5AOX: Signal recognition particle 9 kda protein

Human Alu RNA retrotransposition complex in the ribosome-stalling conformation. Determined by X-ray diffraction at 2.04 Å resolution. Released 11 Nov 2015.

Method: X-ray diffraction
Resolution: 2.04 Å
Organisms: HOMO SAPIENS, SYNTHETIC CONSTRUCT
Chains: 6
Atoms: 6,638
Mol. weight: 98.06 kDa
Ligands: MG
Released: 11 Nov 2015

Explore 5AOX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5AOX contains 10 α-helices and 16 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: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	1
α-helix	7-20	14
β-strand	26-32	7	1
β-strand	37-43	7	1
β-strand	48-53	6	1
α-helix	57-73	17

Chain B: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
α-helix	6-19	14
β-strand	26-32	7	1
β-strand	55-61	7	1
β-strand	66-72	7	1
α-helix	76-90	15

Chain D: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	2
α-helix	7-18	12
α-helix	22-24	3
β-strand	26-32	7	2
α-helix	33-35	3
β-strand	37-43	7	2
β-strand	48-53	6	2
α-helix	57-72	16

Chain E: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	2
α-helix	6-19	14
β-strand	26-33	8	2
β-strand	55-61	7	2
β-strand	66-72	7	2
α-helix	73-90	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Signal recognition particle 9 kda protein	A, D	protein	85	HOMO SAPIENS	P49458 (AlphaFold model)
Signal recognition particle 14 kda protein	B, E	protein	94	HOMO SAPIENS	P37108 (AlphaFold model)
Alu jo consensus RNA	C, F	RNA	87	SYNTHETIC CONSTRUCT

Sequence of entity 1 (A, D), FASTA

>5AOX_1 SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN (chains A, D)
PQYQTWEEFSRAAEKLYLADPMKARVVLKYRHSDGNLCVKVTDDLVSLVYKTDQAQDVKK
IEKFHSQLMRLMVAKEARNVTMETE

Sequence of entity 2 (B, E), FASTA

>5AOX_2 SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN (chains B, E)
GAMESEQFLTELTRLFQKCRTSGSVYITLKKYDGRTKPIPKKGTVEGFEPADNKCLLRAT
DGKKKISTVVSSKEVNKFQMAYSNLLRANMDGLK

Sequence of entity 3 (C, F), FASTA

>5AOX_3 ALU JO CONSENSUS RNA (chains C, F)
GGCCGGGCGCGGUGGCUCACGCCUGUAAUCCCAGCACUUUGGGAGGCCGAGGCGGGAGGA
UCGCGAACACGCGAGACCCCGUCUCUA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4

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

Primary citation

Retrotransposition and Crystal Structure of an Alu Rnp in the Ribosome-Stalling Conformation. Ahl, V., Keller, H., Schmidt, S. et al. Mol Cell (2015) 60:715. DOI 10.1016/J.MOLCEL.2015.10.003 · PubMed

Other PDB entries of the same protein (UniProt P49458 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1E8O 3.2 Å, Core of the Alu domain of the mammalian SRP
7NFX 3.2 Å, Mammalian ribosome nascent chain complex with SRP and SRP receptor in early state A
4UYK 3.22 Å, Crystal structure of a Signal Recognition Particle Alu domain in the elongation arrest…
4UYJ 3.35 Å, Crystal structure of a Signal Recognition Particle Alu domain in the elongation arrest…
1E8S 4.0 Å, Alu domain of the mammalian SRP (potential Alu retroposition intermediate)
1RY1 12.0 Å, Structure of the signal recognition particle interacting with the elongation-arrested…

Browse structure collections

About this viewer

MolViewer shows 5AOX 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.