2XZO: Upf1 helicase - RNA complex

Upf1 helicase - RNA complex. Determined by X-ray diffraction at 2.4 Å resolution. Released 30 Mar 2011.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: HOMO SAPIENS, SYNTHETIC CONSTRUCT
Chains: 2
Atoms: 4,932
Mol. weight: 73.42 kDa
Ligands: MG, ALF, ADP
Released: 30 Mar 2011

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

Secondary structure: helices and β-sheets

2XZO contains 34 α-helices and 31 β-strands across 1 chain. 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: 34 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	299-321	23
β-strand	324	1	1
β-strand	329	1	1
β-strand	332-335	4	1
β-strand	341-345	5	1
β-strand	361-366	6	1
β-strand	374-382	9	1
β-strand	385	1	2
β-strand	388	1	2
β-strand	391-395	5	1
β-strand	409-414	6	1
α-helix	418-432	15
β-strand	437	1	3
α-helix	439-445	7
α-helix	469-471	3
α-helix	473-482	10
β-strand	487-491	5	4
α-helix	498-511	14
α-helix	516	1
β-strand	517-521	5	4
α-helix	524-536	13
β-strand	541-543	3	4
α-helix	547-549	3
α-helix	557-559	3
β-strand	560	1	4
α-helix	561-566	6
α-helix	571-580	10
α-helix	589-609	21
β-strand	612-616	5	4
α-helix	619-621	3
α-helix	623-625	3
β-strand	632-635	4	4
α-helix	638-640	3
α-helix	643-650	8
β-strand	654	1	3
β-strand	656-661	6	4
α-helix	673-675	3
α-helix	676-680	5
α-helix	684-691	8
α-helix	693-695	3
β-strand	696-697	2	4
β-strand	700-701	2	5
α-helix	706-716	11
β-strand	722-723	2	5
α-helix	728-730	3
α-helix	731-732	2
β-strand	746-750	5	6
β-strand	756-757	2	7
β-strand	764-765	2	7
α-helix	767-783	17
α-helix	787-789	3
β-strand	790-794	5	6
α-helix	797-803	7
α-helix	804-808	5
α-helix	815-819	5
β-strand	822-825	4	6
β-strand	834-840	7	6
α-helix	851-854	4
α-helix	856-863	8
β-strand	866-874	9	6
α-helix	876-879	4
α-helix	883-894	12
β-strand	898-900	3	6
α-helix	903-905	3
β-strand	907-908	2	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Regulator of nonsense transcripts 1	A	protein	623	HOMO SAPIENS	Q92900 (AlphaFold model)
5'-r(upupupupupup*up)-3'	D	RNA	7	SYNTHETIC CONSTRUCT

Sequence of entity 1 (A), FASTA

>2XZO_1 REGULATOR OF NONSENSE TRANSCRIPTS 1 (chains A)
GHMRYEDAYQYQNIFGPLVKLEADYDKKLKESQTQDNITVRWDLGLNKKRIAYFTLPKTD
SDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIELRSSVGAPVEVTHNFQV
DFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQGLPDL
NHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLT
EKIHQTGLKVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSAD
EKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVV
LGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAF
PSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAA
NVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQG
REKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNY
YKEQKVLVEGPLNNLRESLMQFS

Sequence of entity 2 (D), FASTA

>2XZO_2 5'-R(*UP*UP*UP*UP*UP*UP*UP)-3' (chains D)
UUUUUUU

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ALF	Tetrafluoroaluminate ion	Al F4	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Water and common crystallization additives (1PE) are not listed.

Primary citation

Molecular Mechanisms for the RNA-Dependent ATPase Activity of Upf1 and its Regulation by Upf2. Chakrabarti, S., Jayachandran, U., Bonneau, F. et al. Mol Cell (2011) 41:693. DOI 10.1016/J.MOLCEL.2011.02.010 · PubMed

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

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…
2IYK 2.95 Å, Crystal structure of the UPF2-interacting domain of nonsense mediated mRNA decay factor…
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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