PDB-3q68: Structure of the Vps75-Rtt109 histone chaperone-lysine acetyltran...

ID or keywords:

Entry

Database: PDB / ID: 3q68

Title

Structure of the Vps75-Rtt109 histone chaperone-lysine acetyltransferase complex (Full-length proteins in space group P212121)

Components

Histone acetyltransferase RTT109
Vacuolar protein sorting-associated protein 75 (VPS75)

Keywords

CHAPERONE/TRANSFERASE / Histone chaperone / Lysine acetyltransferase / CHAPERONE-TRANSFERASE complex

Function / homology

Function and homology information

histone H3K23 acetyltransferase activity / histone H3K56 acetyltransferase activity / H3 histone acetyltransferase complex / DNA replication-dependent chromatin disassembly / histone H3K14 acetyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K9 acetyltransferase activity / maintenance of rDNA / acetyltransferase activator activity / replication-born double-strand break repair via sister chromatid exchange ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.705 Å

Authors

Su, D. / Thompson, J.R. / Mer, G.

Citation

Journal: J.Biol.Chem. / Year: 2011
Title: Structure and histone binding properties of the Vps75-Rtt109 chaperone-lysine acetyltransferase complex.
Authors: Su, D. / Hu, Q. / Zhou, H. / Thompson, J.R. / Xu, R.M. / Zhang, Z. / Mer, G.

History

Deposition	Dec 30, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 23, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 13, 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_conn / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3	Dec 6, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3q68.cif.gz	376 KB	Display	PDBx/mmCIF format
PDB format	pdb3q68.ent.gz	309.2 KB	Display	PDB format
PDBx/mmJSON format	3q68.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3q68_validation.pdf.gz	462.3 KB	Display	wwPDB validaton report
Full document	3q68_full_validation.pdf.gz	490.2 KB	Display
Data in XML	3q68_validation.xml.gz	35.1 KB	Display
Data in CIF	3q68_validation.cif.gz	48.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q6/3q68 ftp://data.pdbj.org/pub/pdb/validation_reports/q6/3q68	HTTPS FTP

-
Related structure data

Related structure data	3q66C 2zd7S 3cz7S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5c55-1 5c54-2 4xky-d 6h2s-d 6h2r-d 5c54-1 5ktl-1 6arh-d 6xgs-d 4mlr-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#122 - Feb 2010 Enhanceosome similarity (4) #67 - Jul 2005 TATA-Binding Protein similarity (1)

Deposited unit

A: Vacuolar protein sorting-associated protein 75 (VPS75)

C: Histone acetyltransferase RTT109

B: Vacuolar protein sorting-associated protein 75 (VPS75)

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	90.988, 98.056, 171.366
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Vacuolar protein sorting-associated protein 75 (VPS75) Mass: 30656.084 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: VPS75, YNL246W, N0890 / Plasmid: pCOLA Duet-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P53853
#2: Protein	Histone acetyltransferase RTT109 / Regulator of Ty1 transposition protein 109 Mass: 50806.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RTT109, KIM2, REM50, YLL002W, L1377 / Plasmid: GST-based pET / Production host: Escherichia coli (E. coli) / References: UniProt: Q07794, histone acetyltransferase
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 3.41 Å³/Da / Density % sol: 63.92 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.8 M sodium citrate, 30% (w/v) 1,6-hexanediol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97901 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97901 Å / Relative weight: 1
Reflection	Resolution: 2.7→50 Å / Num. obs: 40782 / % possible obs: 99.6 % / Redundancy: 8.1 % / R_merge(I) obs: 0.072 / Net I/σ(I): 28.4
Reflection shell	Resolution: 2.7→2.75 Å / Redundancy: 8.3 % / R_merge(I) obs: 0.904 / Mean I/σ(I) obs: 2.5 / % possible all: 100

-
Processing

Software

Name	Version	Classification
HKL-3000		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.6.1_357)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entries 3CZ7 2ZD7

3cz7

2zd7

Resolution: 2.705→47.137 Å / SU ML: 0.36 / σ(F): 0.1 / Phase error: 24.2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2258	510	1.25 %
R_work	0.2016	-	-
obs	0.202	40782	95.65 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 65.472 Å² / k_sol: 0.389 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.2534 Å²	-0 Å²	0 Å²
2-	-	-4.1551 Å²	-0 Å²
3-	-	-	7.4085 Å²

Refinement step

Cycle: LAST / Resolution: 2.705→47.137 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7055	0	0	90	7145

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.022	7225
X-RAY DIFFRACTION	f_angle_d	1.545	9752
X-RAY DIFFRACTION	f_dihedral_angle_d	16.206	2736
X-RAY DIFFRACTION	f_chiral_restr	0.121	1039
X-RAY DIFFRACTION	f_plane_restr	0.012	1251

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 (%)
2.7047-2.9769	0.3127	111	0.2656	9227	X-RAY DIFFRACTION	89
2.9769-3.4075	0.2471	116	0.23	10017	X-RAY DIFFRACTION	96
3.4075-4.2927	0.2333	151	0.1743	10379	X-RAY DIFFRACTION	99
4.2927-47.1439	0.1913	132	0.1937	10649	X-RAY DIFFRACTION	98

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	3.856	3.3351	-1.5666	3.0597	-1.791	6.0623	0.1692	-0.232	1.2006	-0.0443	0.3733	0.9011	0.4311	0.3068	-0.4581	0.5835	0.0161	0.1906	0.9273	-0.0128	0.7141	23.5739	-0.01	-9.675
2	-0.0425	-0.4093	0.065	9.8918	1.2009	0.3891	-0.2073	-0.08	-0.0961	0.127	0.604	-1.846	0.0899	0.3007	-0.3702	0.2301	-0.1464	0.0629	0.7504	-0.1993	0.5308	15.3214	25.3078	-4.7525
3	3.1211	0.1458	1.6524	1.1221	0.5744	0.8533	-0.2036	0.0103	0.3816	0.1461	-0.129	0.0806	-0.232	0.012	0.2565	0.3957	-0.0052	0.0531	0.3644	-0.003	0.3548	10.0137	41.6363	17.073
4	3.1889	3.325	1.0153	6.1027	-1.5075	2.8151	1.1151	1.0805	-1.1043	0.0017	-0.7036	-0.9035	-0.8218	-0.5938	-0.0664	0.3747	-0.0507	-0.061	0.5459	-0.052	0.4978	19.5512	38.2657	0.6538
5	2.7699	0.4558	0.3837	0.4898	-0.4638	0.5353	0.1458	0.44	0.4489	0.135	-0.1274	-0.1621	-0.1387	0.1769	0.0483	0.4119	-0.1025	0.0396	0.3953	0.1149	0.2999	21.0965	43.2986	12.4932
6	4.3132	-0.9797	-0.1602	1.346	0.2631	0.019	-0.4474	-0.2062	0.48	-0.3455	0.137	0.3561	0.2696	0.1181	0.1964	0.5106	0.0889	0.1362	0.6677	-0.0741	0.3648	31.0651	23.7194	5.7176
7	1.7815	1.6081	1.5386	1.934	0.4948	2.5942	-0.0162	0.1062	0.3714	0.0911	-0.058	-0.0977	-0.3462	0.9031	0.0658	0.4599	-0.233	-0.1016	0.6118	-0.0104	0.4758	29.9695	45.0066	26.6902
8	5.317	3.2668	2.9617	8.1751	1.3041	3.3804	0.8118	-0.3634	-1.1547	0.5573	-0.6825	-2.5103	-0.0001	0.3146	-0.0937	0.4857	-0.0765	-0.1687	0.6265	0.1942	1.0439	32.72	35.9492	33.1058
9	1.171	1.7942	1.469	5.2321	0.3046	3.5894	-0.0347	0.0703	-0.4366	0.2246	0.0573	-0.6174	0.123	0.3161	0.024	0.3065	-0.106	0.0209	0.5917	0.005	0.3333	28.1813	34.5726	20.2178
10	5.986	-3.2606	-1.0243	2.0582	0.9348	2.0609	-0.2353	0.4311	-1.1397	-0.1718	-0.0211	0.4726	-0.1729	-0.2765	0.2305	0.3481	-0.0167	0.0208	0.3615	-0.0249	0.4833	6.9705	34.4132	14.5659
11	3.5949	0.9834	-0.5116	2.1689	0.3575	1.0096	0.0122	-0.243	-0.53	0.2275	0.2092	0.0897	0.0014	0.0028	-0.1706	0.3511	-0.0751	-0.0364	0.3904	-0.0223	0.6485	-4.0334	30.4353	23.4127
12	4.8318	-3.1968	4.6836	2.1291	-3.1386	4.5844	1.7642	0.5494	0.741	-2.2678	-2.1152	-0.3277	2.9491	0.7079	-0.0643	1.4477	0.2522	-0.4377	0.7082	-0.1003	1.2155	-8.474	4.6997	22.6284
13	1.7841	-0.2732	0.4143	2.2651	-0.7731	0.635	0.2633	-0.3813	0.0552	0.5985	-0.1491	0.1999	-0.2195	-0.115	-0.0997	0.6198	-0.0794	0.1704	0.4229	-0.039	0.3185	4.4217	27.9749	49.6103
14	0.9337	0.0532	-1.5979	0.0001	-0.195	6.0633	0.2616	-0.0775	0.3772	0.0277	0.5805	0.4988	-0.9153	0.2396	-0.7237	0.4948	0.0442	-0.3408	0.2985	-0.0528	0.9403	-12.8003	5.4532	30.9423
15	4.0491	-1.8492	-2.5869	3.3566	-1.1838	3.8558	-0.5751	1.9352	-4.6907	-0.0994	0.0185	-0.7729	-1.1522	-0.7044	0.3082	0.7839	-0.1543	-0.169	1.4539	-0.0158	1.501	-19.9632	5.2564	35.8613
16	0.4692	-0.1112	0.0486	2.174	-0.4592	-0.0076	0.1394	0.0852	0.1818	0.4423	-0.4419	0.0719	-0.2454	-0.0063	0.1468	0.5314	0.0213	0.0707	0.4255	-0.0137	0.3627	6.336	23.4711	41.924
17	0.7904	0.6078	0.1337	0.6801	-0.2593	0.9864	-0.1599	-0.1614	-0.4097	-0.0039	0.3082	-0.0028	0.4371	-0.1502	-0.0656	0.5823	-0.0695	0.0946	0.2915	0.0015	0.5393	-11.3395	13.5263	41.1596
18	1.9558	0.4913	-1.8916	3.1443	-1.1381	7.258	-0.5002	0.1399	-0.3471	-0.4004	-0.2555	-0.7364	-0.6983	0.6342	-0.559	0.5651	-0.0167	-0.1269	0.3399	0.1703	0.3268	17.7481	20.5712	46.5241
19	0.6983	0.9053	0.5277	1.3456	-0.4309	0.5963	0.4388	0.0273	0.1187	0.1855	-0.2922	0.4968	0.0066	-0.0629	-0.1541	0.5794	-0.029	0.1214	0.3072	-0.0649	0.4152	-4.3718	22.7175	43.2777
20	7.4453	-0.1579	-3.9082	0.2104	0.4025	2.4188	0.3803	0.0327	1.6281	-0.2016	0.761	0.7402	0.3781	0.1484	-1.1377	0.4402	0.0517	-0.0753	1.3158	0.0297	0.8579	-20.7591	34.2014	19.4063
21	0.5022	-0.3728	-0.5595	2.0357	-0.8559	2.5393	0.219	0.2371	-0.4979	0.086	0.017	1.0265	-0.3302	-0.9786	-0.1617	0.3207	0.1109	-0.0102	0.5229	-0.0548	0.392	-11.1507	41.3429	15.6668
22	3.6114	-3.056	-1.2469	8.5155	0.6404	7.3965	-1.0933	-0.2999	-0.5657	-0.0866	2.5353	-0.1595	-0.2378	-0.3579	-0.7109	0.6211	0.0604	0.1862	1.4094	-0.2739	0.8106	-19.3735	36.1541	30.4954
23	0.7465	1.4722	0.0791	4.6524	-1.7285	0.7094	0.42	0.1231	0.0807	-0.1144	-0.233	0.1214	0.2068	-0.175	-0.1407	0.4918	-0.0164	0.072	0.429	-0.1	0.458	-3.8078	15.2307	41.6814
24	1.7398	-0.3506	0.7748	2.456	-1.2636	0.9445	0.2849	-0.1844	-0.0554	0.438	-0.3032	-0.1884	0.0466	0.2746	0.0266	0.5731	-0.1181	-0.0052	0.4318	0.0519	0.3948	10.0455	9.1563	48.8528
25	5.51	4.0295	2.0148	3.131	1.1621	1.8284	-0.1364	0.7812	-1.5165	1.2302	-0.1235	-1.629	0.2438	0.5769	0.3946	0.594	-0.1055	0.1996	0.5485	0.1591	1.0762	8.6105	-6.6991	52.4357
26	2.8609	0.4415	3.4893	0.7367	-1.4302	6.9173	0.6071	0.0133	-0.8505	-0.1338	0.0978	0.1324	0.3216	-0.0667	-0.5863	0.6846	-0.0687	-0.0692	0.4083	-0.0266	0.5243	-4.6573	-0.4671	44.8313
27	3.167	-1.317	0.9121	3.5326	1.0663	3.4985	0.7755	0.4875	-0.175	-0.6576	-0.4085	0.2765	0.862	0.7648	-0.2332	0.8485	0.3023	0.054	0.4825	-0.0537	0.4952	1.2756	-1.6298	30.1379
28	0.6842	1.0906	-0.2424	2.9607	0.1704	-0.018	0.0611	0.0276	0.2082	0.3439	-0.1623	-0.3743	0.0607	-0.0281	0.049	0.5551	0.0179	0.0994	0.4507	-0.0119	0.4994	0.6252	14.6054	45.5139
29	3.3714	0.2021	-0.8666	1.4487	1.0508	0.9092	0.2127	0.5901	-0.5326	-0.0559	-0.1924	-0.1477	-0.3652	0.046	0.0395	0.5281	0.0059	0.1055	0.3945	0.0136	0.4448	12.5939	27.288	32.7387
30	1.1533	0.1795	0.2266	3.5481	-0.2771	0.3906	0.143	0.0773	0.167	0.5975	-0.353	-0.1791	-0.2359	0.052	0.126	0.6156	-0.1247	-0.0199	0.4018	0.053	0.4085	12.2216	34.9315	43.0043
31	0.8471	0.1505	-0.5145	6.0255	1.6844	3.0481	-0.0057	0.2438	-0.0068	0.1376	0.265	0.2151	-0.5295	0.5592	-0.1972	0.6184	0.0016	-0.013	0.6657	0.0441	0.4958	-4.6051	49.8926	9.296
32	0.2986	-0.3472	-0.6431	1.6659	0.9359	1.2327	-0.0957	0.6461	-0.1517	-0.2905	-0.4888	0.375	-0.1125	-0.3703	0.5244	0.2717	-0.1132	-0.0201	0.6149	-0.0286	0.4555	5.8008	23.3693	-5.9654
33	6.1819	-1.668	1.3984	0.9491	0.0362	0.688	-0.1574	-0.4235	-1.8111	-0.358	0.8968	0.3953	0.0651	0.0612	-0.4337	0.6082	0.0083	0.1545	0.9159	-0.0624	1.2208	13.3698	-0.3237	-5.7275
34	1.5745	0.7134	-2.7247	0.7702	-1.2076	5.7599	0.301	-0.8248	0.1395	-0.1774	0.1742	-0.0409	0.9414	1.1922	-0.141	0.9231	0.1754	-0.1554	0.9744	0.1198	0.7354	4.6484	-2.5323	10.3833
35	3.1331	0.4241	-1.0861	0.635	-0.6639	0.4714	-0.4871	0.2948	-0.0713	-0.2917	0.3643	-0.0313	0.158	-0.2208	0.1194	0.4428	-0.1164	0.0061	0.6274	-0.1431	0.4033	-0.98	2.788	-4.3695
36	5.4366	-4.6285	-2.9716	3.9243	2.5055	4.196	1.005	-0.0827	3.1624	-1.9578	0.6239	-1.7578	0.6866	0.0771	-1.2871	0.6168	0.167	-0.1043	0.3214	-0.0023	1.3292	-12.5905	24.6222	7.6367
37	0.1021	0.3676	-0.5385	2.8311	-1.169	1.1563	-0.3171	0.3651	-0.4542	-0.1614	0.5566	0.9945	0.1028	-1.005	-0.1534	0.2175	-0.2249	0.0081	0.7069	-0.137	0.776	-11.0051	-6.4306	3.0882
38	2.7476	0.4695	2.7476	2.2327	0.8707	2.925	-1.6031	1.0612	-1.0029	0.0544	0.8579	0.1632	-0.5432	0.2041	0.5838	1.0223	0.0419	0.4604	1.006	0.2918	1.0648	-18.1659	-9.665	15.8469
39	0.7318	0.7986	-1.3463	2.7492	-0.427	2.1277	-0.9131	-0.4491	-0.1323	0.0407	0.4724	-0.3471	0.1781	0.4599	0.3253	0.4834	0.0584	0.1262	0.7452	0.0949	0.7235	-9.5921	0.6682	8.4063
40	1.201	-0.5165	-2.0048	4.3478	0.3689	3.3429	-0.5519	-1.0778	0.8281	-0.099	0.3064	-1.0308	0.0882	0.8615	0.2761	0.3359	0.0732	-0.0828	0.7142	-0.0616	0.5904	7.7618	7.0687	3.1016
41	5.8359	-6.1377	-1.5094	6.5669	1.0784	3.3529	0.3758	2.1979	-0.2648	0.2475	-0.1281	-2.1643	0.3251	-0.7526	-0.1846	0.7184	0.1124	-0.3453	1.0726	-0.4372	2.0099	22.0666	-0.9566	6.3434

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 2:20)
2	X-RAY DIFFRACTION	2	(chain A and resid 21:42)
3	X-RAY DIFFRACTION	3	(chain A and resid 43:86)
4	X-RAY DIFFRACTION	4	(chain A and resid 87:95)
5	X-RAY DIFFRACTION	5	(chain A and resid 96:125)
6	X-RAY DIFFRACTION	6	(chain A and resid 126:140)
7	X-RAY DIFFRACTION	7	(chain A and resid 141:163)
8	X-RAY DIFFRACTION	8	(chain A and resid 164:177)
9	X-RAY DIFFRACTION	9	(chain A and resid 178:197)
10	X-RAY DIFFRACTION	10	(chain A and resid 198:223)
11	X-RAY DIFFRACTION	11	(chain A and resid 224:231)
12	X-RAY DIFFRACTION	12	(chain A and resid 247:253)
13	X-RAY DIFFRACTION	13	(chain B and resid -1:29)
14	X-RAY DIFFRACTION	14	(chain B and resid 30:38)
15	X-RAY DIFFRACTION	15	(chain B and resid 39:43)
16	X-RAY DIFFRACTION	16	(chain B and resid 44:67)
17	X-RAY DIFFRACTION	17	(chain B and resid 68:84)
18	X-RAY DIFFRACTION	18	(chain B and resid 85:98)
19	X-RAY DIFFRACTION	19	(chain B and resid 99:130)
20	X-RAY DIFFRACTION	20	(chain B and resid 131:136)
21	X-RAY DIFFRACTION	21	(chain B and resid 137:166)
22	X-RAY DIFFRACTION	22	(chain B and resid 167:174)
23	X-RAY DIFFRACTION	23	(chain B and resid 175:199)
24	X-RAY DIFFRACTION	24	(chain B and resid 200:246)
25	X-RAY DIFFRACTION	25	(chain B and resid 247:257)
26	X-RAY DIFFRACTION	26	(chain B and resid 258:284)
27	X-RAY DIFFRACTION	27	(chain B and resid 285:319)
28	X-RAY DIFFRACTION	28	(chain B and resid 320:352)
29	X-RAY DIFFRACTION	29	(chain B and resid 353:374)
30	X-RAY DIFFRACTION	30	(chain B and resid 375:403)
31	X-RAY DIFFRACTION	31	(chain C and resid 3:22)
32	X-RAY DIFFRACTION	32	(chain C and resid 23:44)
33	X-RAY DIFFRACTION	33	(chain C and resid 45:62)
34	X-RAY DIFFRACTION	34	(chain C and resid 63:77)
35	X-RAY DIFFRACTION	35	(chain C and resid 78:128)
36	X-RAY DIFFRACTION	36	(chain C and resid 129:137)
37	X-RAY DIFFRACTION	37	(chain C and resid 138:161)
38	X-RAY DIFFRACTION	38	(chain C and resid 162:172)
39	X-RAY DIFFRACTION	39	(chain C and resid 173:196)
40	X-RAY DIFFRACTION	40	(chain C and resid 197:216)
41	X-RAY DIFFRACTION	41	(chain C and resid 217:223)

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi