4UYJ: Signal recognition particle 9 kda protein

Crystal structure of a Signal Recognition Particle Alu domain in the elongation arrest conformation. Determined by X-ray diffraction at 3.35 Å resolution. Released 5 Nov 2014.

Method: X-ray diffraction
Resolution: 3.35 Å
Organisms: HOMO SAPIENS, PYROCOCCUS HORIKOSHII OT3
Chains: 6
Atoms: 7,256
Mol. weight: 116.56 kDa
Released: 5 Nov 2014

Explore 4UYJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4UYJ contains 10 α-helices and 17 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, 5 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
α-helix	7-20	14
β-strand	26-32	7	1
β-strand	37-43	7	1
β-strand	48-50	3	1
β-strand	53	1	1
α-helix	58-74	17

Chain B: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
α-helix	6-19	14
β-strand	26-33	8	1
β-strand	55-61	7	1
β-strand	66-71	6	1
α-helix	73-75	3
α-helix	76-90	15

Chain C: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	2
α-helix	7-20	14
β-strand	26-32	7	2
β-strand	37-43	7	2
β-strand	48-53	6	2
α-helix	58-74	17

Chain D: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	2
α-helix	6-17	12
β-strand	26-33	8	2
β-strand	55-61	7	2
β-strand	66-72	7	2
α-helix	73-75	3
α-helix	76-90	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Signal recognition particle 9 kda protein	A, C	protein	85	HOMO SAPIENS	P49458 (AlphaFold model)
Signal recognition particle 14 kda protein	B, D	protein	107	HOMO SAPIENS	P37108 (AlphaFold model)
Srp RNA	R, S	RNA	110	PYROCOCCUS HORIKOSHII OT3

Sequence of entity 1 (A, C), FASTA

>4UYJ_1 SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN (chains A, C)
MPQYQTWEEFSRAAEKLYLADPMKARVVLKYRHSDGNLCVKVTDDLVCLVYKTDQAQDVK
KIEKFHSQLMRLMVAKEARNVTMET

Sequence of entity 2 (B, D), FASTA

>4UYJ_2 SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN (chains B, D)
MVLLESEQFLTELTRLFQKCRTSGSVYITLKKYDGRTKPIPKKGTVEGFEPADNKCLLRA
TDGKKKISTVVSSKEVNKFQMAYSNLLRANMDGLKKRDKKNKTKKTK

Sequence of entity 3 (R, S), FASTA

>4UYJ_3 SRP RNA (chains R, S)
GGGGCUAGGCCGGGGGGUUCGGCGUCCCCUGUAACCGGAAACCGCCGAUAUGCCGGGGCC
GAAGCCCGAGGGGCGGUUCCCGUAAGGGUUCCCACCCUCGGGCGUGCCUC

Primary citation

Crystal Structure of a Signal Recognition Particle Alu Domain in the Elongation Arrest Conformation. Bousset, L., Mary, C., Brooks, M.A. et al. RNA (2014) 20:1955. DOI 10.1261/RNA.047209.114 · PubMed

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

5AOX 2.04 Å, Human Alu RNA retrotransposition complex in the ribosome-stalling conformation
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…
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…

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