PDB-5v4r: Crystal structure of LARP1-unique domain DM15 bound to m7GTP

ID or keywords:

Entry

Database: PDB / ID: 5v4r

Title

Crystal structure of LARP1-unique domain DM15 bound to m7GTP

Components

La-related protein 1

Keywords

RNA BINDING PROTEIN / Cap-binding / RNA-binding /

DM15

Function / homology

Function and homology information

cellular response to rapamycin / translation activator activity / eukaryotic initiation factor 4E binding /

RNA cap binding / TORC1 signaling / response to amino acid starvation / RNA 7-methylguanosine cap binding / mRNA stabilization / post-transcriptional regulation of gene expression /

TOR signaling ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.77 Å

Authors

Berman, A.J. / Lahr, R.M.

Citation

Journal: Elife / Year: 2017
Title: La-related protein 1 (LARP1) binds the mRNA cap, blocking eIF4F assembly on TOP mRNAs.
Authors: Lahr, R.M. / Fonseca, B.D. / Ciotti, G.E. / Al-Ashtal, H.A. / Jia, J.J. / Niklaus, M.R. / Blagden, S.P. / Alain, T. / Berman, A.J.

History

Deposition	Mar 10, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 19, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5v4r.cif.gz	159.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5v4r.ent.gz	125.6 KB	Display	PDB format
PDBx/mmJSON format	5v4r.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v4/5v4r ftp://data.pdbj.org/pub/pdb/validation_reports/v4/5v4r	HTTPS FTP

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Related structure data

Related structure data	5v7cC 5v87C 4zc4S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5qrn-d 6vil-3 5qsh-d 4dvl-2 4mcu-2 2zf9-2 5qrv-d 5qrm-d 5qrs-d 3x0k-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#227 - Nov 2018 Telomerase similarity (5)

Deposited unit

A: La-related protein 1

B: La-related protein 1

hetero molecules

39.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: La-related protein 1

hetero molecules

defined by author
Evidence: gel filtration
20.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: La-related protein 1

defined by author
19.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	48.177, 60.163, 60.609
Angle α, β, γ (deg.)	90.00, 101.28, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	La-related protein 1 / La ribonucleoprotein domain family member 1 Mass: 19616.281 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LARP1, KIAA0731, LARP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6PKG0
#2: Chemical	ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE Mass: 539.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₂₀N₅O₁₄P₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 43.98 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH 7.5 and 10% PEG 6000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
Detector	Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Aug 18, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.77→33.895 Å / Num. obs: 28525 / % possible obs: 86 % / Redundancy: 2.9 % / Net I/σ(I): 2.45

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
Coot		model building
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4ZC4

4zc4

Resolution: 1.77→33.895 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.93

	R_factor	Num. reflection	% reflection
R_free	0.2094	1923	7.06 %
R_work	0.1763	-	-
obs	0.1787	27251	81.92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.77→33.895 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2626	0	33	175	2834

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	2769
X-RAY DIFFRACTION	f_angle_d	0.481	3722
X-RAY DIFFRACTION	f_dihedral_angle_d	13.357	1618
X-RAY DIFFRACTION	f_chiral_restr	0.029	348
X-RAY DIFFRACTION	f_plane_restr	0.002	468

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.7701-1.8144	0.2686	121	0.237	1601	X-RAY DIFFRACTION	73
1.8144-1.8634	0.245	146	0.2192	1861	X-RAY DIFFRACTION	85
1.8634-1.9182	0.2948	92	0.2351	1158	X-RAY DIFFRACTION	53
1.9182-1.9801	0.2429	105	0.2101	1400	X-RAY DIFFRACTION	64
1.9801-2.0509	0.2393	159	0.2032	2073	X-RAY DIFFRACTION	94
2.0509-2.133	0.2455	159	0.1967	2079	X-RAY DIFFRACTION	95
2.133-2.2301	0.2155	136	0.1862	1784	X-RAY DIFFRACTION	93
2.2301-2.3476	0.1964	83	0.1785	1122	X-RAY DIFFRACTION	93
2.3476-2.4947	0.2035	164	0.177	2193	X-RAY DIFFRACTION	99
2.4947-2.6872	0.2177	165	0.1877	2179	X-RAY DIFFRACTION	99
2.6872-2.9575	0.2203	166	0.1797	2207	X-RAY DIFFRACTION	100
2.9575-3.3851	0.2203	165	0.1721	2195	X-RAY DIFFRACTION	99
3.3851-4.2636	0.1442	97	0.1525	1267	X-RAY DIFFRACTION	57
4.2636-33.9016	0.2101	165	0.1614	2209	X-RAY DIFFRACTION	97

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	5.601	-2.2679	0.1153	1.0356	-0.3748	1.0356	0.0847	0.8095	-0.7447	-0.0355	0.6732	-0.5396	0.4018	0.5723	-0.4838	0.4028	0.1004	0.0397	0.5424	-0.2035	0.5208	15.8839	0.2537	-11.4321
2	4.719	-1.4164	1.0746	8.2822	1.2242	5.4461	0.0127	-0.0543	-0.0181	0.5511	-0.0197	-0.5478	0.2879	0.578	-0.0136	0.2608	0.0157	-0.0501	0.2917	0.0251	0.2984	14.5844	8.8531	0.8806
3	2.3745	-0.2448	0.8459	2.1956	-0.6284	2.3593	0.0093	-0.033	-0.0311	0.0704	-0.0129	0.0004	-0.0058	-0.0821	0.0044	0.2202	-0.0016	0.0096	0.2077	0.0057	0.1949	-1.7859	8.7394	-5.3898
4	2.2884	-0.3254	0.1669	9.3064	2.353	3.0492	-0.0118	0.1142	0.1033	-0.3911	0.0537	-0.0162	-0.0662	-0.0251	-0.0203	0.2299	0.0005	-0.0153	0.25	0.0231	0.2466	-11.7905	11.5351	-14.8555
5	2.4624	0.4961	0.7245	4.6106	4.5854	4.5948	-0.0913	-0.288	-0.6332	0.4061	-0.0399	0.9625	0.7646	-0.5068	0.162	0.4494	-0.0572	0.0078	0.4765	0.059	0.4889	-18.9085	0.1757	-11.5267
6	0.2323	0.806	-0.7239	2.8007	-2.9046	8.2576	0.0557	0.2565	0.3403	-0.1377	-0.094	0.9392	-0.3397	-0.649	-0.0978	0.2451	0.0647	-0.0057	0.4577	0.136	0.5522	-21.2137	14.483	-13.0644
7	7.7847	2.6753	-3.6853	2.3028	-0.2854	3.7099	-0.375	0.269	-0.0361	-0.3379	0.0867	0.913	0.3071	-0.8001	0.0413	0.3691	0.0168	-0.0504	0.4366	0.0205	0.5067	-22.2806	21.2342	-28.8666
8	4.1317	-1.3922	2.2572	1.9621	0.1896	3.8554	0.6409	0.9051	-0.2768	-1.485	-0.3589	0.3273	0.5947	0.2211	-0.2806	0.6272	0.083	-0.1028	0.4796	0.0148	0.3624	-18.6203	22.7627	-37.619
9	2.2816	0.5587	1.7945	3.0786	2.4302	2.8315	-0.1345	-0.0563	0.3252	-0.2658	-0.1528	0.176	-0.394	-0.4887	0.2821	0.3105	0.0551	-0.0598	0.3384	0.0358	0.3379	-20.522	33.3011	-23.1146
10	3.3882	-0.3205	0.9907	2.5524	-0.1369	5.0063	0.0214	0.3526	0.338	-0.108	-0.0244	-0.0927	-0.2353	-0.0236	0.0426	0.2971	0.0345	-0.0194	0.2814	0.0537	0.3216	-9.4979	28.9528	-22.9021
11	5.4652	-0.0636	-0.4198	3.9647	-1.1038	4.1999	-0.0078	0.6154	0.0488	-0.2059	-0.0784	-0.1311	0.1601	0.1639	0.0955	0.2278	0.0215	-0.0032	0.286	0.0278	0.2203	-2.8662	22.4132	-22.4599
12	1.7689	0.1569	-0.6962	4.3802	-0.4736	2.6276	0.079	0.7914	0.705	-0.263	-0.3005	-0.3149	-0.6193	0.3621	0.1263	0.2884	0.0036	0.0355	0.4723	0.1827	0.3789	6.1246	27.8255	-24.8287
13	3.863	-0.3899	-0.2457	3.4682	1.1254	9.0658	0.1072	0.3227	-0.0616	-0.0434	-0.1219	-0.1903	0.5162	0.5212	0.1123	0.2432	0.0423	0.0095	0.2817	0.0383	0.2337	6.0404	17.8062	-20.731
14	9.1076	5.9185	3.5631	9.2637	5.2565	7.6635	-0.2648	1.651	-0.084	-0.4688	-0.3134	-0.2181	-0.071	0.5973	0.5671	0.5406	0.012	0.0985	0.8372	0.1143	0.457	13.1353	21.7128	-31.7603
15	1.6	-1.8519	0.5967	7.9061	-1.6176	2.0909	0.1594	0.3162	0.1073	0.0617	-0.3488	-0.7131	0.4011	0.4207	0.2523	0.3832	-0.0367	-0.0025	0.7376	0.113	0.4992	15.7386	17.5793	-17.9443

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 794 through 809 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 810 through 827 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 828 through 906 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 907 through 922 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 923 through 931 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 932 through 944 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 795 through 803 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 804 through 809 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 810 through 827 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 828 through 868 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 869 through 887 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 888 through 906 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 907 through 922 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 923 through 931 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 932 through 946 )

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