PDB-3md1: Crystal Structure of the Second RRM Domain of Yeast Poly(U)-Bindi...

ID or keywords:

Entry

Database: PDB / ID: 3md1

Title

Crystal Structure of the Second RRM Domain of Yeast Poly(U)-Binding Protein (Pub1)

Components

Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

Keywords

RNA BINDING PROTEIN / RRM / RBD / RNP / poly(U) binding / Pub1 / Nucleus / RNA-binding

Function / homology

Function and homology information

nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / poly(U) RNA binding / translational termination / cellular response to glucose starvation / regulation of mRNA stability / stress granule assembly / P-body / cytoplasmic stress granule / ribosome binding / mRNA binding ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Li, H. / Shi, H. / Li, Y. / Cui, Y. / Niu, L. / Teng, M.

Citation

Journal: To be published
Title: Crystal Structure of the Second RRM Domain of Yeast Poly(U)-Binding Protein (Pub1)
Authors: Li, H. / Shi, H. / Li, Y. / Cui, Y. / Niu, L. / Teng, M.

History

Deposition	Mar 29, 2010	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	May 5, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3md1.cif.gz	51.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3md1.ent.gz	38.2 KB	Display	PDB format
PDBx/mmJSON format	3md1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3md1_validation.pdf.gz	445.3 KB	Display	wwPDB validaton report
Full document	3md1_full_validation.pdf.gz	445.9 KB	Display
Data in XML	3md1_validation.xml.gz	10.4 KB	Display
Data in CIF	3md1_validation.cif.gz	13.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/md/3md1 ftp://data.pdbj.org/pub/pdb/validation_reports/md/3md1	HTTPS FTP

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Related structure data

Related structure data	1cvjS 3md3 S: Starting model for refinement
Similar structure data	2l4n-d 3pz8-8 2h3m-d 2uwq-d 3qu6-2 2mj8-d 2eo2-d 1jic-d 2gpe-1 2xi1-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

1cvjS

3md3

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#106 - Oct 2008 Poly(A) Polymerase similarity (2)

Deposited unit

A: Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

B: Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

hetero molecules

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

1

A: Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

hetero molecules

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

2

B: Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

hetero molecules

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

3

A: Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

hetero molecules

A: Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

hetero molecules

A: Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

hetero molecules

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

4

B: Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

hetero molecules

B: Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

hetero molecules

B: Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

hetero molecules

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

Unit cell

Length a, b, c (Å)	72.661, 72.661, 81.989
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

#1: Protein	Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 / ARS consensus-binding protein ACBP-60 / Poly uridylate-binding protein / Poly(U)-binding protein Mass: 9385.273 Da / Num. of mol.: 2 / Fragment: second RRM domain / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32588
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.22 Å³/Da / Density % sol: 44.57 %
Crystal grow	Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 25% (w/v) polyethylene glycol 4000 (PEG4000), 0.1 M sodium acetate , pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
Detector	Type: MAR CCD 130 mm / Detector: CCD / Date: Jan 12, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.6→50 Å / Num. obs: 20050 / Redundancy: 5.7 % / B_iso Wilson estimate: 13.1 Å²
Reflection shell	Resolution: 1.6→50 Å / Redundancy: 5.7 % / R_merge(I) obs: 0.34 / Num. unique all: 20050

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Processing

Software

Name	Version	Classification
MAR345dtb		data collection
PHASES		phasing
REFMAC	5	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1CVJ

1cvj

Resolution: 1.6→49.92 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.958 / SU B: 4.52 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22051	1083	5.1 %	RANDOM
R_work	0.19812	-	-	-
obs	0.19929	20050	99.09 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 13.106 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.15 Å²	0.07 Å²	0 Å²
2-	-	0.15 Å²	0 Å²
3-	-	-	-0.22 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→49.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1280	0	12	151	1443

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.021	1345
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.105	1.911	1819
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.221	5	166
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.528	24.868	76
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.176	15	207
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.169	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	184
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	1074
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	0.584	1.5	816
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.033	2	1303
X-RAY DIFFRACTION	r_scbond_it	1.56	3	529
X-RAY DIFFRACTION	r_scangle_it	2.214	4.5	516
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.6→1.641 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.355	77	-
R_work	0.33	1380	-
obs	-	-	91.69 %

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	3.4872	0.3158	0.3389	2.5986	1.1601	3.241	-0.2651	0.1952	0.2131	-0.1509	0.0399	-0.0647	-0.1976	0.1852	0.2252	0.0864	0.0155	-0.0396	0.1021	0.028	0.1254	-20.1103	14.1332	-3.309
2	0.8209	-0.3533	1.1247	0.4769	0.4548	4.2553	-0.054	-0.0483	-0.099	0.0608	-0.0206	0.1133	0.0312	-0.1878	0.0746	0.0716	0.0365	0.0353	0.0922	0.0304	0.1467	-33.5625	4.4666	1.1461
3	5.8222	1.5616	-0.8544	0.545	0.4217	4.0778	-0.1209	-0.4123	0.1447	-0.0005	-0.1061	0.099	-0.1118	-0.3782	0.227	0.2016	0.1879	0.0678	0.2254	0.0165	0.0695	-35.4486	11.2992	7.0605
4	5.1194	1.5128	1.2611	2.2794	-1.7786	2.8369	-0.027	-0.111	0.1105	0.4053	0.062	0.0999	-0.4964	-0.1112	-0.0351	0.1704	0.0964	-0.0072	0.0895	-0.0234	0.05	-27.5659	12.9179	8.351
5	5.5083	1.3379	-0.7106	9.6517	-0.5524	8.509	-0.1842	-0.3517	0.1299	0.3272	0.0491	-0.1262	-0.1473	0.0216	0.1351	0.1629	0.039	-0.1057	0.0462	-0.0261	0.0697	-19.0495	14.2448	10.4035
6	9.1917	2.7808	2.2308	3.1184	1.0788	0.6154	-0.2196	0.0383	0.2233	0.3308	0.1567	0.0948	0.0055	0.0222	0.0629	0.1723	0.0645	-0.0387	0.0957	-0.0229	0.0845	-26.3582	17.7606	3.5463
7	12.7364	-5.7942	5.3899	7.7122	-1.0068	3.7551	-0.0386	0.2457	-0.0787	-0.0623	0.0157	0.0299	-0.1511	0.0682	0.0229	0.0795	0.017	0.0215	0.0697	0.0318	0.104	-40.1021	14.8388	-6.3817
8	8.3803	-4.0493	3.8896	4.4281	-2.5858	2.026	-0.0519	-0.1061	-0.2822	-0.1407	0.1469	0.206	0.0339	-0.029	-0.095	0.0949	0.0419	0.0171	0.1116	0.0364	0.1388	-37.8426	9.8303	-4.7023
9	13.9925	4.1711	8.0166	3.3962	2.7015	4.6381	-0.186	0.0286	0.2303	0.0118	0.0551	0.0681	-0.0991	0.0212	0.1309	0.1014	0.0178	-0.0169	0.0876	0.0007	0.1034	-23.5448	14.6328	0.2248
10	1.2639	1.3628	-2.0193	10.964	0.4668	3.9763	-0.0082	-0.0395	0.0723	-0.101	0.2444	-0.5484	-0.0404	0.157	-0.2362	0.0733	-0.0071	-0.112	0.0962	0.016	0.2576	-12.5291	14.7419	1.4455
11	6.1689	2.8398	-0.343	3.0185	-1.6723	1.5086	-0.2339	0.2036	0.0967	0.0908	0.1381	-0.225	-0.0026	-0.0437	0.0959	0.1997	0.0387	-0.12	0.0855	-0.008	0.1721	-16.0771	5.9798	3.3461
12	15.0889	-2.1527	-1.7466	2.5337	0.8102	1.8927	0.085	-0.525	-0.2912	0.1982	-0.0337	-0.0258	-0.1332	-0.0104	-0.0513	0.1186	0.0355	0.003	0.0848	0.0302	0.0503	-26.778	1.1414	6.4137
13	8.7605	1.8075	-2.4386	1.3246	0.198	1.2079	-0.1304	0.0984	-0.158	0.1367	0.0589	0.0105	0.1679	-0.0421	0.0715	0.1172	0.0188	0.0182	0.1228	0.0361	0.0879	-29.0555	0.079	2.3485
14	3.5317	1.0293	0.6517	6.5945	-3.272	2.0602	-0.1592	0.2629	-0.0165	-0.2406	-0.0514	-0.3933	0.1475	0.1388	0.2106	0.1425	0.0339	0.0196	0.1291	0.0211	0.0888	-19.7236	8.1822	-4.5691
15	2.1688	0.0257	-2.1541	7.1873	5.7122	6.7246	-0.1917	0.0182	0.0121	-0.1433	0.1406	0.1752	-0.0075	0.1664	0.0511	0.1716	-0.0233	0.0169	0.1275	-0.0397	0.0973	-26.9508	8.2746	-15.565
16	3.9248	-0.867	2.105	6.8846	-0.776	2.8102	0.1118	-0.0572	-0.3062	-0.3386	0.052	-0.2777	0.3175	-0.2147	-0.1639	0.0687	-0.0595	-0.0027	0.1032	0.0412	0.1323	-14.5621	-9.9548	10.3377
17	0.3439	-0.0295	-0.918	0.0028	0.0602	4.5051	0.0241	-0.0577	0.0802	0.0012	0.0229	-0.0105	-0.2973	-0.4375	-0.047	0.0647	0.0657	-0.0194	0.189	-0.0344	0.1174	-15.4212	6.3707	14.653
18	0.4684	1.3518	-0.5826	6.6365	0.202	2.073	0.1034	-0.1343	-0.0375	0.1343	-0.0902	-0.2084	-0.3438	0.2846	-0.0132	0.1048	0.0234	-0.0548	0.2695	-0.0448	0.0806	-8.2188	4.4905	20.1553
19	0.2169	-0.727	-0.0938	2.979	-0.7178	2.8775	-0.0726	-0.1026	0.0241	0.3108	0.1783	-0.1081	-0.1056	-0.012	-0.1058	0.0337	0.0057	-0.0159	0.2564	0.0417	0.0635	-11.713	-2.9132	21.9768
20	11.6673	-3.7006	0.3843	9.0833	1.9158	0.6626	0.0104	-0.9523	-0.6001	-0.0252	0.2163	-0.2762	-0.0461	-0.2161	-0.2266	0.059	0.0073	0.0024	0.3328	0.1966	0.1384	-14.9527	-10.4358	24.2739
21	1.9887	0.6292	0.7444	5.1699	-2.8492	2.1976	0.0019	-0.4244	-0.2428	-0.2783	-0.0443	-0.2511	0.15	-0.1868	0.0423	0.0558	-0.0213	-0.0155	0.1681	0.0515	0.1308	-8.3584	-8.0246	17.9819
22	7.2194	5.684	-4.2859	5.5561	-4.6711	4.1006	-0.1061	0.0457	-0.1962	-0.0176	0.0549	-0.0903	-0.0199	-0.051	0.0513	0.0527	0.0158	-0.0138	0.0751	-0.0258	0.1587	-4.4902	4.5478	8.9554
23	14.2844	1.6666	-1.3962	0.2418	-0.4786	3.7725	-0.1215	0.2496	0.7969	-0.0403	0.0732	0.1172	-0.1579	-0.1288	0.0484	0.1182	-0.0166	-0.0325	0.0672	0.0157	0.1997	-4.8546	9.5306	7.4508
24	2.4913	0.6443	0.3537	10.9488	-4.9103	2.3712	-0.048	-0.2425	0.0531	-0.1111	0.0321	-0.0491	0.0447	-0.0939	0.0159	0.0691	-0.009	-0.0026	0.1267	0.0138	0.1071	-12.0895	-1.9632	11.5356
25	30.073	-6.0485	0.2175	3.5231	-3.7845	6.0694	-0.4405	-0.2658	-1.467	-0.2043	0.4033	0.3189	0.5034	-0.417	0.0372	0.0956	-0.0962	-0.0412	0.1602	0.1379	0.2409	-16.9	-15.9371	15.7853
26	2.4066	0.3263	-1.502	5.5799	3.8615	3.9416	0.0569	-0.1081	-0.1432	-0.1452	-0.1634	0.0365	-0.1147	-0.1239	0.1065	0.0196	-0.0527	-0.0408	0.2337	0.1665	0.1348	-22.6045	-10.813	16.1132
27	1.0221	-0.0535	1.0941	5.1537	0.1296	6.7552	0.0151	0.037	0.023	0.2336	-0.0916	0.1431	-0.0047	-0.306	0.0765	0.0142	0.0163	0.0129	0.2059	0.0813	0.075	-24.658	-2.5981	19.0404
28	3.6521	2.1268	1.9532	4.8467	0.6165	2.9777	0.1748	-0.4975	0.2294	0.1324	-0.0028	0.1811	-0.2975	-0.418	-0.172	0.1311	0.0602	0.0453	0.2006	-0.0319	0.0842	-19.7939	7.1734	19.5885
29	4.183	-3.0322	0.9467	10.8779	6.2859	6.4447	0.0985	-0.0467	-0.2519	-0.422	-0.0042	0.2546	-0.3201	-0.4652	-0.0943	0.0626	0.0094	0.0012	0.2762	0.0756	0.069	-20.1522	-3.9631	10.2437

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	161 - 165
2	X-RAY DIFFRACTION	2	A	166 - 171
3	X-RAY DIFFRACTION	3	A	172 - 177
4	X-RAY DIFFRACTION	4	A	178 - 182
5	X-RAY DIFFRACTION	5	A	183 - 187
6	X-RAY DIFFRACTION	6	A	188 - 193
7	X-RAY DIFFRACTION	7	A	194 - 198
8	X-RAY DIFFRACTION	8	A	199 - 205
9	X-RAY DIFFRACTION	9	A	206 - 210
10	X-RAY DIFFRACTION	10	A	211 - 216
11	X-RAY DIFFRACTION	11	A	217 - 223
12	X-RAY DIFFRACTION	12	A	224 - 229
13	X-RAY DIFFRACTION	13	A	230 - 234
14	X-RAY DIFFRACTION	14	A	235 - 238
15	X-RAY DIFFRACTION	15	A	239 - 243
16	X-RAY DIFFRACTION	16	B	161 - 165
17	X-RAY DIFFRACTION	17	B	166 - 171
18	X-RAY DIFFRACTION	18	B	172 - 177
19	X-RAY DIFFRACTION	19	B	178 - 182
20	X-RAY DIFFRACTION	20	B	183 - 187
21	X-RAY DIFFRACTION	21	B	188 - 192
22	X-RAY DIFFRACTION	22	B	193 - 197
23	X-RAY DIFFRACTION	23	B	198 - 203
24	X-RAY DIFFRACTION	24	B	204 - 209
25	X-RAY DIFFRACTION	25	B	210 - 215
26	X-RAY DIFFRACTION	26	B	216 - 220
27	X-RAY DIFFRACTION	27	B	221 - 226
28	X-RAY DIFFRACTION	28	B	227 - 232
29	X-RAY DIFFRACTION	29	B	233 - 239

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