2WJV: Regulator of nonsense transcripts 1

Crystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2. Determined by X-ray diffraction at 2.85 Å resolution. Released 7 Jul 2009.

Method: X-ray diffraction
Resolution: 2.85 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 13,187
Mol. weight: 203.85 kDa
Ligands: ZN
Released: 7 Jul 2009

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

Secondary structure: helices and β-sheets

2WJV contains 91 α-helices and 84 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: 47 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	131-133	3
β-strand	134-137	4	1
β-strand	142-145	4	1
α-helix	155-163	9
β-strand	168-170	3	1
β-strand	180	1	1
β-strand	194-198	5	2
α-helix	199	1
β-strand	204-209	6	2
α-helix	226-228	3
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	259-268	10
α-helix	289-293	5
α-helix	299-321	23
β-strand	326-329	4	4
β-strand	331-334	4	5
α-helix	336-338	3
β-strand	342-345	4	5
β-strand	361-366	6	4
β-strand	374-379	6	4
β-strand	380-382	3	5
β-strand	391-393	3	5
β-strand	409-413	5	4
α-helix	418-432	15
β-strand	437	1	6
α-helix	439-445	7
α-helix	457-460	4
α-helix	465	1
α-helix	469-471	3
α-helix	473-483	11
β-strand	487-491	5	7
α-helix	498-510	13
α-helix	516	1
β-strand	517-521	5	7
α-helix	524-535	12
β-strand	541-543	3	7
α-helix	547-549	3
α-helix	557-559	3
β-strand	560	1	7
α-helix	561-566	6
α-helix	572-582	11
α-helix	589-608	20
β-strand	612-616	5	7
α-helix	618-621	4
α-helix	623-625	3
β-strand	632-635	4	7
α-helix	638-640	3
α-helix	643-650	8
β-strand	654	1	6
β-strand	656-661	6	7
α-helix	673-675	3
α-helix	676-680	5
α-helix	684-691	8
α-helix	695	1
β-strand	696-697	2	7
α-helix	698	1
β-strand	700-701	2	8
α-helix	706-716	11
β-strand	722-723	2	8
α-helix	728-730	3
α-helix	732	1
β-strand	741	1	9
β-strand	744	1	9
β-strand	746-750	5	10
α-helix	753-755	3
β-strand	756-758	3	11
β-strand	763-765	3	11
α-helix	767-783	17
α-helix	787-789	3
β-strand	790-793	4	10
α-helix	797-810	14
α-helix	815-819	5
β-strand	822-824	3	10
α-helix	827-829	3
β-strand	834-840	7	10
α-helix	851-853	3
α-helix	856-862	7
β-strand	866-874	9	10
α-helix	876-879	4
α-helix	883-894	12
β-strand	898-900	3	10
α-helix	903-905	3
β-strand	907-908	2	10

Chain B: 41 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	131-133	3
β-strand	134-137	4	12
β-strand	142-145	4	12
α-helix	155-163	9
β-strand	168-170	3	12
β-strand	180	1	12
β-strand	194-198	5	13
β-strand	204-209	6	13
α-helix	210-214	5
α-helix	226-228	3
β-strand	230-231	2	13
β-strand	233-234	2	14
β-strand	237-238	2	14
α-helix	244-247	4
α-helix	248-253	6
α-helix	259-268	10
α-helix	277-279	3
α-helix	289-293	5
α-helix	299-321	23
β-strand	326-329	4	15
β-strand	331-332	2	15
β-strand	342-345	4	15
β-strand	361-366	6	15
β-strand	374-382	9	15
β-strand	391-395	5	15
β-strand	409-413	5	15
α-helix	418-432	15
β-strand	437	1	16
α-helix	439-445	7
α-helix	465	1
α-helix	469-471	3
α-helix	473-483	11
β-strand	487-491	5	17
α-helix	498-510	13
α-helix	516	1
β-strand	517-521	5	17
α-helix	524-536	13
β-strand	541-543	3	17
α-helix	547-549	3
α-helix	557-559	3
β-strand	560	1	17
α-helix	561-566	6
α-helix	572-584	13
α-helix	589-608	20
β-strand	612-616	5	17
α-helix	618-621	4
α-helix	623-625	3
β-strand	632-635	4	17
α-helix	638-640	3
α-helix	643-650	8
β-strand	654	1	16
β-strand	656-661	6	17
α-helix	673-675	3
α-helix	676-680	5
α-helix	684-691	8
β-strand	696-697	2	17
β-strand	700-701	2	18
α-helix	706-716	11
β-strand	722-723	2	18
β-strand	741	1	19
β-strand	744	1	19
β-strand	746-750	5	20
β-strand	756	1	21
β-strand	765	1	21
α-helix	767-783	17
α-helix	787-789	3
β-strand	790-793	4	20
α-helix	797-810	14
β-strand	813	1	5
α-helix	815-819	5
β-strand	822-824	3	20
α-helix	826-829	4
β-strand	834-840	7	20
α-helix	851-853	3
α-helix	856-862	7
β-strand	866-874	9	20
α-helix	876-879	4
α-helix	883-894	12
β-strand	898-900	3	20
α-helix	903-905	3
β-strand	907-908	2	20

Chain D: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1108-1126	19
β-strand	1168-1174	7	2
β-strand	1183-1189	7	2
α-helix	1193-1197	5

Chain E: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1108-1128	21
β-strand	1168-1177	10	13
β-strand	1180-1189	10	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Regulator of nonsense transcripts 1	A, B	protein	800	HOMO SAPIENS	Q92900 (AlphaFold model)
Regulator of nonsense transcripts 2	D, E	protein	97	HOMO SAPIENS	Q9HAU5 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2WJV_1 REGULATOR OF NONSENSE TRANSCRIPTS 1 (chains A, B)
TKDLPIHACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDG
PLGETVLECYNCGCRNVFLLGFIPAKADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQ
DRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKENPSATLEDLEKPGVDEEPQHVLL
RYEDAYQYQNIFGPLVKLEADYDKKLKESQTQDNITVRWDLGLNKKRIAYFTLPKTDSDM
RLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIELRSSVGAPVEVTHNFQVDFV
WKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQGLPDLNHS
QVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQLTEKI
HQTGLKVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSADEKR
YRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPVVLGA
KQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSAFPSN
IFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEAANVE
KITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREK
DFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLNYYKE
QKVLVEGPLNNLRESLMQFS

Sequence of entity 2 (D, E), FASTA

>2WJV_2 REGULATOR OF NONSENSE TRANSCRIPTS 2 (chains D, E)
AMGVPCVEDEDFIQALDKMMLENLQQRSGESVKVHQLDVAIPLHLKSQLRKGPPLGGGEG
EAESADTMPFVMLTRKGNKQQFKILNVPMSSQLAANH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Water and common crystallization additives (SO4) are not listed.

Primary citation

Unusual Bipartite Mode of Interaction between the Nonsense-Mediated Decay Factors, Upf1 and Upf2. Clerici, M., Mourao, A., Gutsche, I. et al. EMBO J (2009) 28:2293. DOI 10.1038/EMBOJ.2009.175 · 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
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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