2IYK: Regulator of nonsense transcripts 1

Crystal structure of the UPF2-interacting domain of nonsense mediated mRNA decay factor UPF1. Determined by X-ray diffraction at 2.95 Å resolution. Released 30 Aug 2006.

Method: X-ray diffraction
Resolution: 2.95 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 2,458
Mol. weight: 36.82 kDa
Ligands: ZN
Released: 30 Aug 2006

Explore 2IYK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2IYK contains 12 α-helices and 18 β-strands across 2 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: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	1
β-strand	32-35	4	1
α-helix	45-52	8
β-strand	58-60	3	1
β-strand	70	1	1
β-strand	84-87	4	2
α-helix	88-89	2
β-strand	96-99	4	2
α-helix	106-109	4
α-helix	116-118	3
β-strand	120-121	2	2
β-strand	123-124	2	3
β-strand	127-128	2	3
α-helix	134-137	4
α-helix	138-143	6
α-helix	149-160	12

Chain B: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	4
β-strand	32-35	4	4
α-helix	45-52	8
β-strand	58-60	3	4
β-strand	70	1	4
β-strand	84-89	6	5
β-strand	92-99	8	5
α-helix	116-118	3
β-strand	120-121	2	5
β-strand	123-124	2	6
β-strand	127-128	2	6
α-helix	134-137	4
α-helix	138-143	6
α-helix	149-160	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Regulator of nonsense transcripts 1	A, B	protein	162	HOMO SAPIENS	Q92900 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2IYK_1 REGULATOR OF NONSENSE TRANSCRIPTS 1 (chains A, B)
GAMGTKDLPIHACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTL
HKDGPLGETVLECYNCGCRNVFLLGFIPAKADSVVVLLCRQPCASQSSLKDINWDSSQWQ
PLIQDRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKEN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Primary citation

Crystal Structure of the Upf2-Interacting Domain of Nonsense-Mediated Mrna Decay Factor Upf1. Kadlec, J., Guilligay, D., Ravelli, R.B. et al. RNA (2006) 12:1817. DOI 10.1261/RNA.177606 · PubMed

Other PDB entries of the same protein (UniProt Q92900 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2XZO 2.4 Å, Upf1 helicase - RNA complex
2GK6 2.4 Å, Structural and Functional insights into the human Upf1 helicase core
2WJY 2.5 Å, Crystal structure of the complex between human nonsense mediated decay factors UPF1 and…
2GJK 2.6 Å, Structural and functional insights into the human Upf1 helicase core
8RXB 2.6 Å, Human UPF1 CH domain in complex with SMG6 peptide
2XZP 2.72 Å, Upf1 helicase
2GK7 2.8 Å, Structural and Functional insights into the human Upf1 helicase core
2WJV 2.85 Å, Crystal structure of the complex between human nonsense mediated decay factors UPF1 and…
6Z3R 2.97 Å, Structure of SMG1-8-9 kinase complex bound to UPF1-LSQ
6EJ5 3.34 Å, A conserved structural element in the RNA helicase UPF1 regulates its catalytic activity…
9QWN 3.6 Å, Human UPF1 in complex with the histone stem loop RNA

Browse structure collections

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