PDB-3to1: Two surfaces on Rtt106 mediate histone binding and chaperone activity

ID or keywords:

Entry

Database: PDB / ID: 3to1

Title

Two surfaces on Rtt106 mediate histone binding and chaperone activity

Components

Histone chaperone RTT106

Keywords

CHAPERONE / histone chaperone

Function / homology

Function and homology information

transposition / DNA replication-dependent chromatin assembly / heterochromatin formation / nucleosome binding / transcription elongation by RNA polymerase II / chromatin organization / chromosome / histone binding / double-stranded DNA binding / negative regulation of transcription by RNA polymerase II ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Zunder, R.M. / Antczak, A.J. / Berger, J.M. / Rine, J.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Two surfaces on the histone chaperone Rtt106 mediate histone binding, replication, and silencing.
Authors: Zunder, R.M. / Antczak, A.J. / Berger, J.M. / Rine, J.

History

Deposition	Sep 2, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 21, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jan 25, 2012	Group: Database references
Revision 1.2	Jul 18, 2012	Group: Database references
Revision 1.3	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.4	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3to1.cif.gz	184 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3to1_validation.pdf.gz	437.9 KB	Display	wwPDB validaton report
Full document	3to1_full_validation.pdf.gz	444 KB	Display
Data in XML	3to1_validation.xml.gz	17.2 KB	Display
Data in CIF	3to1_validation.cif.gz	22.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/to/3to1 ftp://data.pdbj.org/pub/pdb/validation_reports/to/3to1	HTTPS FTP

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Related structure data

Similar structure data	3fq6-d 1th8-d 5v8t-1 6vcv-d 5uq0-2 2ykh-2 6ml0-d 4edj-1 4ote-2 6qw0-2 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	#32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: Histone chaperone RTT106

B: Histone chaperone RTT106

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

1

A: Histone chaperone RTT106

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

2

B: Histone chaperone RTT106

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

Unit cell

Length a, b, c (Å)	71.977, 60.703, 76.411
Angle α, β, γ (deg.)	90.00, 104.52, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Histone chaperone RTT106 / Regulator of Ty1 transposition protein 106 Mass: 26888.770 Da / Num. of mol.: 2 / Fragment: UNP residues 69-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: RTT106, YNL206C, N1346 / Production host: Escherichia coli (E. coli) / References: UniProt: P40161
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Histone chaperone RTT106 / Regulator of Ty1 transposition protein 106

Mass: 26888.770 Da / Num. of mol.: 2 / Fragment: UNP residues 69-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RTT106, YNL206C, N1346 / Production host:

Escherichia coli (E. coli) / References: UniProt: P40161

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 29 / 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: 3 Å³/Da / Density % sol: 59.07 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM Hepes pH 7.5, 10% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2007
Radiation	Monochromator: KOHZU DUAL DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.11587 Å / Relative weight: 1
Reflection	Resolution: 2.6→23.227 Å / Num. obs: 19832 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 2.6→2.74 Å / % possible all: 99.8

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Processing

Software

Name	Version	Classification
Blu-Ice	Ice	data collection
PHASER		phasing
PHENIX	(phenix.refine: dev_810)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: model not deposited

Resolution: 2.6→23.227 Å / SU ML: 0.77 / σ(F): 1.34 / Phase error: 28.42 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2574	1012	5.11 %	RANDOM
R_work	0.2095	-	-	-
obs	0.212	19808	99.87 %	-
all	-	19808	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 46.856 Å² / k_sol: 0.33 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.1718 Å²	-0 Å²	2.7632 Å²
2-	-	-5.6075 Å²	-0 Å²
3-	-	-	10.7793 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→23.227 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3420	0	0	29	3449

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	3488
X-RAY DIFFRACTION	f_angle_d	0.845	4709
X-RAY DIFFRACTION	f_dihedral_angle_d	11.904	1302
X-RAY DIFFRACTION	f_chiral_restr	0.047	546
X-RAY DIFFRACTION	f_plane_restr	0.004	587

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 (%)
2.6-2.737	0.4261	149	0.3689	2649	X-RAY DIFFRACTION	100
2.737-2.9081	0.4165	124	0.3224	2670	X-RAY DIFFRACTION	100
2.9081-3.1322	0.3057	152	0.2645	2684	X-RAY DIFFRACTION	100
3.1322-3.4465	0.3025	147	0.2277	2657	X-RAY DIFFRACTION	100
3.4465-3.9431	0.2424	135	0.2012	2693	X-RAY DIFFRACTION	100
3.9431-4.9599	0.2055	148	0.1571	2701	X-RAY DIFFRACTION	100
4.9599-23.227	0.236	157	0.1973	2742	X-RAY DIFFRACTION	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	1.2569	0.1617	0.6226	1.2998	0.4466	0.9393	0.1041	-0.1123	0.3362	0.239	-0.008	0.3708	-0.0455	0.0274	0	0.4603	-0.047	0.0164	0.5732	-0.0245	0.6214	30.1604	2.3386	9.8674
2	1.5808	-1.0015	1.0092	3.5465	0.4722	2.1672	-0.2259	-0.1439	0.2711	0.0769	0.0721	0.1428	-0.192	0.1694	0	0.2902	-0.0164	-0.0245	0.3205	0.0109	0.4939	19.7869	1.6684	1.8238
3	0.5396	0.4734	0.0422	0.5764	0.3654	0.5674	-0.0401	-0.0345	-0.2491	0.1817	-0.3123	0.1187	0.0424	-0.2641	-0	0.373	0.001	-0.029	0.4098	-0.0217	0.5305	14.1898	-18.5453	-1.0787
4	0.523	-0.1129	0.0597	0.2573	-0.0476	0.5736	0.0967	0.2305	0.5316	0.2781	-0.2397	-0.0845	-0.0843	1.1041	-0.001	0.3533	-0.0375	-0.0803	0.3798	-0.0198	0.4909	21.5295	-15.0459	-1.8204
5	0.5626	-0.0431	0.272	1.0561	0.9034	0.8847	0.2263	0.1655	0.1487	0.5094	-0.1235	0.0301	0.2013	0.2035	0	0.3795	-0.0078	-0.0423	0.3962	-0.0186	0.4874	16.1696	-25.2328	-9.003
6	0.0157	0.057	-0.0279	0.1804	-0.0851	0.0497	0.3898	0.178	-0.4657	-0.7926	-0.0434	-0.2864	0.1306	0.3877	0.0045	0.4961	-0.0266	-0.0552	0.5429	-0.0532	0.642	20.0691	-27.0452	-8.7687
7	0.0751	0.1623	0.0242	0.5323	0.1398	0.2085	0.4167	0.5781	-0.0495	0.0818	-0.0065	-0.1376	0.0391	-0.0643	-0	0.4864	-0.0109	0.0091	0.4305	0.0038	0.5149	20.1724	-26.1879	-5.7896
8	0.0825	0.0082	-0.0498	-0.0049	-0.0049	0.0126	-0.4697	0.3317	0.7394	-0.6472	0.2863	0.7203	-0.2787	-0.6236	-0	0.4568	-0.0121	-0.0937	0.4618	-0.0242	0.5463	10.1985	-20.613	-13.0737
9	0.9139	0.5433	1.0386	1.0505	0.5549	2.4188	-0.0121	0.0694	-0.0025	-0.1265	-0.1827	0.4687	0.6717	-0.2065	-0	0.6112	-0.0718	0.0824	0.5943	-0.0469	0.4552	-3.5233	-5.2099	-37.8633
10	1.6202	1.0725	0.7927	0.9376	0.0274	1.2472	-0.1166	0.6883	0.4324	0.3112	-0.154	0.1209	0.0985	-0.361	-0.0001	0.542	-0.0809	0.0974	0.5108	-0.0207	0.3687	0.3359	3.0315	-26.9821
11	0.8005	-0.5931	-0.1632	1.8396	1.0375	0.9119	0.2782	-0.1785	-0.4	0.0724	-0.2558	0.7364	0.4429	-0.8198	0.1923	0.5004	-0.3487	-0.1138	0.644	0.0288	0.4971	-12.2428	-5.0654	-24.6343
12	2.0294	0.1593	-1.0798	0.8301	0.8297	1.6299	0.1355	0.3205	-0.0209	0.2761	-0.1074	0.0876	1.2854	-0.2738	0.7166	1.0469	-0.1334	-0.018	0.5723	0.1043	0.3713	-1.1025	-6.3854	-21.1926
13	1.3955	0.9083	-0.3246	0.9446	0.5569	1.5954	0.0889	0.0495	0.1885	-0.0564	-0.2765	0.2615	0.3263	0.0981	0	0.5395	0.0166	0.0105	0.3973	0.0073	0.349	5.5085	15.6737	-22.121
14	0.3618	-0.1762	-0.3312	0.0864	0.1846	0.7512	-0.0833	0.2969	0.7126	-0.2647	0.2361	0.1891	-1.2895	0.3258	0.0082	0.4218	-0.0418	-0.0388	0.5482	-0.0885	0.5514	1.5036	31.3358	-13.2381
15	0.4614	0.0546	0.2226	0.1584	-0.0542	0.1372	0.2743	-0.1649	-0.1984	-0.2314	-0.1007	0.4127	-0.3098	0.1806	0	0.429	-0.0208	-0.0173	0.4021	0.0227	0.44	10.5476	22.3998	-22.3644
16	0.3069	0.2222	0.0208	0.2159	0.05	0.3528	-0.3578	-0.9256	-0.0048	0.9026	0.3466	0.183	0.2494	-0.4589	0.0007	0.6191	-0.0365	-0.045	0.5407	0.055	0.4466	7.944	17.9213	-10.3378

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 70:118)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 119:205)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 218:235)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 236:248)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 249:269)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 270:275)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 276:287)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 288:299)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 71:118)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 119:146)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 154:181)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 182:205)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 218:262)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 263:269)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 270:287)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 288:300)

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