PDB-3o4z: Tel2 structure and function in the Hsp90-dependent maturation of ...

ID or keywords:

Entry

Database: PDB / ID: 3o4z

Title

Tel2 structure and function in the Hsp90-dependent maturation of mTOR and ATR complexes

Components

Telomere length regulation protein TEL2

Keywords

PROTEIN BINDING / HEAT like helical repeats

Function / homology

Function and homology information

positive regulation of DNA damage checkpoint / 'de novo' cotranslational protein folding / protein localization to chromosome / TTT Hsp90 cochaperone complex / telomeric DNA binding / telomere maintenance via telomerase / telomere maintenance / Hsp90 protein binding / chromosome, telomeric region / protein stabilization ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.1 Å

Authors

Xie, Y. / Pavletich, N.P.

Citation

Journal: Genes Dev. / Year: 2010
Title: Tel2 structure and function in the Hsp90-dependent maturation of mTOR and ATR complexes.
Authors: Takai, H. / Xie, Y. / de Lange, T. / Pavletich, N.P.

History

Deposition	Jul 27, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 15, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Aug 9, 2017	Group: Data collection / Refinement description / Source and taxonomy Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3o4z.cif.gz	919.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3o4z.ent.gz	782 KB	Display	PDB format
PDBx/mmJSON format	3o4z.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3o4z_validation.pdf.gz	478.1 KB	Display	wwPDB validaton report
Full document	3o4z_full_validation.pdf.gz	627.6 KB	Display
Data in XML	3o4z_validation.xml.gz	93.8 KB	Display
Data in CIF	3o4z_validation.cif.gz	124.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o4/3o4z ftp://data.pdbj.org/pub/pdb/validation_reports/o4/3o4z	HTTPS FTP

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Related structure data

Similar structure data	4lo7-4 3ia4-d 6bw2-d 4zu4-d 4lo7-6 5bqu-d 1p7h-2 2op5-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) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Telomere length regulation protein TEL2

B: Telomere length regulation protein TEL2

C: Telomere length regulation protein TEL2

D: Telomere length regulation protein TEL2

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

1

A: Telomere length regulation protein TEL2

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

2

B: Telomere length regulation protein TEL2

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

3

C: Telomere length regulation protein TEL2

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

4

D: Telomere length regulation protein TEL2

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

5

A: Telomere length regulation protein TEL2

C: Telomere length regulation protein TEL2

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

6

B: Telomere length regulation protein TEL2

D: Telomere length regulation protein TEL2

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

Unit cell

Length a, b, c (Å)	91.400, 123.300, 162.300
Angle α, β, γ (deg.)	90.00, 95.17, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

ID
1
2
3
4
5
6
7
8

#1: Protein	Telomere length regulation protein TEL2 Mass: 74345.922 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TEL2, YGR099W / Cell line (production host): HI-5 INSECT CELLS / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P53038

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.06 Å³/Da / Density % sol: 59.84 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-HCl, 7% (w/v) polyethylene glycol (PEG) 8000, 0.8 M NaCl and 1.5% (v/v) ethanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Relative weight: 1
Reflection	Resolution: 3.1→39.2 Å / Num. obs: 60224 / Redundancy: 4.8 % / R_sym value: 0.05 / Net I/σ(I): 24.2
Reflection shell	Resolution: 3.1→3.21 Å / Mean I/σ(I) obs: 2.5 / R_sym value: 0.42 / % possible all: 97.6

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
SHELXS		phasing
REFMAC	5.4.0069	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 3.1→39.2 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.935 / SU B: 41.947 / SU ML: 0.326 / Cross valid method: THROUGHOUT / ESU R Free: 0.42 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23857	2526	4 %	RANDOM
R_work	0.222	-	-	-
obs	0.22267	60224	96.23 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 105.176 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.26 Å²	0 Å²	-0.2 Å²
2-	-	2.2 Å²	0 Å²
3-	-	-	-1.98 Å²

Refinement step

Cycle: LAST / Resolution: 3.1→39.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18452	0	0	0	18452

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	18784
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.186	1.98	25324
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.571	5	2260
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.323	23.942	832
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.303	15	3544
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.496	15	116
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	2948
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	13656
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	0.592	0.75	11396
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.185	1.5	18436
X-RAY DIFFRACTION	r_scbond_it	1.296	1.5	7388
X-RAY DIFFRACTION	r_scangle_it	2.273	2.5	6888
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	224	TIGHT POSITIONAL	0.01	0.03
1	2	B	224	TIGHT POSITIONAL	0.01	0.03
1	3	C	224	TIGHT POSITIONAL	0.01	0.03
1	4	D	224	TIGHT POSITIONAL	0.01	0.03
1	1	A	224	TIGHT THERMAL	1.36	10
1	2	B	224	TIGHT THERMAL	0.91	10
1	3	C	224	TIGHT THERMAL	1.21	10
1	4	D	224	TIGHT THERMAL	0.9	10
2	1	A	400	TIGHT POSITIONAL	0.01	0.03
2	2	B	400	TIGHT POSITIONAL	0.01	0.03
2	3	C	400	TIGHT POSITIONAL	0.01	0.03
2	4	D	400	TIGHT POSITIONAL	0.01	0.03
2	1	A	400	TIGHT THERMAL	1.4	10
2	2	B	400	TIGHT THERMAL	1.11	10
2	3	C	400	TIGHT THERMAL	1.03	10
2	4	D	400	TIGHT THERMAL	1.02	10
3	1	A	1026	TIGHT POSITIONAL	0.01	0.03
3	2	B	1026	TIGHT POSITIONAL	0.01	0.03
3	3	C	1026	TIGHT POSITIONAL	0.01	0.03
3	4	D	1026	TIGHT POSITIONAL	0.01	0.03
3	1	A	1026	TIGHT THERMAL	1.57	10
3	2	B	1026	TIGHT THERMAL	1.32	10
3	3	C	1026	TIGHT THERMAL	1.15	10
3	4	D	1026	TIGHT THERMAL	1.53	10
4	1	A	513	TIGHT POSITIONAL	0.01	0.03
4	2	B	513	TIGHT POSITIONAL	0.01	0.03
4	3	C	513	TIGHT POSITIONAL	0.01	0.03
4	4	D	513	TIGHT POSITIONAL	0.01	0.03
4	1	A	513	TIGHT THERMAL	1.8	10
4	2	B	513	TIGHT THERMAL	1.57	10
4	3	C	513	TIGHT THERMAL	1.4	10
4	4	D	513	TIGHT THERMAL	1.87	10
5	1	A	793	TIGHT POSITIONAL	0.02	0.03
5	2	B	793	TIGHT POSITIONAL	0.01	0.03
5	3	C	793	TIGHT POSITIONAL	0.01	0.03
5	4	D	793	TIGHT POSITIONAL	0.01	0.03
5	1	A	793	TIGHT THERMAL	2.04	10
5	2	B	793	TIGHT THERMAL	1.93	10
5	3	C	793	TIGHT THERMAL	1.98	10
5	4	D	793	TIGHT THERMAL	1.98	10
6	1	A	98	TIGHT POSITIONAL	0.01	0.03
6	2	B	98	TIGHT POSITIONAL	0.01	0.03
6	3	C	98	TIGHT POSITIONAL	0.01	0.03
6	4	D	98	TIGHT POSITIONAL	0.01	0.03
6	1	A	98	TIGHT THERMAL	2.54	10
6	2	B	98	TIGHT THERMAL	1.99	10
6	3	C	98	TIGHT THERMAL	1.96	10
6	4	D	98	TIGHT THERMAL	1.2	10
7	1	A	687	TIGHT POSITIONAL	0.01	0.03
7	2	B	687	TIGHT POSITIONAL	0.01	0.03
7	3	C	687	TIGHT POSITIONAL	0.01	0.03
7	4	D	687	TIGHT POSITIONAL	0.02	0.03
7	1	A	687	TIGHT THERMAL	1.46	10
7	2	B	687	TIGHT THERMAL	1.32	10
7	3	C	687	TIGHT THERMAL	1.44	10
7	4	D	687	TIGHT THERMAL	2.48	10
8	1	A	872	TIGHT POSITIONAL	0.01	0.03
8	2	B	872	TIGHT POSITIONAL	0.01	0.03
8	3	C	872	TIGHT POSITIONAL	0.01	0.03
8	4	D	872	TIGHT POSITIONAL	0.01	0.03
8	1	A	872	TIGHT THERMAL	1.83	10
8	2	B	872	TIGHT THERMAL	1.68	10
8	3	C	872	TIGHT THERMAL	1.69	10
8	4	D	872	TIGHT THERMAL	1.88	10

LS refinement shell

Resolution: 3.1→3.18 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.386	168	-
R_work	0.335	3934	-
obs	-	-	86.03 %

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	1.3331	-0.7425	-1.7459	6.0339	-1.5262	11.0688	-0.0728	0.9006	-0.3181	-1.2595	-0.2237	-0.4966	0.651	0.5408	0.2965	0.3259	0.1932	0.185	0.4196	-0.1699	-0.063	60.673	60.543	17.881
2	6.7323	-1.6293	-2.3244	4.4999	1.2312	7.1674	-0.1575	0.8555	-0.1317	-0.5819	-0.1075	0.0874	0.406	-0.0145	0.2651	-0.2164	0.1579	-0.1228	-0.2529	-0.0217	-0.4794	48.657	66.654	36.441
3	1.1838	0.2247	-1.7364	1.6503	-1.1515	7.0408	0.0092	0.0798	-0.0099	-0.201	0.0017	0.1785	-0.0743	-0.3777	-0.0109	-0.4354	0.1373	-0.056	-0.3129	-0.0529	-0.2706	31.032	72.379	67.838
4	5.1132	1.8474	3.8012	2.6165	2.7251	8.4016	-0.1594	0.283	0.4438	-0.4648	0.0868	0.0548	-0.4252	-0.0618	0.0727	-0.2514	0.0462	-0.0402	-0.4609	0.1271	-0.0232	66.053	97.006	63.368
5	4.6774	-3.1893	0.95	4.9876	-0.3039	10.5422	-0.5329	-0.924	0.3945	1.0204	0.4077	0.4325	-0.6301	-0.5378	0.1252	0.5183	0.0867	0.2512	0.6997	-0.0176	-0.1126	40.484	69.895	154.033
6	4.1879	-1.5388	-1.3153	7.0632	1.8169	6.6287	-0.0545	-0.5764	-0.0856	0.5542	-0.1214	0.4017	0.1658	-0.4554	0.1758	-0.067	-0.1337	0.1051	0.1626	0.1873	-0.4056	46.526	58.759	134.873
7	1.9019	0.0848	0.7207	0.7181	-0.5157	10.0282	0.2258	-0.314	-0.4124	0.1629	-0.2077	-0.0047	0.535	-0.0194	-0.0181	-0.1764	-0.0488	0.0216	-0.2841	0.1465	-0.131	52.281	43.295	102.508
8	4.3878	2.7611	-3.0031	4.9172	-2.8891	6.4554	0.2471	-0.6418	-0.0377	0.4481	-0.1225	-0.2591	-0.0003	0.1144	-0.1246	-0.3314	-0.0275	-0.0944	-0.1907	-0.0147	-0.1611	81.96	72.868	112.715
9	4.8029	-0.3282	1.3387	2.1462	0.2926	6.0798	-0.0946	-1.8123	-0.6311	1.815	0.0539	0.1522	1.301	0.7427	0.0406	1.6644	0.1672	-0.2146	1.3757	0.293	0.498	74.556	75.176	156.984
10	4.3123	-1.348	0.5295	8.3768	-1.0194	6.7118	0.072	-1.1028	0.0117	1.4604	-0.1436	-0.3953	0.1588	0.6355	0.0717	0.2393	-0.173	-0.0603	0.3856	-0.0869	-0.138	71.764	87.738	137.756
11	2.0602	-0.0422	-1.4882	1.7169	-0.342	7.5586	0.1355	-0.3788	0.3836	0.2377	-0.2713	0.1559	-0.1106	-0.3419	0.1359	-0.3163	-0.1593	-0.0592	-0.2581	-0.1344	0.1208	70.487	105.553	105.884
12	4.0188	1.4507	2.6866	3.6284	2.2285	7.581	0.2063	-0.5539	0.2811	0.3871	-0.317	0.3129	-0.004	-0.1221	0.1106	-0.3362	-0.0126	0.1227	-0.2321	0.0653	-0.3614	39.676	75.798	110.315
13	1.2823	0.5714	1.7758	2.8143	-3.1257	10.5353	-0.0003	1.59	0.5543	-1.3171	-0.2272	0.6599	-1.339	-0.7385	0.2276	1.1611	0.2617	-0.1037	1.1672	0.4551	0.4728	71.685	92.887	19.001
14	7.4885	-1.7356	0.4483	4.1797	-0.943	6.4843	-0.0214	1.4615	0.7468	-0.9763	-0.0063	-0.0612	-0.8305	0.0944	0.0278	0.1097	-0.0888	0.1079	-0.0356	0.2725	-0.0869	81.401	86.337	38.783
15	1.1603	0.0476	0.8707	1.6354	1.6437	9.2411	-0.0632	0.0818	-0.0092	-0.2427	0.0915	-0.2909	-0.1908	0.2176	-0.0283	-0.4198	-0.0479	0.0116	-0.4193	0.0332	-0.0132	95.294	79.242	71.766
16	5.6261	0.9914	-3.0458	2.8167	-1.1391	6.4248	-0.1426	0.2888	-0.3263	-0.1314	0.0848	0.0705	0.1504	-0.143	0.0577	-0.4742	0.093	-0.1149	-0.4952	-0.0369	-0.4473	61.238	54.773	61.76

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 78
2	X-RAY DIFFRACTION	2	A	83 - 209
3	X-RAY DIFFRACTION	3	A	210 - 386
4	X-RAY DIFFRACTION	4	A	428 - 688
5	X-RAY DIFFRACTION	5	B	1 - 78
6	X-RAY DIFFRACTION	6	B	83 - 209
7	X-RAY DIFFRACTION	7	B	210 - 386
8	X-RAY DIFFRACTION	8	B	428 - 688
9	X-RAY DIFFRACTION	9	C	1 - 78
10	X-RAY DIFFRACTION	10	C	83 - 209
11	X-RAY DIFFRACTION	11	C	210 - 386
12	X-RAY DIFFRACTION	12	C	428 - 688
13	X-RAY DIFFRACTION	13	D	1 - 78
14	X-RAY DIFFRACTION	14	D	83 - 209
15	X-RAY DIFFRACTION	15	D	210 - 386
16	X-RAY DIFFRACTION	16	D	428 - 688

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