9QWN: Human UPF1

Human UPF1 in complex with the histone stem loop RNA. Determined by electron microscopy at 3.6 Å resolution. Released 3 Dec 2025.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 6,825
Mol. weight: 102.07 kDa
Ligands: ZN
Released: 3 Dec 2025

Explore 9QWN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9QWN contains 35 α-helices and 40 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: 35 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	123	1	1
α-helix	131-133	3
β-strand	134-137	4	1
β-strand	142-145	4	1
α-helix	155-163	9
β-strand	169	1	1
β-strand	180	1	1
β-strand	194-198	5	2
β-strand	205-209	5	2
β-strand	230-231	2	2
β-strand	233-234	2	3
β-strand	237-238	2	3
α-helix	244-247	4
α-helix	248-253	6
α-helix	259-271	13
α-helix	278-281	4
α-helix	288-293	6
α-helix	299-322	24
β-strand	325-329	5	4
β-strand	334	1	4
β-strand	341-345	5	4
β-strand	361-366	6	4
β-strand	374-382	9	4
β-strand	391-395	5	4
β-strand	409-413	5	4
α-helix	418-432	15
β-strand	437	1	5
α-helix	439-445	7
α-helix	458-460	3
α-helix	469-471	3
α-helix	473-482	10
β-strand	487-491	5	6
α-helix	498-512	15
β-strand	517-521	5	6
α-helix	524-535	12
β-strand	541-543	3	6
α-helix	557-559	3
β-strand	560	1	6
α-helix	561-566	6
α-helix	572-583	12
α-helix	589-609	21
β-strand	612-616	5	6
α-helix	619-621	3
β-strand	632-636	5	6
α-helix	638-640	3
α-helix	643-650	8
β-strand	654	1	5
β-strand	656-661	6	6
α-helix	673-678	6
α-helix	684-691	8
α-helix	693-695	3
β-strand	696-697	2	6
β-strand	700-701	2	7
α-helix	706-716	11
β-strand	722-723	2	7
α-helix	728-730	3
β-strand	741	1	8
β-strand	744	1	8
β-strand	746-750	5	9
β-strand	756-757	2	10
β-strand	764-765	2	10
α-helix	767-782	16
β-strand	790-793	4	9
α-helix	797-808	12
α-helix	815-820	6
β-strand	822-824	3	9
α-helix	826-830	5
β-strand	836-840	5	9
α-helix	852-854	3
α-helix	856-864	9
β-strand	869-874	6	9
α-helix	876-879	4
α-helix	883-894	12
β-strand	898-900	3	9
β-strand	907-908	2	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 2 of Regulator of nonsense transcripts 1	A	protein	800	Homo sapiens	Q92900 (AlphaFold model)
RNA stem loop	D	RNA	38	synthetic construct

Sequence of entity 1 (A), FASTA

>9QWN_1 Isoform 2 of Regulator of nonsense transcripts 1 (chains A)
TKDLPIHACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDG
PLGETVLECYNCGCRNVFLLGFIPAKADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQ
DRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKENPSATLEDLEKPGVDEEPQHVLL
RYEDAYQYQNIFGPLVKLEADYDKKLKESQTQDNITVRWDLGLNKKRIAYFTLPKTDSDM
RLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIELRSSVGAPVETVHNFQVDFV
WKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVITKCQLPKRFTAQGLPDLNHS
QVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKI
HQTGLKVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKR
YRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLGA
KQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSN
IFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVE
KITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREK
DFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKE
QKVLVEGPLNNLRESLMQFS

Sequence of entity 2 (D), FASTA

>9QWN_2 RNA stem loop (chains D)
UUUUUUUUUUUUCCAAAGGCUCUUUUCAGAGCCACCCA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

Primary citation

Mechanistic insights into recruitment and regulation of the RNA helicase UPF1 in replication-dependent histone mRNA decay. Machado de Amorim, A., Xue, G., He, W. et al. Nat Commun (2026) 17:155-155. DOI 10.1038/s41467-025-67991-z · 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…
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…

Browse structure collections

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