PDB-4a76: The Lin28b Cold shock domain in complex with heptathymidine

ID or keywords:

Entry

Database: PDB / ID: 4a76

Title

The Lin28b Cold shock domain in complex with heptathymidine

Components

5'-D(*TP*TP*TP*TP*TP*TP*TP)-3'
LIN28 COLD SHOCK DOMAIN

Keywords

CHAPERONE/DNA / CHAPERONE-DNA COMPLEX

Function / homology

Function and homology information

regulatory ncRNA-mediated gene silencing /

nucleic acid binding /

nucleolus / zinc ion binding
Similarity search - Function

Biological species

XENOPUS TROPICALIS

Method

X-RAY DIFFRACTION /

SYNCHROTRON / OTHER / Resolution: 1.92 Å

Authors

Mayr, F. / Schuetz, A. / Doege, N. / Heinemann, U.

Citation

Journal: Nucleic Acids Res. / Year: 2012
Title: The Lin28 Cold-Shock Domain Remodels Pre-Let-7 Microrna.
Authors: Mayr, F. / Schutz, A. / Doge, N. / Heinemann, U.

History

Deposition	Nov 11, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 5, 2012	Provider: repository / Type: Initial release
Revision 1.1	Apr 4, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.2	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

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4a76.cif.gz	171.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4a76.ent.gz	138.3 KB	Display	PDB format
PDBx/mmJSON format	4a76.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/a7/4a76 ftp://data.pdbj.org/pub/pdb/validation_reports/a7/4a76	HTTPS FTP

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Related structure data

Related structure data	3uljC 4a4iC 4a75C 4alpC C: citing same article (ref.)
Similar structure data	6b4a-2 4hbm-3 6q9l-2 1fbz-1 2e4q-2 4k6y-1 4y00-3 4mdn-d 6fmb-d 5d13-4 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

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: LIN28 COLD SHOCK DOMAIN

B: 5'-D(*TP*TP*TP*TP*TP*TP*TP)-3'

C: LIN28 COLD SHOCK DOMAIN

D: 5'-D(*TP*TP*TP*TP*TP*TP*TP)-3'

E: LIN28 COLD SHOCK DOMAIN

F: 5'-D(*TP*TP*TP*TP*TP*TP*TP)-3'

G: LIN28 COLD SHOCK DOMAIN

H: 5'-D(*TP*TP*TP*TP*TP*TP*TP)-3'

48.1 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: LIN28 COLD SHOCK DOMAIN

B: 5'-D(*TP*TP*TP*TP*TP*TP*TP)-3'

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

2

C: LIN28 COLD SHOCK DOMAIN

D: 5'-D(*TP*TP*TP*TP*TP*TP*TP)-3'

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

3

E: LIN28 COLD SHOCK DOMAIN

F: 5'-D(*TP*TP*TP*TP*TP*TP*TP)-3'

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

4

G: LIN28 COLD SHOCK DOMAIN

H: 5'-D(*TP*TP*TP*TP*TP*TP*TP)-3'

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

Unit cell

Length a, b, c (Å)	51.610, 77.575, 100.231
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	LIN28 COLD SHOCK DOMAIN Mass: 9942.231 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) XENOPUS (SILURANA) TROPICALIS (tropical clawed frog) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: B4F6I0
#2: DNA chain	5'-D(TPTPTPTPTPTPTP)-3' / HEPTATHYMIDINE Mass: 2084.392 Da / Num. of mol.: 4 / Source method*: obtained synthetically
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.09 Å³/Da / Density % sol: 41.02 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: BL14-1 / Type: BESSY / Wavelength: 0.98141
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98141 Å / Relative weight: 1
Reflection	Resolution: 1.92→45.9 Å / Num. obs: 30854 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 3 % / R_merge(I) obs: 0.07

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Processing

Software

Name: REFMAC / Version: 5.5.0109 / Classification: refinement

Refinement

Method to determine structure: OTHER
Starting model: NONE

Resolution: 1.92→45.88 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.923 / SU B: 8.373 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24543	1567	5 %	RANDOM
R_work	0.20736	-	-	-
obs	0.20925	29769	100 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 24.861 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.91 Å²	0 Å²	0 Å²
2-	-	2.97 Å²	0 Å²
3-	-	-	-2.06 Å²

Refinement step

Cycle: LAST / Resolution: 1.92→45.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2695	435	0	345	3475

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	3292
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2266
X-RAY DIFFRACTION	r_angle_refined_deg	1.4	2.125	4515
X-RAY DIFFRACTION	r_angle_other_deg	2.073	3	5511
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.702	5	362
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.644	23.125	128
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.69	15	489
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.624	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	462
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	3390
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	666
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	2.877	5	1731
X-RAY DIFFRACTION	r_mcbond_other	0.576	5	726
X-RAY DIFFRACTION	r_mcangle_it	3.883	7	2784
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	5.1	9	1561
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	6.141	11	1721
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: 1.919→1.969 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.312	108	-
R_work	0.267	2053	-
obs	-	-	100 %

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	9.3403	-4.7813	3.0554	2.5057	-1.7637	17.3534	-0.1166	0.1369	0.5612	0.089	-0.2448	-0.4126	2.2446	-1.9744	0.3614	0.527	-0.4637	-0.1726	0.4516	0.2167	0.3364	-3.842	-18.09	45.377
2	1.2118	0.0035	0.2048	0.7339	0.8185	1.021	-0.0062	-0.1059	-0.2212	0.1038	0.0605	-0.0423	0.0426	0.0593	-0.0543	0.0998	0.0143	-0.003	0.0748	0.0211	0.1181	7.004	-9.715	40.539
3	2.3851	-0.39	2.6681	2.0829	-1.298	5.7982	-0.0598	0.1217	0.0736	-0.1256	0.006	-0.1029	-0.2925	0.0292	0.0538	0.106	0.0115	0.0111	0.0544	-0.0025	0.0732	5.136	-0.04	37.926
4	5.6875	2.0134	-2.3319	3.2052	-0.5501	4.0288	-0.3656	0.2983	-0.7869	-0.2462	0.0658	-0.1207	0.517	-0.0131	0.2997	0.102	0.0026	0.0291	0.0257	-0.0386	0.1419	1.608	-16.52	39.931
5	1.9679	0.0281	-0.1683	1.9905	1.3396	2.7346	0.0011	-0.1182	0.0538	-0.1152	-0.0088	-0.0879	-0.2056	-0.128	0.0076	0.1078	0.0149	-0.016	0.0609	0.0089	0.0932	0.273	-1.601	42.548
6	2.0164	1.7891	0.4561	1.7605	-0.2825	3.5661	-0.0828	0.0608	-0.1249	-0.0349	0.045	-0.0808	-0.0955	0.1812	0.0377	0.0482	0.0171	0.0162	0.0862	-0.0099	0.0853	7.853	-8.953	28.384
7	7.6328	-5.1804	2.0027	4.8452	-2.2899	3.7667	0.0127	0.3492	0.0377	-0.4699	-0.0864	-0.2203	0.3686	0.2134	0.0736	0.1744	-0.0429	0.0302	0.0617	-0.037	0.1185	1.405	-12.408	-1.999
8	0.4388	-0.2681	1.1976	0.8031	0.3958	5.4253	-0.0909	-0.0312	-0.0684	0.0525	-0.0304	0.1934	-0.1531	-0.2356	0.1213	0.0551	-0.0071	0.0219	0.1038	0.0066	0.1314	-10.901	-4.895	12.309
9	1.9692	-0.3206	0.2962	0.9035	-0.3349	1.2088	-0.0812	0.0854	-0.1559	-0.0997	0.0245	0.1181	-0.0993	-0.0714	0.0566	0.0877	-0.0183	0.011	0.0612	-0.0071	0.1148	-5.572	-5.898	3.84
10	5.8563	-0.5453	-0.5559	10.6187	2.5852	0.9629	-0.164	-0.2592	-0.6265	0.4374	-0.0258	0.3711	0.1636	0.1292	0.1898	0.0933	-0.0071	0.0404	0.1092	0.0116	0.1182	-0.814	-13.552	3.383
11	2.0886	-0.6573	-0.6757	2.73	0.1872	1.7319	-0.0687	-0.0331	-0.1468	0.0768	0.0173	0.1929	-0.0124	-0.0359	0.0513	0.0796	-0.0049	-0.0124	0.062	-0.003	0.0882	-1.423	-4.422	5.009
12	1.9325	-1.0111	-0.6782	1.2681	-0.3288	3.2574	-0.179	-0.1524	-0.1304	0.0651	0.0223	0.0322	-0.1731	0.0198	0.1567	0.0491	0.0241	0.0201	0.067	0.0278	0.118	-8.366	-8.33	17.158
13	1.6831	0.5141	-0.3882	1.326	0.4665	3.3821	-0.0303	-0.052	-0.0064	0.0705	0.021	-0.0561	0.0336	-0.0305	0.0094	0.0874	0.0058	0.0218	0.0246	-0.0049	0.1409	-18.282	-7.811	35.437
14	2.9819	-0.8009	-1.0796	1.644	0.7764	1.7233	-0.1636	-0.0294	-0.2519	0.1003	-0.0456	0.1107	0.2228	0.0078	0.2093	0.0848	-0.005	0.0123	0.031	0.0065	0.086	-19.41	-10.966	36.065
15	4.0549	-0.2215	-0.0396	4.1353	2.2546	4.8648	-0.1518	-0.0599	-0.0634	-0.1562	-0.0936	0.1408	-0.0428	0.0564	0.2454	0.101	-0.0072	0.0104	0.052	0.0382	0.107	-15.252	-9.809	37.688
16	0.8409	-0.7327	0.134	1.3906	-0.6499	1.0687	0.013	-0.0091	-0.0628	-0.0959	0.0122	0.0145	0.1312	-0.0855	-0.0251	0.0788	-0.0056	0.0023	0.0659	0.0053	0.0994	17.913	-6.405	8.986
17	1.9992	0.213	-0.7387	1.5377	-0.2792	0.892	-0.0657	0.1711	-0.0935	-0.1833	-0.0494	-0.1035	0.0985	0.0558	0.115	0.0894	0.004	-0.001	0.0932	0.0137	0.0908	20.049	-6.849	7.778
18	1.226	-0.0257	-0.5027	2.6344	-0.2287	2.5734	-0.054	-0.0583	-0.0946	0.1316	-0.0411	0.002	0.24	0.0035	0.0952	0.1266	-0.0015	0.0221	0.0819	-0.0161	0.1349	16.369	-12.217	12.044
19	1.8412	-0.113	-0.4656	4.6116	-1.6346	1.5402	0.0471	0.0044	-0.0957	0.3364	-0.0636	0.1064	-0.0653	0.07	0.0165	0.1041	-0.009	-0.0091	0.0825	0.0043	0.0595	15.032	-8.669	8.7

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	28 - 32
2	X-RAY DIFFRACTION	2	A	33 - 74
3	X-RAY DIFFRACTION	3	A	75 - 86
4	X-RAY DIFFRACTION	4	A	87 - 99
5	X-RAY DIFFRACTION	5	A	100 - 113
6	X-RAY DIFFRACTION	6	B	1 - 6
7	X-RAY DIFFRACTION	7	C	29 - 35
8	X-RAY DIFFRACTION	8	C	36 - 47
9	X-RAY DIFFRACTION	9	C	48 - 86
10	X-RAY DIFFRACTION	10	C	87 - 94
11	X-RAY DIFFRACTION	11	C	95 - 113
12	X-RAY DIFFRACTION	12	D	1 - 6
13	X-RAY DIFFRACTION	13	E	27 - 45
14	X-RAY DIFFRACTION	14	E	46 - 88
15	X-RAY DIFFRACTION	15	E	89 - 113
16	X-RAY DIFFRACTION	16	G	26 - 43
17	X-RAY DIFFRACTION	17	G	44 - 74
18	X-RAY DIFFRACTION	18	G	75 - 91
19	X-RAY DIFFRACTION	19	G	92 - 113

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