8RXB: Human UPF1 CH domain

Human UPF1 CH domain in complex with SMG6 peptide. Determined by X-ray diffraction at 2.6 Å resolution. Released 15 May 2024.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 12
Atoms: 7,195
Mol. weight: 127.39 kDa
Ligands: ZN
Released: 15 May 2024

Explore 8RXB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8RXB contains 32 α-helices and 62 β-strands across 12 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: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	20-23	4	4
β-strand	28-31	4	4
α-helix	41-49	9
β-strand	54-56	3	4
β-strand	65-66	2	4
β-strand	80-84	5	5
β-strand	90-95	6	5
β-strand	116-117	2	5
β-strand	119-120	2	6
β-strand	123-124	2	6
α-helix	130-133	4
α-helix	134-138	5
α-helix	141-142	2
α-helix	145-157	13

Chains B, F, G and N: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	408-410	3	5

Chain D: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	20-23	4	7
β-strand	28-31	4	7
α-helix	41-49	9
β-strand	54-56	3	7
β-strand	65-66	2	7
β-strand	80-83	4	8
β-strand	90-95	6	8
β-strand	116-117	2	8
β-strand	119-120	2	9
β-strand	123-124	2	9
α-helix	130-133	4
α-helix	134-139	6
α-helix	141-142	2
α-helix	145-155	11

Chain E: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	20-23	4	1
β-strand	28-31	4	1
α-helix	41-49	9
β-strand	54-56	3	1
β-strand	65-66	2	1
β-strand	80-84	5	2
β-strand	90-95	6	2
β-strand	116-117	2	2
β-strand	119-120	2	3
β-strand	123-124	2	3
α-helix	130-133	4
α-helix	134-139	6
α-helix	141-142	2
α-helix	145-154	10

Chain I: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	17-19	3
β-strand	20-23	4	10
β-strand	28-31	4	10
α-helix	41-49	9
β-strand	54-56	3	10
β-strand	65-66	2	10
β-strand	80-82	3	11
β-strand	91-92	2	12
β-strand	93-95	3	11
β-strand	116-117	2	11
β-strand	119-120	2	13
β-strand	123-124	2	13
α-helix	130-133	4
α-helix	134-138	5
α-helix	141-142	2
α-helix	145-154	10

Chain J: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	408-409	2	12

Chain L: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	17-19	3
β-strand	20-23	4	14
β-strand	28-31	4	14
α-helix	41-49	9
β-strand	54-56	3	14
β-strand	65-66	2	14
β-strand	80-82	3	15
β-strand	90-92	3	16
β-strand	93-95	3	15
β-strand	116-117	2	15
β-strand	119-120	2	17
β-strand	123-124	2	17
α-helix	130-133	4
α-helix	134-138	5
α-helix	145-154	10

Chain P: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	20-23	4	18
β-strand	28-31	4	18
α-helix	41-49	9
β-strand	54-56	3	18
β-strand	66	1	18
β-strand	80-84	5	19
β-strand	91-95	5	19
β-strand	116-117	2	19
β-strand	119-120	2	20
β-strand	123-124	2	20
α-helix	130-133	4
α-helix	134-139	6
α-helix	141-142	2
α-helix	145-155	11

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Regulator of nonsense transcripts 1	A, D, E, I, L, P	protein	173	Homo sapiens	Q92900 (AlphaFold model)
Telomerase-binding protein EST1A	B, F, G, J, N, Q	protein	15	Homo sapiens	Q86US8 (AlphaFold model)

Sequence of entity 1 (A, D, E, I, L, P), FASTA

>8RXB_1 Regulator of nonsense transcripts 1 (chains A, D, E, I, L, P)
TKDLPIHACSYCGIHDPACVVYCNTSKKWFCNGRGNTSGSHIVNHLVRAKCKEVTLHKDG
PLGETVLECYNCGCRNVFLLGFIPAKADSVVVLLCRQPCASQSSLKDINWDSSQWQPLIQ
DRCFLSWLVKIPSEQEQLRARQITAQQINKLEELWKENPSATLEDLEKPGVDE

Sequence of entity 2 (B, F, G, J, N, Q), FASTA

>8RXB_2 Telomerase-binding protein EST1A (chains B, F, G, J, N, Q)
RGRGILILPAHTTLS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	13

Primary citation

UPF1 helicase orchestrates mutually exclusive interactions with the SMG6 endonuclease and UPF2. Langer, L.M., Kurscheidt, K., Basquin, J. et al. Nucleic Acids Res (2024) 52:6036-6048. DOI 10.1093/nar/gkae323 · 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
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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