PDB-5v87: Crystal structure of LARP1-unique domain DM15 bound to m7GpppC

ID or keywords:

Entry

Database: PDB / ID: 5v87

Title

Crystal structure of LARP1-unique domain DM15 bound to m7GpppC

Components

La-related protein 1

Keywords

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

DM15 / 5'TOP

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 / positive regulation of macroautophagy ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.692 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 21, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 19, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software / Item: _software.classification
Revision 1.2	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	5v87.cif.gz	152.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5v87.ent.gz	119.1 KB	Display	PDB format
PDBx/mmJSON format	5v87.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/v8/5v87 ftp://data.pdbj.org/pub/pdb/validation_reports/v8/5v87	HTTPS FTP

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Related structure data

Related structure data	5v4rC 5v7cC 5c0vS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1u9b-d 4bqa-1 6usd-d 6us0-d 4tky-1 1pp6-1 5qm3-2 5f6w-d 5cog-2 4cj2-1 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

40.5 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&software
20.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: La-related protein 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	47.959, 59.962, 60.321
Angle α, β, γ (deg.)	90.00, 100.65, 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: Chemical	ChemComp-91P / [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-9-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate / dinucleotide triphosphate cap analog m7GpppC Mass: 763.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₀H₃₀N₈O₁₈P₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.17 Å³/Da / Density % sol: 43.39 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.05 M Sodium cacodylate trihydrate pH 6.5, 30% w/v Polyethylene glycol 4,000 (#25 Index-116)

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Data collection

Diffraction	Mean temperature: 90 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54 Å
Detector	Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 4, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.69→30 Å / Num. obs: 34328 / % possible obs: 92.2 % / Redundancy: 3.4 % / Net I/σ(I): 19.85

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5C0V

5c0v

Resolution: 1.692→24.986 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.09

	R_factor	Num. reflection	% reflection
R_free	0.2035	1970	5.74 %
R_work	0.1815	-	-
obs	0.1828	34328	91.18 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.692→24.986 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2529	0	82	224	2835

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2710
X-RAY DIFFRACTION	f_angle_d	0.884	3649
X-RAY DIFFRACTION	f_dihedral_angle_d	11.513	1556
X-RAY DIFFRACTION	f_chiral_restr	0.045	345
X-RAY DIFFRACTION	f_plane_restr	0.005	455

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 (%)
1.6916-1.7339	0.256	144	0.2252	2360	X-RAY DIFFRACTION	94
1.7339-1.7807	0.2087	149	0.2031	2463	X-RAY DIFFRACTION	97
1.7807-1.8331	0.2171	150	0.1876	2458	X-RAY DIFFRACTION	98
1.8331-1.8923	0.2327	147	0.1935	2390	X-RAY DIFFRACTION	95
1.8923-1.9599	0.2277	133	0.1991	2222	X-RAY DIFFRACTION	88
1.9599-2.0383	0.204	150	0.1823	2462	X-RAY DIFFRACTION	99
2.0383-2.131	0.2081	154	0.1846	2537	X-RAY DIFFRACTION	99
2.131-2.2433	0.2181	118	0.1867	1902	X-RAY DIFFRACTION	75
2.2433-2.3838	0.2071	119	0.176	1951	X-RAY DIFFRACTION	77
2.3838-2.5677	0.2067	154	0.1866	2521	X-RAY DIFFRACTION	100
2.5677-2.8257	0.1973	153	0.1868	2539	X-RAY DIFFRACTION	100
2.8257-3.2339	0.2055	154	0.1807	2528	X-RAY DIFFRACTION	99
3.2339-4.0715	0.1968	96	0.1694	1580	X-RAY DIFFRACTION	62
4.0715-24.9883	0.1855	149	0.1722	2445	X-RAY DIFFRACTION	94

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	6.6932	-2.5081	-1.6078	1.4977	0.9214	0.5678	0.3113	1.3683	-0.5966	0.2594	0.5743	-0.9006	0.245	0.6463	0.3614	0.4266	0.1193	-0.0379	0.7226	-0.2718	0.5952	16.4008	1.0255	-10.9074
2	3.62	0.7829	2.2358	3.8932	1.4033	4.4361	0.0041	0.2218	0.0741	0.2765	-0.0316	-0.3841	0.0666	0.5373	0.0861	0.165	0.0034	-0.0098	0.2438	0.0476	0.1997	10.714	9.7165	-3.1509
3	2.7726	0.4831	0.5026	5.6368	-0.7329	3.7001	0.0266	-0.0649	0.0619	0.2923	-0.0588	-0.0505	0.0449	-0.0207	0.0186	0.1674	-0.0056	-0.004	0.1354	-0.005	0.1256	0.0634	9.0836	-0.6704
4	6.2995	2.9262	1.319	7.5981	3.0007	6.7752	0.1102	0.2205	-0.2371	-0.2549	-0.0695	-0.1117	0.1833	0.0105	-0.021	0.1347	0.028	-0.0085	0.1449	0.0062	0.1275	-3.3893	6.9654	-10.8925
5	4.7704	-1.1048	1.489	2.4092	-2.4368	2.4962	0.1226	-0.3531	-0.281	0.1212	0.092	0.3198	0.0273	-0.273	-0.2233	0.1709	-0.0231	0.0048	0.2589	0.0205	0.1854	-11.9995	6.5203	-5.1178
6	3.6477	2.6302	1.4825	4.4865	3.7362	5.3424	-0.0537	0.2952	-0.1145	-0.3985	0.0964	-0.0062	0.0512	-0.1499	-0.0069	0.1481	0.0051	-0.0039	0.1954	0.0178	0.1691	-11.3973	11.0043	-14.8739
7	8.7053	-3.0137	-2.5237	3.3231	3.4962	7.7364	-0.0918	0.1492	0.1207	-0.1492	0.0508	0.8036	0.2019	-0.5434	-0.0048	0.2278	-0.0564	-0.0109	0.4344	0.0599	0.396	-20.2403	6.8703	-11.3202
8	8.7675	0.4989	5.0047	3.0388	1.7422	3.5711	0.2139	0.2974	-1.4995	-0.1797	-0.5815	1.1454	0.2377	-1.3855	0.445	0.4296	0.0058	-0.0357	0.5649	-0.0114	0.6446	-23.5974	20.629	-29.0533
9	6.1922	-0.8799	1.062	3.2085	4.0523	5.9118	0.7416	1.3714	-0.4491	-1.6674	-0.7982	0.1577	0.8447	0.36	0.0406	0.6629	0.1528	-0.1093	0.525	-0.0036	0.3125	-18.6426	22.3191	-37.4961
10	4.7202	-0.2271	1.9893	2.8894	2.7343	8.1502	-0.1843	-0.0148	0.5053	-0.1699	-0.0519	0.2615	-0.855	-0.6217	0.2389	0.3653	0.1081	-0.0572	0.3104	0.0356	0.3754	-20.5296	32.8806	-22.7735
11	6.3686	-2.8948	-3.4473	3.5036	1.4771	3.4203	-0.0746	0.1372	0.2526	0.0257	0.091	-0.0226	0.0592	-0.0833	-0.0056	0.2397	0.02	-0.0726	0.195	0.0195	0.2115	-13.1201	25.4969	-21.8085
12	2.741	-0.3213	0.4378	3.0683	0.0701	5.6169	-0.0429	0.3191	0.4619	-0.1184	0.011	-0.0726	-0.3253	0.2432	0.0217	0.2157	-0.0294	-0.0227	0.2463	0.0834	0.2625	-4.9356	27.4116	-23.0485
13	0.3696	-0.0663	-0.6348	2.0918	-0.9023	1.5906	-0.0425	0.7032	0.4765	-0.1004	-0.2015	-0.2484	-0.4395	0.2106	-0.1659	0.2811	-0.0788	-0.0066	0.5365	0.2195	0.3515	6.0614	27.8969	-24.4426
14	4.9766	0.9121	-1.1183	5.9209	2.6519	5.2993	0.0575	0.7231	-0.1213	-0.0793	-0.0903	-0.4887	0.426	0.2636	0.0284	0.1718	0.0401	0.02	0.3291	0.0655	0.2156	5.8354	17.6329	-20.9875
15	7.1946	6.3106	4.1258	8.2324	3.5833	2.3667	-0.0522	1.3723	0.5953	-0.3835	-0.3399	-0.1203	0.5309	0.7896	0.3985	0.5531	0.1292	0.1969	0.9122	0.2142	0.5157	12.7539	22.7842	-30.1745
16	1.5458	-0.171	-0.8673	1.2835	-0.0327	0.6768	0.028	-0.1961	-0.0397	-0.0268	-0.1611	-0.4912	0.0115	0.2737	-0.1387	0.2768	-0.1216	0.0329	0.7997	0.2233	0.5037	15.9475	22.8223	-18.5757
17	3.2286	-0.7861	0.2029	0.2871	-0.3494	0.9532	0.1454	0.0179	0.3241	-0.204	0.3164	-0.4826	-0.421	1.2726	-0.3477	0.4026	-0.1397	-0.0085	0.8373	-0.0575	1.3807	14.796	10.2914	-16.4278

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 847 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 848 through 871 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 872 through 887 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 888 through 906 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 907 through 922 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 923 through 941 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 794 through 803 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 804 through 809 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 810 through 827 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 828 through 847 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 848 through 887 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 888 through 906 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 907 through 922 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 923 through 931 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 932 through 940 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 941 through 944 )

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