PDB-4uyk: Crystal structure of a Signal Recognition Particle Alu domain in ...

ID or keywords:

Entry

Database: PDB / ID: 4uyk

Title

Crystal structure of a Signal Recognition Particle Alu domain in the elongation arrest conformation

Components

SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN
SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN
SRP RNA

Keywords

SIGNALING PROTEIN / SIGNAL RECOGNITION PARTICLE / TRANSLATION / RNA / RNA FOLDING

Function / homology

Function and homology information

signal recognition particle receptor complex / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / cotranslational protein targeting to membrane / protein targeting to ER / negative regulation of translational elongation / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

PYROCOCCUS HORIKOSHII OT3 (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 3.22 Å

Authors

Bousset, L. / Mary, C. / Brooks, M.A. / Scherrer, A. / Strub, K. / Cusack, S.

Citation

Journal: RNA / Year: 2014
Title: Crystal Structure of a Signal Recognition Particle Alu Domain in the Elongation Arrest Conformation.
Authors: Bousset, L. / Mary, C. / Brooks, M.A. / Scherrer, A. / Strub, K. / Cusack, S.

History

Deposition	Sep 1, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 5, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 3, 2014	Group: Database references
Revision 1.2	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4uyk.cif.gz	232.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4uyk.ent.gz	185.5 KB	Display	PDB format
PDBx/mmJSON format	4uyk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4uyk_validation.pdf.gz	465.7 KB	Display	wwPDB validaton report
Full document	4uyk_full_validation.pdf.gz	467.7 KB	Display
Data in XML	4uyk_validation.xml.gz	13.2 KB	Display
Data in CIF	4uyk_validation.cif.gz	17.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uy/4uyk ftp://data.pdbj.org/pub/pdb/validation_reports/uy/4uyk	HTTPS FTP

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Related structure data

Related structure data	4uyjC C: citing same article (ref.)
Similar structure data	4iov-d 6ih9-d 7kp3-d 2qa0-d 3ra2-d 3j1q-d 7jot-d 6u2v-d 3ra9-d 3raa-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (2) #130 - Oct 2010 Riboswitches similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (2) #253 - Jan 2021 Expressome similarity (2) #260 - Aug 2021 Ribonuclease P similarity (2) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (2) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #10 - Oct 2000 Ribosome similarity (2) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (2) #245 - May 2020 Spliceosomes similarity (2) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (2) #65 - May 2005 Self-splicing RNA similarity (2) #105 - Sep 2008 Ribonuclease A similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (3) #161 - May 2013 Ricin similarity (2) #227 - Nov 2018 Telomerase similarity (2) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

PDB pages

PDBj /

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Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (2)
#130 - Oct 2010
Riboswitches
similarity (2)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
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#157 - Jan 2013
Transfer-Messenger RNA
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#253 - Jan 2021
Expressome
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#260 - Aug 2021
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#181 - Jan 2015
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#229 - Jan 2019
Fluorescent RNA Aptamers
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#146 - Feb 2012
Aminoglycoside Antibiotics
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#15 - Mar 2001
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similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
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#10 - Oct 2000
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#210 - Jun 2017
Adenine Riboswitch in Action
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#87 - Mar 2007
Zinc Fingers
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#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (2)
#245 - May 2020
Spliceosomes
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#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (2)
#65 - May 2005
Self-splicing RNA
similarity (2)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
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#161 - May 2013
Ricin
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#227 - Nov 2018
Telomerase
similarity (2)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
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Elongation Factors
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#89 - May 2007
Aconitase and Iron Regulatory Protein 1
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Deposited unit

A: SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN

B: SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN

R: SRP RNA

66.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	100.860, 100.860, 197.470
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN / SRP9 Mass: 10233.126 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-85 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEH9 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49458
#2: Protein	SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN / SRP14 / 18 KDA ALU RNA-BINDING PROTEIN Mass: 12386.117 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-107 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEH14DELTAR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37108
#3: RNA chain	SRP RNA Mass: 43523.797 Da / Num. of mol.: 1 / Fragment: ALU DOMAIN, RESIDUES 1-89 AND RESIDUES 289-314 / Source method: obtained synthetically / Source: (synth.) PYROCOCCUS HORIKOSHII OT3 (archaea) / References: GenBank: HG323574
Has protein modification	Y
Sequence details	HUMAN SRP9 RESIDUES 1 TO 85 WERE EXPRESSED IN THIS WORK HUMAN SRP14 RESIDUES 1 TO 107 WERE ...HUMAN SRP9 RESIDUES 1 TO 85 WERE EXPRESSED IN THIS WORK HUMAN SRP14 RESIDUES 1 TO 107 WERE EXPRESSED IN THIS WORK THE P. HORIKOSHII SRP ALU RNA SEQUENCE HAS THE S-DOMAIN DELETED, AND REPLACED BY A TETRA LOOP. CCC (CYCLIC CYTIDINE), PRODUCED DURING IN-VITRO TRANSCRIPTION.

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.12 Å³/Da / Density % sol: 73.3 % / Description: NONE
Crystal grow	pH: 5 Details: 17.5% PEG 400, 5% GLYCEROL BUFFERED IN 100 MM SODIUM ACETATE PH 5.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
Detector	Type: ADSC CCD / Detector: CCD / Date: Apr 16, 2004
Radiation	Monochromator: DIAMOND (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.934 Å / Relative weight: 1
Reflection	Resolution: 3.2→30 Å / Num. obs: 30821 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 2.18 % / R_merge(I) obs: 0.08 / Net I/σ(I): 9.09
Reflection shell	Resolution: 3.2→3.4 Å / Redundancy: 2.18 % / R_merge(I) obs: 0.64 / Mean I/σ(I) obs: 1.74 / % possible all: 95.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0071	refinement
XDS		data reduction
XSCALE		data scaling
SHARP		phasing

Refinement

Method to determine structure:

MAD
Starting model: NONE

Resolution: 3.22→89.82 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.936 / SU B: 48.231 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23315	854	5 %	RANDOM
R_work	0.1916	-	-	-
obs	0.19365	16238	99.3 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 123.705 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.44 Å²	0 Å²	0 Å²
2-	-	3.44 Å²	0 Å²
3-	-	-	-6.89 Å²

Refinement step

Cycle: LAST / Resolution: 3.22→89.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1377	2882	0	0	4259

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.014	4624
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	2738
X-RAY DIFFRACTION	r_angle_refined_deg	1.116	1.478	6910
X-RAY DIFFRACTION	r_angle_other_deg	1.071	3	6462
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.991	5	171
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.828	23.966	58
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.484	15	265
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.631	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	752
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3158
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1049
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.79	6.421	690
X-RAY DIFFRACTION	r_mcbond_other	2.788	6.419	689
X-RAY DIFFRACTION	r_mcangle_it	4.816	9.598	859
X-RAY DIFFRACTION	r_mcangle_other	4.813	9.602	860
X-RAY DIFFRACTION	r_scbond_it	2.52	7.392	3934
X-RAY DIFFRACTION	r_scbond_other	2.519	7.392	3935
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.189	11.068	6051
X-RAY DIFFRACTION	r_long_range_B_refined	7.091	71.367	5914
X-RAY DIFFRACTION	r_long_range_B_other	7.091	71.368	5915
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 3.22→3.304 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.445	59	-
R_work	0.338	1136	-
obs	-	-	96.6 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.0204	-0.0338	-0.108	3.9951	-1.0708	1.7651	0.067	-0.0514	0.0489	-0.1309	-0.4436	-0.8341	-0.2435	0.8179	0.3766	0.4897	-0.0016	0.0586	0.8557	0.0068	0.7557	93.9689	57.9997	9.2527
2	5.4347	-1.784	-2.0727	3.0253	1.0933	4.3278	-0.1229	-0.832	0.1467	-0.0876	0.73	-0.2189	0.4075	0.0072	-0.6071	0.5762	0.0649	-0.1105	0.7538	-0.2454	0.2898	89.2823	51.2755	12.3263
3	2.0998	0.1659	1.5837	0.7287	1.2374	3.3652	0.2997	-0.36	0.0861	0.0555	-0.108	0.0813	0.5004	-0.2427	-0.1917	0.604	0.0874	-0.0155	0.6956	0.027	0.3819	76.7156	43.7815	7.3572
4	2.5155	-1.553	0.8181	3.1019	1.5459	2.2616	-0.1611	-0.4413	-0.0585	0.348	0.0837	0.1876	0.3494	-0.3395	0.0774	0.8135	0.0758	0.0583	0.8449	0.0401	0.1325	78.9886	46.8283	13.929
5	0.4647	-0.8709	-0.5516	1.6873	1.0188	0.817	-0.0738	-0.1026	-0.0465	-0.0528	0.2524	0.0908	0.0829	0.0631	-0.1786	0.697	-0.0422	-0.0276	0.5738	0.0121	0.3764	81.6864	37.3684	-12.4402
6	3.5925	-0.7722	4.345	0.2228	-1.1131	6.5571	0.206	0.4723	-0.7438	0.2407	-0.0493	0.0984	-1.0379	0.9666	-0.1568	1.6038	0.0731	-0.566	0.9007	0.2101	0.5646	124.5581	30.715	16.442
7	2.4602	-2.0134	-0.2286	2.0884	0.5075	0.5654	0.3062	0.0607	0.1972	-0.4767	-0.0479	-0.2728	-0.2233	0.3315	-0.2583	0.6851	-0.0062	0.0835	0.5483	0.0159	0.2626	83.9587	51.5996	-21.0442

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 25
2	X-RAY DIFFRACTION	2	A	26 - 82
3	X-RAY DIFFRACTION	3	B	1 - 42
4	X-RAY DIFFRACTION	4	B	50 - 97
5	X-RAY DIFFRACTION	5	R	6 - 85
6	X-RAY DIFFRACTION	6	R	86 - 117
7	X-RAY DIFFRACTION	7	R	118 - 139

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