PDB-4a9a: Structure of Rbg1 in complex with Tma46 dfrp domain

ID or keywords:

Entry

Database: PDB / ID: 4a9a

Title

Structure of Rbg1 in complex with Tma46 dfrp domain

Components

RIBOSOME-INTERACTING GTPASE 1
TRANSLATION MACHINERY-ASSOCIATED PROTEIN 46

Keywords

TRANSLATION / DRG-DFRP COMPLEX / RIBOSOME BINDING GTPASE

Function / homology

Function and homology information

: / positive regulation of cellular response to amino acid starvation / cytoplasmic stress granule / cytoplasmic translation /

mRNA binding / GTP binding /

metal ion binding /

cytosol /

cytoplasm
Similarity search - Function

Biological species

SACCHAROMYCES CEREVISIAE (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 2.67 Å

Authors

Francis, S.M. / Gas, M. / Daugeron, M. / Seraphin, B. / Bravo, J.

Citation

Journal: Nucleic Acids Res. / Year: 2012
Title: Rbg1-Tma46 Dimer Structure Reveals New Functional Domains and Their Role in Polysome Recruitment.
Authors: Francis, S.M. / Gas, M. / Daugeron, M. / Bravo, J. / Seraphin, B.

History

Deposition	Nov 25, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 3, 2012	Provider: repository / Type: Initial release
Revision 1.1	Dec 19, 2012	Group: Database references
Revision 1.2	Jan 25, 2017	Group: Data collection
Revision 1.3	May 8, 2024	Group: Data collection / Database references / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4a9a.cif.gz	366.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4a9a.ent.gz	304.2 KB	Display	PDB format
PDBx/mmJSON format	4a9a.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/a9/4a9a ftp://data.pdbj.org/pub/pdb/validation_reports/a9/4a9a	HTTPS FTP

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Related structure data

Similar structure data	6wys-d 4ccg-d 6flo-d 2od7-2 3brs-d 3nk6-d 3rzz-d 3hmo-2 1z0a-d 6h80-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	#16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (5) #245 - May 2020 Spliceosomes similarity (4) #117 - Sep 2009 Xanthine Oxidoreductase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #82 - Oct 2006 Cytochrome p450 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: RIBOSOME-INTERACTING GTPASE 1

B: RIBOSOME-INTERACTING GTPASE 1

C: TRANSLATION MACHINERY-ASSOCIATED PROTEIN 46

D: TRANSLATION MACHINERY-ASSOCIATED PROTEIN 46

116 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: RIBOSOME-INTERACTING GTPASE 1

C: TRANSLATION MACHINERY-ASSOCIATED PROTEIN 46

defined by author&software
57.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: RIBOSOME-INTERACTING GTPASE 1

D: TRANSLATION MACHINERY-ASSOCIATED PROTEIN 46

defined by author&software
57.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	86.200, 224.890, 84.890
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	RIBOSOME-INTERACTING GTPASE 1 / GTP-BINDING PROTEIN RBG1 / GENETICALLY INTERACTS WITH RIBOSOMAL GENES PROTEIN 1 / RBG1 Mass: 41717.035 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PBS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIPL / References: UniProt: P39729
#2: Protein	TRANSLATION MACHINERY-ASSOCIATED PROTEIN 46 / DRG FAMILY-REGULATORY PROTEIN 1 / TMA46 Mass: 16039.022 Da / Num. of mol.: 2 / Fragment: DFRP DOMAIN, RESIDUES 205-345 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PBS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIPL / References: UniProt: Q12000
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 3.55 Å³/Da / Density % sol: 65.41 % / Description: NONE
Crystal grow	pH: 7 Details: 2.38 SODIUM FORMATE, 0.2-0.25 SODIUM CITRATE PH 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
Detector	Type: ADSC CCD / Detector: CCD / Date: Nov 5, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.67→79.42 Å / Num. obs: 47671 / % possible obs: 99.9 % / Observed criterion σ(I): 1.9 / Redundancy: 7.14 % / R_merge(I) obs: 0.08 / Net I/σ(I): 6.5
Reflection shell	Resolution: 2.67→2.82 Å / Redundancy: 7 % / R_merge(I) obs: 0.4 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
MOSFLM		data reduction
SCALA		data scaling
SHARP		phasing

Refinement

Method to determine structure:

SIRAS
Starting model: NONE

Resolution: 2.67→56.22 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.948 / SU B: 18.68 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.331 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22212	1200	2.5 %	RANDOM
R_work	0.1959	-	-	-
obs	0.19655	46457	99.96 %	-

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: 76.935 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.39 Å²	0 Å²	0 Å²
2-	-	0.15 Å²	0 Å²
3-	-	-	0.24 Å²

Refinement step

Cycle: LAST / Resolution: 2.67→56.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7030	0	0	77	7107

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	7132
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.233	1.983	9613
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.648	5	893
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.642	24.637	289
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.555	15	1367
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.193	15	43
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	1128
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	5145
X-RAY DIFFRACTION	r_gen_planes_other
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.672→2.741 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.349	92	-
R_work	0.35	3140	-
obs	-	-	99.91 %

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	5.4334	0.0287	-0.7547	5.4165	1.2894	20.3922	0.1269	-0.0308	-0.8751	0.2576	-0.5051	-0.3205	1.1734	0.7407	0.3782	0.4191	-0.0262	-0.1985	0.5623	-0.0348	0.2879	71.0576	17.0394	71.5766
2	2.6596	1.7799	-0.4397	2.5903	-0.3357	1.9384	0.0723	-0.1282	-0.062	0.1876	-0.0467	-0.211	-0.038	0.2761	-0.0256	0.0703	0.0089	-0.0333	0.1103	-0.0371	0.0775	54.7808	16.0026	47.4237
3	12.9989	-3.7393	6.255	9.1015	1.5144	12.3432	-0.5121	-1.0011	1.2415	0.6659	-0.0357	0.2786	-1.4867	-0.1742	0.5478	0.6844	-0.0854	-0.084	0.4513	-0.1905	0.2843	64.3488	34.1675	73.0216
4	9.6433	0.2457	-2.1733	12.8158	-0.94	5.0223	0.2993	0.3254	0.3208	-1.267	-0.1593	-0.7876	-0.3994	0.1248	-0.14	0.3851	0.014	0.147	0.092	-0.0462	0.4359	55.5183	44.3417	33.9234
5	10.6415	8.9861	4.9774	11.2573	5.5185	9.3982	0.7364	-0.7385	1.649	1.5675	-0.8073	1.6539	-0.321	-0.2583	0.0709	0.4494	-0.0903	0.3074	0.4356	-0.0833	0.3794	35.6465	11.6347	62.3998
6	5.6294	1.4642	-1.1814	28.9172	-0.073	5.6312	-0.036	0.0493	1.0584	0.7619	0.1925	1.1165	-1.0111	-0.0341	-0.1566	0.2288	0.0516	0.0034	0.1682	-0.0367	0.3126	31.6107	21.188	45.9349
7	1.2923	4.2219	-0.2111	15.5173	2.6548	13.6519	0.078	0.098	0.9325	-0.4977	0.0899	2.8361	0.0724	-2.1258	-0.1679	0.5415	-0.0735	-0.0811	0.5332	-0.0216	1.2461	39.0827	43.5014	34.9632
8	2.6909	1.7131	1.9561	51.6725	-3.1645	1.8849	-0.1194	-0.3258	0.2249	-2.4572	0.2081	0.5396	-0.1774	-0.4358	-0.0887	1.636	0.4767	0.8246	0.5492	0.1821	0.8671	59.0984	40.3208	22.0759
9	11.1905	5.0717	-0.1882	17.626	-6.5159	4.0506	-0.4162	0.6226	0.0369	-1.9338	0.1189	-0.5952	0.5571	0.0215	0.2973	0.3278	-0.0029	-0.0068	0.2138	-0.0127	0.083	50.6133	18.15	29.1142
10	2.4912	1.2621	2.7792	7.3272	-0.0311	21.1623	-0.0269	-0.0335	-0.3416	0.2398	-0.039	0.3383	0.4875	-1.1116	0.0659	0.2869	-0.0628	-0.1482	0.5559	0.0212	0.262	71.6971	23.7672	10.6398
11	11.3142	1.8578	3.3587	10.4619	-0.7911	10.2838	-0.7736	1.151	1.2781	-0.3285	0.0443	-0.2818	-1.7574	0.2971	0.7293	0.719	-0.1429	-0.2045	0.4764	0.1767	0.3413	80.0584	39.8054	9.2382
12	3.4354	-1.2046	0.2274	2.4989	-0.1809	1.9865	0.0941	0.2886	-0.2604	-0.1771	-0.0402	0.1089	0.1261	0.0037	-0.0538	0.1411	-0.0525	-0.0865	0.1546	-0.035	0.1975	89.1989	18.6151	32.3649
13	7.1871	-1.5611	-0.7142	21.3414	3.2244	3.8756	0.2007	-0.4124	0.6017	0.2159	-0.2685	0.7241	-0.3482	-0.3284	0.0678	0.302	-0.0354	-0.0219	0.1235	-0.0957	0.5102	87.9392	44.5982	47.5347
14	8.3654	-6.9164	1.2669	6.9963	-4.9804	12.4941	0.6921	1.0129	1.0082	-0.8104	-0.9294	-0.9649	0.5265	0.4186	0.2374	0.5917	0.1498	0.1694	1.0251	-0.1826	0.5611	107.9117	12.0016	17.9984
15	9.0622	3.5264	0.0297	24.1105	6.0121	8.5323	-0.0501	-0.0241	1.378	-2.4499	-0.2913	0.4009	-1.2262	0.2184	0.3414	0.3425	-0.0602	-0.1035	0.3698	0.0572	0.4749	111.9903	20.0446	35.5057
16	13.2671	-11.091	10.2338	30.587	4.4562	15.9116	-0.1494	0.4538	0.8022	1.5861	2.1404	-4.6685	0.6814	2.0809	-1.991	0.5199	-0.0805	-0.3082	0.858	-0.6132	1.9843	104.1092	42.5049	51.1755
17	29.3956	-5.0723	13.5293	23.7403	7.1162	10.1661	-0.9584	-0.3782	-0.167	1.6195	0.7601	0.384	0.1161	0.1515	0.1982	0.3122	0.0169	-0.1164	0.224	0.1631	0.308	96.113	17.1278	48.7571

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 45
2	X-RAY DIFFRACTION	2	A	53 - 125
3	X-RAY DIFFRACTION	2	A	131 - 174
4	X-RAY DIFFRACTION	2	A	233 - 299
5	X-RAY DIFFRACTION	3	A	175 - 232
6	X-RAY DIFFRACTION	4	A	300 - 369
7	X-RAY DIFFRACTION	5	C	214 - 240
8	X-RAY DIFFRACTION	6	C	241 - 267
9	X-RAY DIFFRACTION	7	C	268 - 282
10	X-RAY DIFFRACTION	8	C	302 - 313
11	X-RAY DIFFRACTION	9	C	314 - 339
12	X-RAY DIFFRACTION	10	B	2 - 53
13	X-RAY DIFFRACTION	11	B	175 - 232
14	X-RAY DIFFRACTION	12	B	54 - 91
15	X-RAY DIFFRACTION	12	B	98 - 125
16	X-RAY DIFFRACTION	12	B	133 - 174
17	X-RAY DIFFRACTION	12	B	233 - 299
18	X-RAY DIFFRACTION	13	B	300 - 369
19	X-RAY DIFFRACTION	14	D	214 - 240
20	X-RAY DIFFRACTION	15	D	241 - 267
21	X-RAY DIFFRACTION	16	D	268 - 282
22	X-RAY DIFFRACTION	17	D	320 - 339

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