nck SH3.1 domain, 1.8A, triclinic
2CUB Solution structure of the SH3 domain of the human cytoplasmic protein Nck1
2JS0 Solution structure of second SH3 domain of adaptor Nck

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