2GK6: Regulator of nonsense transcripts 1

Structural and Functional insights into the human Upf1 helicase core. Determined by X-ray diffraction at 2.4 Å resolution. Released 9 Jan 2007.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 9,795
Mol. weight: 141.21 kDa
Ligands: PO4, ADP, MG
Released: 9 Jan 2007

Explore 2GK6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2GK6 contains 62 α-helices and 53 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: 30 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	299-323	25
β-strand	326-329	4	1
β-strand	331-335	5	1
β-strand	341-346	6	1
β-strand	361-366	6	1
β-strand	375-382	8	1
β-strand	390-395	6	1
β-strand	409-413	5	1
α-helix	418-432	15
β-strand	437	1	2
α-helix	440-445	6
α-helix	473-483	11
β-strand	487-491	5	3
α-helix	498-510	13
α-helix	516	1
β-strand	517-521	5	3
α-helix	524-535	12
β-strand	541-543	3	3
α-helix	548-550	3
β-strand	560	1	3
α-helix	561-565	5
α-helix	572-578	7
α-helix	589-608	20
β-strand	612-616	5	3
α-helix	618-621	4
α-helix	623-625	3
β-strand	632-635	4	3
α-helix	638-640	3
α-helix	643-650	8
β-strand	654	1	2
β-strand	656-661	6	3
α-helix	673-675	3
α-helix	676-680	5
α-helix	684-690	7
α-helix	694-695	2
β-strand	696-697	2	3
β-strand	700-701	2	4
α-helix	706-716	11
β-strand	722-723	2	4
α-helix	728-730	3
β-strand	746-750	5	5
β-strand	755-756	2	6
β-strand	765-766	2	6
α-helix	767-781	15
α-helix	787-789	3
β-strand	790-793	4	5
α-helix	797-809	13
α-helix	815-820	6
β-strand	822-824	3	5
α-helix	826-829	4
β-strand	834-841	8	5
α-helix	856-862	7
β-strand	866-874	9	5
α-helix	876-879	4
α-helix	883-894	12
α-helix	903-905	3

Chain B: 32 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	299-322	24
β-strand	326-329	4	7
β-strand	331-335	5	7
β-strand	341-346	6	7
β-strand	361-366	6	7
β-strand	375-382	8	7
β-strand	390-395	6	7
β-strand	409-413	5	7
α-helix	414-415	2
α-helix	418-432	15
β-strand	437	1	8
α-helix	440-445	6
α-helix	469-472	4
α-helix	473-482	10
β-strand	487-491	5	9
α-helix	498-510	13
α-helix	516	1
β-strand	517-521	5	9
α-helix	524-535	12
β-strand	541-543	3	9
β-strand	560	1	9
α-helix	561-565	5
α-helix	572-578	7
α-helix	589-608	20
β-strand	612-616	5	9
α-helix	618-621	4
α-helix	623-625	3
β-strand	632-635	4	9
α-helix	638-640	3
α-helix	643-650	8
β-strand	654	1	8
β-strand	656-661	6	9
α-helix	673-675	3
α-helix	676-680	5
α-helix	684-691	8
α-helix	694-695	2
β-strand	696-697	2	9
α-helix	698	1
β-strand	700-701	2	10
α-helix	710-716	7
β-strand	722-723	2	10
β-strand	746-750	5	11
β-strand	755-756	2	12
β-strand	765-766	2	12
α-helix	767-781	15
α-helix	787-789	3
β-strand	790-793	4	11
α-helix	797-809	13
α-helix	815-819	5
β-strand	822-824	3	11
α-helix	826-829	4
β-strand	834-841	8	11
α-helix	851-853	3
α-helix	856-862	7
β-strand	866-874	9	11
α-helix	876-879	4
α-helix	883-894	12
β-strand	898-899	2	11
α-helix	903-905	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Regulator of nonsense transcripts 1	A, B	protein	624	Homo sapiens	Q92900 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2GK6_1 Regulator of nonsense transcripts 1 (chains A, B)
PLGSRYEDAYQYQNIFGPLVKLEADYDKKLKESQTQDNITVRWDLGLNKKRIAYFTLPKT
DSDMRLMQGDEICLRYKGDLAPLWKGIGHVIKVPDNYGDEIAIELRSSVGAPVEVTHNFQ
VDFVWKSTSFDRMQSALKTFAVDETSVSGYIYHKLLGHEVEDVIIKCQLPKRFTAQGLPD
LNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPSNIAVDQL
TEKIHQTGLKVVRLCAKSREAIDSPVSFLALHNQIRNMDSMPELQKLQQLKDETGELSSA
DEKRYRALKRTAERELLMNADVICCTCVGAGDPRLAKMQFRSILIDESTQATEPECMVPV
VLGAKQLILVGDHCQLGPVVMCKKAAKAGLSQSLFERLVVLGIRPIRLQVQYRMHPALSA
FPSNIFYEGSLQNGVTAADRVKKGFDFQWPQPDKPMFFYVTQGQEEIASSGTSYLNRTEA
ANVEKITTKLLKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQ
GREKDFIILSCVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGNPKALSKQPLWNHLLN
YYKEQKVLVEGPLNNLRESLMQFS

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
MG	Magnesium ion	Mg	2

Primary citation

Structural and functional insights into the human Upf1 helicase core. Cheng, Z., Muhlrad, D., Lim, M.K. et al. EMBO J (2007) 26:253-264. DOI 10.1038/sj.emboj.7601464 · 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
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

About this viewer

MolViewer shows 2GK6 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.