1RY1: SRP9

Structure of the signal recognition particle interacting with the elongation-arrested ribosome. Determined by electron microscopy at 12.0 Å resolution. Released 20 Apr 2004.

Method: Electron microscopy
Resolution: 12.0 Å
Organisms: Canis lupus familiaris, Triticum aestivum
Chains: 14
Atoms: 11,794
Mol. weight: 179.85 kDa
Released: 20 Apr 2004

Explore 1RY1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1RY1 contains 35 α-helices and 28 β-strands across 6 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 B: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	16-18	3	4
α-helix	20-23	4
β-strand	24	1	5
β-strand	41	1	5
α-helix	46-53	8
α-helix	54-56	3
β-strand	59-63	5	4
β-strand	81-85	5	4
β-strand	87	1	6
β-strand	93	1	6
α-helix	102-111	10
α-helix	112-114	3
α-helix	116-119	4

Chain C: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	6-20	15
β-strand	26-29	4	1
β-strand	31	1	2
β-strand	32	1	3
β-strand	37	1	3
β-strand	38-43	6	1
β-strand	49-53	5	1
α-helix	56-58	3
α-helix	59-74	16

Chain D: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
α-helix	6-18	13
β-strand	26	1	2
β-strand	27-33	7	1
β-strand	55-61	7	1
β-strand	66-72	7	1
α-helix	76-90	15

Chain S: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	51-64	14

Chain U: 16 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	3-14	12
α-helix	17-19	3
α-helix	24-40	17
α-helix	45-61	17
α-helix	64-66	3
α-helix	70-85	16
β-strand	90	1	7
β-strand	99-104	6	8
α-helix	111-123	13
β-strand	129-133	5	8
α-helix	139-152	14
β-strand	156-158	3	8
α-helix	159-160	2
α-helix	165-179	15
β-strand	183-187	5	8
α-helix	188-190	3
α-helix	196-209	14
β-strand	213-219	7	8
α-helix	220-222	3
α-helix	225-236	12
β-strand	241-245	5	8
α-helix	254-263	10
β-strand	267-271	5	8
β-strand	279-281	3	8
α-helix	284-292	9

Chain W: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	329-341	13
α-helix	346-349	4
β-strand	351	1	7
α-helix	366-379	14
α-helix	384-388	5
α-helix	392-398	7
α-helix	401-409	9
α-helix	414-432	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SRP Alu domain	E	RNA	50	Canis lupus familiaris
SRP S domain	A	RNA	128	Canis lupus familiaris
Srp RNA	M	RNA	27	Canis lupus familiaris
Srp RNA	N	RNA	31	Canis lupus familiaris
Srp RNA	O	RNA	24	Canis lupus familiaris
Srp RNA	P	RNA	20	Canis lupus familiaris
Srp RNA	Q	RNA	12	Canis lupus familiaris
Srp RNA	R	RNA	12	Canis lupus familiaris
SRP9	C	protein	85	Canis lupus familiaris	P49458 (AlphaFold model)
SRP14	D	protein	106	Canis lupus familiaris	P37108 (AlphaFold model)
SRP19	B	protein	108	Canis lupus familiaris	P09132 (AlphaFold model)
SRP54NG	U	protein	296	Canis lupus familiaris	O07347 (AlphaFold model)

2 more molecules are not listed.

Sequence of entity 1 (E), FASTA

>1RY1_1 SRP Alu domain (chains E)
GGGCCGGGCGCGGUGGCGCGCGCCUGUAGUCCCAGCUACUCGGGAGGCUC

Sequence of entity 2 (A), FASTA

>1RY1_2 SRP S domain (chains A)
GACACUAAGUUCGGCAUCAAUAUGGUGACCUCCCGGGAGCGGGGGACCACCAGGUUGCCU
AAGGAGGGGUGAACCGGCCCAGGUCGGAAACGGAGCAGGUCAAAACUCCCGUGCUGAUCA
GUAGUGUC

Sequence of entity 3 (M), FASTA

>1RY1_3 SRP RNA (chains M)
AGGCUGGAGGAUCGCUUGAGUCCAGGA

Sequence of entity 4 (N), FASTA

>1RY1_4 SRP RNA (chains N)
CCUGUGCAACAUAGCGAGACCCCGUCUCUUU

Sequence of entity 5 (O), FASTA

>1RY1_5 SRP RNA (chains O)
GUUCUGGGCUGUAGUGCGCUAUGC

Sequence of entity 6 (P), FASTA

>1RY1_6 SRP RNA (chains P)
CAAUAGCCACUGCACUCCAG

Sequence of entity 7 (Q), FASTA

>1RY1_7 SRP RNA (chains Q)
CGAUCGGGUGUC

Sequence of entity 8 (R), FASTA

>1RY1_8 SRP RNA (chains R)
AUCGCGCCUGUG

Sequence of entity 9 (C), FASTA

>1RY1_9 SRP9 (chains C)
PQYQTWEEFSRAAEKLYLADPMKARVVLKYRHSDGNLCVKVTDDLVCLVYKTDQAQDVKK
IEKFHSQLMRLMVAKEARNVTMETE

Sequence of entity 10 (D), FASTA

>1RY1_10 SRP14 (chains D)
VLLESEQFLTELTRLFQKCRTSGSVYITLKKYDGRTKPIPKKGTVEGFEPADNKCLLRAT
DGKKKISTVVSSKEVNKFQMAYSNLLRANMDGLKKRDKKNKTKKTK

Sequence of entity 11 (B), FASTA

>1RY1_11 SRP19 (chains B)
MRFICIYPAYLNNKKTIAEGRRIPISKAVENPTATEIQDVCSAVGLNVFLEKNKMYSREW
NRDVQYRGRVRVQLKQEDGSLCLVQFPSRKSVMLYAAEMIPKLKTRTQ

Sequence of entity 12 (U), FASTA

>1RY1_12 SRP54NG (chains U)
MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEAL
GKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLAL
YYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEA
RDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVT
GLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGD

Primary citation

Structure of the signal recognition particle interacting with the elongation-arrested ribosome. Halic, M., Becker, T., Pool, M.R. et al. Nature (2004) 427:808-814. DOI 10.1038/nature02342 · 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…
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)

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