PDB-6o09: Structure of AtPCNA in complex with the PIP motif of ATXR6

ID or keywords:

Entry

Database: PDB / ID: 6o09

Title

Structure of AtPCNA in complex with the PIP motif of ATXR6

Components

Proliferating cellular nuclear antigen 1
Uncharacterized protein

Keywords

NUCLEAR PROTEIN / histone / methylation / nucleosome / PCNA / PIP / DNA replication / atxr5 / atxr6

Function / homology

Function and homology information

DNA polymerase processivity factor activity / regulation of DNA replication / DNA replication / regulation of cell cycle / nucleolus / DNA binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Glycine max (soybean)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.06 Å

Authors

Couture, J.F. / Davarinejad, H.

Citation

Journal: J. Mol. Biol. / Year: 2019
Title: ATXR5/6 Forms Alternative Protein Complexes with PCNA and the Nucleosome Core Particle.
Authors: Davarinejad, H. / Joshi, M. / Ait-Hamou, N. / Munro, K. / Couture, J.F.

History

Deposition	Feb 15, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 27, 2019	Provider: repository / Type: Initial release
Revision 1.1	Apr 10, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6o09.cif.gz	623 KB	Display	PDBx/mmCIF format
PDB format	pdb6o09.ent.gz	510.9 KB	Display	PDB format
PDBx/mmJSON format	6o09.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6o09_validation.pdf.gz	524.3 KB	Display	wwPDB validaton report
Full document	6o09_full_validation.pdf.gz	533.9 KB	Display
Data in XML	6o09_validation.xml.gz	57.5 KB	Display
Data in CIF	6o09_validation.cif.gz	81.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o0/6o09 ftp://data.pdbj.org/pub/pdb/validation_reports/o0/6o09	HTTPS FTP

-
Related structure data

Related structure data	2zvvS S: Starting model for refinement
Similar structure data	6e49-d 3ggr-d 6j8y-d 6j0j-2 6k2m-2 3p91-1 6ap4-3 5fve-1 6j0j-1 4yhr-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) 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	#7 - Jul 2000 Nucleosome similarity (2) #150 - Jun 2012 Sliding Clamps similarity (9) #241 - Jan 2020 Twenty Years of Molecules similarity (8)

Deposited unit

C: Proliferating cellular nuclear antigen 1

I: Uncharacterized protein

A: Proliferating cellular nuclear antigen 1

B: Uncharacterized protein

D: Proliferating cellular nuclear antigen 1

E: Uncharacterized protein

F: Proliferating cellular nuclear antigen 1

G: Uncharacterized protein

H: Proliferating cellular nuclear antigen 1

J: Uncharacterized protein

K: Proliferating cellular nuclear antigen 1

L: Uncharacterized protein

222 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: Proliferating cellular nuclear antigen 1

I: Uncharacterized protein

D: Proliferating cellular nuclear antigen 1

E: Uncharacterized protein

H: Proliferating cellular nuclear antigen 1

J: Uncharacterized protein

defined by author&software
Evidence: gel filtration
111 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Proliferating cellular nuclear antigen 1

B: Uncharacterized protein

K: Proliferating cellular nuclear antigen 1

L: Uncharacterized protein

F: Proliferating cellular nuclear antigen 1

G: Uncharacterized protein

defined by author&software
111 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	72.902, 90.549, 90.510
Angle α, β, γ (deg.)	60.05, 73.46, 73.59
Int Tables number	1
Space group name H-M	P1

#1: Protein	Proliferating cellular nuclear antigen 1 / PCNA 1 Mass: 34573.148 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PCNA, PCNA1, At1g07370, F22G5.29 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9M7Q7
#2: Protein/peptide	Uncharacterized protein Mass: 2424.814 Da / Num. of mol.: 6 / Fragment: residues 77-96 / Source method: obtained synthetically / Source: (synth.) Glycine max (soybean) / References: UniProt: K7MRE7
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44.18 %
Crystal grow	Temperature: 294.15 K / Method: vapor diffusion / Details: 0.2 M sodium malonate 20% PEG3350 / Temp details: room temperature

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 1, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.06→29.652 Å / Num. obs: 219871 / % possible obs: 94.4 % / Redundancy: 1.9 % / Net I/σ(I): 9.2
Reflection shell	Resolution: 2.06→2.13 Å / Num. unique obs: 10607

-
Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998)	refinement
d*TREK		data reduction
d*TREK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2ZVV

2zvv

Resolution: 2.06→29.652 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 2.08 / Phase error: 26.97

	R_factor	Num. reflection	% reflection
R_free	0.2343	2006	1.82 %
R_work	0.1965	-	-
obs	0.1972	110486	94.35 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.06→29.652 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11905	0	0	402	12307

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	12081
X-RAY DIFFRACTION	f_angle_d	0.933	16386
X-RAY DIFFRACTION	f_dihedral_angle_d	3.291	7279
X-RAY DIFFRACTION	f_chiral_restr	0.058	2024
X-RAY DIFFRACTION	f_plane_restr	0.005	2057

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 (%)
2.06-2.1115	0.2925	136	0.2634	7429	X-RAY DIFFRACTION	91
2.1115-2.1686	0.2953	136	0.2455	7462	X-RAY DIFFRACTION	91
2.1686-2.2324	0.2896	141	0.2387	7572	X-RAY DIFFRACTION	92
2.2324-2.3044	0.2979	137	0.2379	7666	X-RAY DIFFRACTION	93
2.3044-2.3867	0.3005	145	0.239	7675	X-RAY DIFFRACTION	93
2.3867-2.4822	0.3056	142	0.2365	7660	X-RAY DIFFRACTION	94
2.4822-2.5952	0.2801	145	0.2384	7796	X-RAY DIFFRACTION	94
2.5952-2.7319	0.281	148	0.2395	7769	X-RAY DIFFRACTION	95
2.7319-2.9029	0.2982	144	0.2281	7890	X-RAY DIFFRACTION	96
2.9029-3.1268	0.2794	146	0.2208	7848	X-RAY DIFFRACTION	96
3.1268-3.4411	0.247	141	0.2015	7906	X-RAY DIFFRACTION	96
3.4411-3.938	0.1961	150	0.1731	7913	X-RAY DIFFRACTION	96
3.938-4.9577	0.178	145	0.1469	7935	X-RAY DIFFRACTION	97
4.9577-29.6555	0.197	150	0.1817	7959	X-RAY DIFFRACTION	97

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	3.2208	2.3666	-3.6749	2.603	-2.9985	4.2117	-0.0636	0.1245	0.5946	-0.2543	-0.1792	0.8224	-0.2702	-0.0019	0.1854	0.3904	0.0464	-0.0995	0.3394	-0.0168	0.5657	21.7391	-28.9111	-9.3086
2	4.4962	-3.1156	-4.5731	6.7848	4.0298	4.8289	-0.2557	-0.0484	0.2184	0.3802	-0.0261	0.3138	0.5664	0.3161	0.2721	0.3762	0.015	-0.0099	0.3591	0.0086	0.3398	19.8793	-50.9672	-11.3729
3	4.8361	-3.1814	-2.6564	6.2108	5.3229	6.1656	-0.1179	-0.0837	0.3151	-0.1391	0.0957	-0.0856	-0.3604	0.085	0.0453	0.3	0.004	-0.024	0.2732	0.0669	0.3208	21.8083	-41.8536	-18.0339
4	5.7931	-5.8569	-0.8514	6.0216	1.3365	2.3501	-0.4934	-0.5101	0.4191	0.0354	0.5972	0.6192	-0.5753	0.2572	-0.0827	0.4561	-0.0596	-0.051	0.3851	0.0186	0.6434	27.199	-34.6991	-14.0244
5	3.0094	-0.048	0.429	2.5976	0.5668	6.346	-0.0555	0.0575	0.1817	-0.1034	-0.0337	0.0806	-0.0074	0.02	0.0313	0.2798	0.0013	-0.0156	0.3374	0.0253	0.3279	24.5566	-41.8005	-4.1008
6	2.6001	1.4339	0.1968	2.1203	0.5349	2.2017	-0.0668	0.0866	0.1006	0.0173	0.1213	0.0707	-0.0273	-0.0584	-0.0565	0.2427	0.0241	-0.0167	0.24	0.0153	0.3133	13.9103	-60.1431	-28.385
7	6.5319	-4.2084	-0.9343	4.9901	1.0886	1.4297	-0.0515	-0.0725	0.1444	0.1912	0.0089	0.0004	0.2433	-0.0504	0.0521	0.2603	-0.0307	-0.0117	0.2815	0.0028	0.3089	6.3235	-67.7372	-28.6404
8	2.8229	1.1056	0.3792	3.0651	1.8385	3.549	0.0775	0.2315	0.0561	-0.199	-0.0216	0.1643	-0.1558	-0.0818	-0.0747	0.2412	0.0309	0.005	0.2598	0.0446	0.253	14.6144	-56.0242	-27.1612
9	4.9025	-0.4329	0.3684	2.62	-4.2183	6.8234	-0.246	1.3286	-1.1392	-0.2401	0.3229	-0.4505	0.9087	0.4539	-0.0946	0.3006	0.0301	0.0348	0.4554	-0.1735	0.5418	29.588	-62.7793	-34.4926
10	7.264	-0.3375	-0.0629	6.6089	-1.2994	5.5314	-0.2025	0.627	0.9725	-0.7342	0.0424	-0.6168	-0.3283	1.4328	0.139	0.4604	-0.1255	0.1003	0.5664	0.1443	0.3564	28.1971	-49.0651	-34.1974
11	5.2159	3.8933	5.6499	3.5958	4.412	6.1726	-0.4097	0.2703	0.0287	0.4867	-0.0054	-0.3562	-0.5858	0.3438	0.4002	0.5679	-0.0278	0.0279	0.5939	-0.0603	0.3744	-15.3581	-42.012	-24.7183
12	2.5634	-0.5142	0.9484	5.9201	1.5288	3.7924	-0.0901	0.0181	-0.0903	0.2668	0.2549	-0.0095	0.0981	-0.0001	-0.0918	0.2807	-0.0418	0.0476	0.3071	0.005	0.2991	-7.26	-31.8011	-2.6844
13	5.6596	-3.912	-3.504	3.5449	2.2017	3.4668	0.1254	0.5122	0.193	-0.3436	-0.154	-0.4933	0.0444	-0.188	0.087	0.3237	-0.0084	0.0356	0.3846	0.0002	0.2995	-7.109	-27.4059	-10.1006
14	4.852	-0.0496	-1.0137	7.1293	-0.9734	4.8933	-0.1327	0.1419	-0.0306	-0.1584	0.1565	0.0621	-0.1412	-0.2989	-0.0316	0.3034	-0.0576	0.0155	0.2943	-0.0064	0.3181	-11.4818	-37.9072	-4.0893
15	3.6678	-0.1305	0.2566	9.1413	-2.1771	3.6518	0.3193	-0.0229	-0.4426	-0.5907	-0.1805	0.2827	0.5835	-0.0061	-0.2362	0.3657	-0.0299	0.0278	0.4002	0.0043	0.2844	-11.3406	-41.7549	-2.7028
16	1.7656	0.4776	0.7957	3.0177	0.5119	1.2144	-0.0358	0.1075	0.1102	-0.0306	0.0476	-0.0159	0.0977	0.1967	-0.0017	0.2485	-0.0074	0.0292	0.3458	-0.0154	0.2629	-0.6887	-9.6304	2.4972
17	2.9231	0.0723	-1.2869	2.4242	1.2023	2.2413	-0.0982	0.0242	0.0668	0.096	0.188	-0.1134	0.0151	0.0522	-0.1071	0.2738	-0.0359	-0.0188	0.3367	-0.0075	0.335	7.778	-6.5878	6.7738
18	3.1651	0.8235	0.7712	4.9591	0.5964	1.9865	0.0407	0.08	0.2114	-0.1612	0.0076	0.1161	-0.1414	0.0649	-0.0286	0.197	0.0255	0.0207	0.2589	0.0249	0.2033	-3.4377	-13.1766	-0.4298
19	0.6885	-0.6404	-0.6583	2.7745	2.768	2.7577	-0.069	0.4292	0.5841	0.1309	0.1184	-0.3119	-0.673	0.2168	-0.1419	0.5364	-0.1851	-0.1007	0.4348	0.0212	0.6153	-14.1113	-27.9133	-45.2508
20	2.8531	0.8324	-2.8555	3.3266	-1.402	5.6793	-0.0629	0.1193	0.0373	-0.0526	0.0154	0.1013	-0.1643	-0.0774	0.0715	0.2048	0.0054	-0.0177	0.2538	0.0023	0.2364	-22.1158	-47.3135	-39.5544
21	2.3692	0.6357	-2.4088	5.4985	-1.7143	4.1846	-0.0386	-0.1126	0.3737	0.1338	-0.3961	-0.1471	-0.9454	0.6004	0.3759	0.4394	-0.0775	-0.0508	0.4475	-0.0002	0.3868	-12.8913	-39.3915	-42.4271
22	5.6689	1.0705	-0.21	2.7656	-1.2183	4.7497	0.0391	0.046	-0.1056	0.0063	-0.1716	-0.0496	-0.1557	0.1829	0.101	0.3311	-0.0134	-0.0059	0.3122	-0.023	0.2641	-21.8299	-42.9685	-51.0161
23	4.7012	-2.2218	-1.1162	4.729	0.4337	7.5032	0.1126	0.2246	0.078	0.0536	-0.16	-0.4527	0.0982	0.1202	-0.022	0.3084	-0.0326	-0.0217	0.2395	-0.0189	0.3314	-20.8483	-41.9322	-53.6265
24	1.351	0.5673	-0.3739	2.9115	-0.2022	1.7192	-0.1278	-0.1506	-0.166	0.0118	0.0194	-0.0213	0.1225	0.0018	0.1219	0.2613	0.0349	-0.0244	0.2671	0.0143	0.3239	-22.7996	-67.0407	-27.1748
25	2.7075	-0.3055	0.8633	5.3865	1.8121	2.0842	0.2814	0.1858	-0.2071	-0.3701	-0.0046	-0.7256	-0.0026	0.4876	-0.0945	0.3783	0.1307	-0.0021	0.4025	0.0026	0.5619	-8.3927	-69.4763	-28.5943
26	1.6097	-0.0172	-0.1585	3.1875	-0.7607	3.7589	-0.0224	-0.1204	-0.0237	0.0576	-0.0134	-0.0882	-0.0219	0.1184	0.0308	0.2106	0.0172	0.0063	0.2404	0.004	0.2467	-21.6176	-58.4181	-29.2144
27	1.9343	1.5348	-0.67	2.3135	0.143	5.5306	0.7123	-1.4563	-0.2427	0.6167	-1.206	0.4613	0.523	-0.9711	0.3088	0.3742	-0.1438	0.0246	0.5202	-0.0317	0.4293	-35.1454	-57.8276	-20.0992
28	7.8416	3.0246	0.7536	1.8047	-1.2367	6.4929	0.2674	-0.6857	0.9049	0.7746	-0.3556	0.929	-1.0505	-1.4366	0.0244	0.3963	0.1174	0.0218	0.4292	-0.0811	0.2888	-26.6437	-46.0108	-20.5441
29	2.8368	-0.2262	0.2726	1.9705	1.982	2.0673	-0.311	0.7492	0.2974	-0.8838	0.2213	0.6689	0.1049	0.1822	0.0251	0.5733	-0.1837	-0.106	0.5634	-0.0054	0.4001	27.2013	-9.2412	-33.8572
30	3.0117	-2.7215	2.0567	5.2111	-2.1679	4.3934	-0.0876	0.07	-0.0465	-0.2412	0.1756	0.1636	-0.0319	-0.1022	-0.0791	0.231	-0.0321	0.011	0.2704	-0.0054	0.2602	32.3681	-5.3231	-15.2339
31	4.3864	-4.0903	2.0111	5.4222	-4.6519	5.7075	-0.2195	0.1065	-0.1294	-0.4704	-0.144	0.3148	1.331	-1.5884	0.5308	0.625	-0.1354	0.1348	0.7267	-0.1988	0.3834	32.0804	-9.7851	-26.1507
32	5.2056	0.0183	-0.1957	2.8853	-1.05	5.2996	0.025	0.0515	0.23	-0.1419	0.019	-0.0682	0.1065	-0.2974	-0.0572	0.3087	-0.0142	-0.0111	0.228	-0.0074	0.2955	34.3071	3.9913	-24.0334
33	1.7445	-1.8773	-2.5505	1.9759	2.642	3.8052	-0.1309	0.2366	-0.3161	-0.1991	-0.2185	0.1475	0.2042	-0.3774	0.3743	0.3234	-0.0063	0.0231	0.4036	0.0155	0.4072	29.3381	-15.5613	0.048
34	5.0532	1.9209	1.4047	5.6899	0.1482	3.5473	0.0773	-0.5405	0.2171	0.4243	-0.1208	-0.066	-0.3323	0.1094	-0.0023	0.3048	0.0093	0.036	0.2965	-0.0567	0.1783	37.8581	-4.0954	10.5053
35	8.6837	-0.5236	0.966	2.853	0.8705	3.3157	0.0892	-0.1944	-0.1156	0.3557	-0.1889	0.2484	-0.0489	-0.3663	0.1314	0.3317	0.0145	0.0809	0.365	-0.03	0.2487	34.2019	-3.8156	15.0247
36	1.9076	0.5479	-0.4031	2.9048	-0.2006	3.2749	0.0057	-0.145	-0.019	0.1274	-0.1015	0.1591	-0.0562	-0.066	0.0709	0.2133	0.023	0.0077	0.2445	-0.0086	0.223	33.4262	-9.3796	1.9013
37	3.5287	0.3312	3.5341	9.6258	1.2347	3.6096	0.4206	0.0232	-0.5526	0.2074	-0.1491	-1.1087	0.1849	0.4689	-0.335	0.2562	-0.0403	-0.0315	0.3313	0.0478	0.4253	46.7639	-18.3475	1.3731
38	3.1662	0.936	1.8948	9.3771	4.7019	3.1331	0.5523	0.7801	-1.3976	-0.5806	-0.132	-0.9363	1.2536	0.6493	-0.0906	0.4578	0.0615	0.0418	0.3291	-0.0166	0.4872	39.6917	-23.648	-6.7168
39	9.3176	5.6623	-0.299	9.358	-5.7793	5.281	-0.0853	-0.972	0.5207	-0.073	-0.4129	-0.132	-0.1088	0.5516	0.4472	0.6031	0.0894	0.0854	0.3795	-0.0546	0.4548	-5.4398	-13.4955	-21.7835
40	4.3156	1.234	1.6904	1.0317	2.099	4.3483	0.0206	-0.2554	0.0313	0.446	-0.083	-0.0158	0.6647	-0.181	0.039	0.5713	-0.0555	0.0217	0.2781	0.0028	0.3892	-8.0995	-7.2731	-39.4582
41	6.6658	-1.9923	-0.3152	4.9914	0.4412	6.0097	0.0106	-0.1025	0.2551	0.1702	0.1207	-0.2046	0.4362	0.2135	-0.1374	0.4752	-0.0549	-0.0229	0.2781	-0.065	0.3556	-2.4458	1.6622	-32.0845
42	4.1208	1.3416	0.061	5.6441	2.5875	5.6677	-0.106	-0.4956	0.5725	0.2872	-0.0745	0.4387	0.2298	-0.4423	0.1315	0.4951	-0.0394	0.0339	0.3665	0.007	0.3525	-8.2481	1.7679	-29.531
43	1.5307	0.3772	-2.5496	0.2279	-0.9745	5.188	-0.0582	-0.1521	-0.1116	0.0751	-0.0545	0.1503	1.4522	-0.2065	0.1131	0.8118	-0.0589	0.0591	0.3774	-0.055	0.5072	-11.9248	-18.3755	-55.503
44	3.6983	-0.4169	0.7169	3.2101	-0.9132	2.4	-0.0826	0.0471	0.1397	-0.1356	-0.1123	-0.1074	0.0789	0.0719	0.2054	0.4501	0.0037	0.0531	0.3669	0.0707	0.3747	-11.2417	-4.0182	-66.8568
45	6.6887	-3.5477	1.8034	6.2491	-1.6618	5.6753	-0.3776	-0.5246	0.5731	-0.1586	0.4408	-0.2801	0.8896	0.1554	0.0206	0.4156	0.0776	0.0188	0.3942	0.0376	0.4375	-13.0313	-2.7364	-72.7192
46	3.1366	1.3914	0.6384	2.5711	1.0581	5.3726	0.0806	0.263	-0.1858	0.2027	-0.0881	-0.0353	0.6453	0.0059	-0.0088	0.4108	0.0116	0.0302	0.2485	0.0165	0.3077	-10.7557	-10.5235	-57.5923
47	2.2101	-1.0262	-0.6414	7.1846	-1.3148	8.8922	0.0871	-0.2047	0.901	0.6077	-0.4609	0.7443	-0.5827	-0.7164	0.0539	0.3107	0.0036	0.0521	0.4156	-0.0845	0.5051	-16.4307	-2.9675	2.0773
48	2.3126	-0.8736	-0.7055	9.429	2.8183	1.8137	0.4129	1.3653	-0.1647	-2.0631	-0.2754	0.6776	-0.3103	-0.5431	-0.2415	0.6049	0.0548	-0.1732	0.6089	0.1139	0.4697	-14.9505	-10.207	-11.6705
49	2.1485	-0.2111	2.9515	2.0245	0.0207	8.2493	0.487	0.5297	1.091	-0.5617	-0.0137	0.5384	0.7965	-1.4814	-0.4092	0.5059	-0.1104	0.0186	0.7839	0.057	0.457	-28.0334	-9.6093	-60.1585
50	2.5776	-0.8918	-0.6155	5.6911	-4.8748	4.958	0.0871	-0.4942	-0.3793	0.8629	-0.2881	0.2873	1.3801	-1.817	0.1398	1.0218	-0.3723	0.04	0.589	0.0094	0.4172	-23.4899	-17.4639	-49.0591
51	3.1937	-4.8017	3.6208	7.239	-5.468	4.0882	0.5418	-0.1847	-0.6825	-0.5446	0.2605	0.2049	0.3835	-0.0696	-0.8675	0.5704	-0.0252	0.025	0.5482	0.0246	0.42	17.0803	-35.9636	-37.4581
52	9.9134	4.0312	-1.842	4.6342	-1.3517	2.4022	-0.2782	0.5057	-0.5622	-0.0249	0.2009	-0.4893	-0.5082	0.3256	0.139	0.5487	-0.0523	-0.0191	0.413	-0.0939	0.3925	18.7596	-23.4295	-57.1415
53	4.0894	2.0136	-0.2668	7.7363	-1.9201	3.4152	0.3245	-0.2306	-0.317	1.0848	-0.3415	-0.6416	0.3033	-0.2587	0.0152	0.5975	-0.0218	-0.1458	0.3664	-0.0599	0.3618	27.1193	-20.4503	-48.1912
54	6.7454	0.7277	-2.6824	2.8047	-0.6301	2.1556	0.0168	-0.7039	-0.3844	1.2595	0.076	0.0684	0.0919	0.1364	-0.0311	0.7993	-0.0286	0.007	0.4997	-0.0207	0.2949	16.2983	-27.1536	-42.9215
55	4.1917	0.6844	-1.0357	4.3824	0.4106	4.1377	0.1938	0.1489	0.0877	0.3391	-0.108	0.111	-0.2057	0.272	-0.0696	0.4884	-0.014	-0.042	0.2871	-0.0592	0.3379	18.176	-33.3373	-54.0933
56	6.3686	1.5356	0.7442	6.0291	0.1443	4.4925	0.3143	-0.6683	-0.0269	0.6472	-0.215	0.2331	-0.0831	-0.2087	-0.001	0.5026	0.041	0.041	0.4027	-0.0413	0.3276	17.7584	-35.9564	-53.1615
57	2.9542	-2.5943	2.176	3.6442	-3.2624	2.9256	-0.0561	-0.025	-0.0803	1.2844	0.0273	-0.1794	-0.5326	-0.0205	-0.0433	0.7591	0.0015	-0.0393	0.4236	-0.0621	0.4154	24.2483	-4.3746	-47.8771
58	1.7335	1.0935	-0.0407	3.5678	-0.9437	2.2931	0.032	-0.0205	0.1874	0.4922	-0.0189	-0.0194	-0.1641	-0.1106	-0.0002	0.3696	0.0561	-0.0113	0.3263	-0.0158	0.2632	24.2156	-3.4249	-59.3813
59	5.769	3.0921	-4.2206	6.8323	1.1198	5.2901	0.1971	0.3863	-0.7681	0.1278	-0.2933	-0.0635	-1.139	0.0436	0.1369	0.6028	-0.058	-0.1136	0.4815	0.0254	0.4994	40.6642	-4.6398	-56.85
60	3.8393	0.0791	2.4207	1.418	2.0829	4.4594	0.0657	-1.0464	0.3468	1.4259	-0.5803	-1.7002	-0.4826	0.655	0.1653	0.9236	-0.1537	-0.3465	0.5075	0.0508	0.5968	36.7049	-10.0679	-44.7204

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid -5:8)
2	X-RAY DIFFRACTION	2	(chain A and resid 9:23)
3	X-RAY DIFFRACTION	3	(chain A and resid 24:62)
4	X-RAY DIFFRACTION	4	(chain A and resid 63:70)
5	X-RAY DIFFRACTION	5	(chain A and resid 71:124)
6	X-RAY DIFFRACTION	6	(chain A and resid 125:164)
7	X-RAY DIFFRACTION	7	(chain A and resid 165:191)
8	X-RAY DIFFRACTION	8	(chain A and resid 192:257)
9	X-RAY DIFFRACTION	9	(chain B and resid 78:83)
10	X-RAY DIFFRACTION	10	(chain B and resid 84:90)
11	X-RAY DIFFRACTION	11	(chain C and resid -5:1)
12	X-RAY DIFFRACTION	12	(chain C and resid 2:29)
13	X-RAY DIFFRACTION	13	(chain C and resid 30:63)
14	X-RAY DIFFRACTION	14	(chain C and resid 64:101)
15	X-RAY DIFFRACTION	15	(chain C and resid 102:124)
16	X-RAY DIFFRACTION	16	(chain C and resid 125:164)
17	X-RAY DIFFRACTION	17	(chain C and resid 165:200)
18	X-RAY DIFFRACTION	18	(chain C and resid 201:257)
19	X-RAY DIFFRACTION	19	(chain D and resid -4:4)
20	X-RAY DIFFRACTION	20	(chain D and resid 5:50)
21	X-RAY DIFFRACTION	21	(chain D and resid 51:70)
22	X-RAY DIFFRACTION	22	(chain D and resid 71:100)
23	X-RAY DIFFRACTION	23	(chain D and resid 101:124)
24	X-RAY DIFFRACTION	24	(chain D and resid 125:184)
25	X-RAY DIFFRACTION	25	(chain D and resid 185:200)
26	X-RAY DIFFRACTION	26	(chain D and resid 201:258)
27	X-RAY DIFFRACTION	27	(chain E and resid 78:83)
28	X-RAY DIFFRACTION	28	(chain E and resid 84:90)
29	X-RAY DIFFRACTION	29	(chain F and resid -4:4)
30	X-RAY DIFFRACTION	30	(chain F and resid 5:61)
31	X-RAY DIFFRACTION	31	(chain F and resid 62:70)
32	X-RAY DIFFRACTION	32	(chain F and resid 71:124)
33	X-RAY DIFFRACTION	33	(chain F and resid 125:140)
34	X-RAY DIFFRACTION	34	(chain F and resid 141:166)
35	X-RAY DIFFRACTION	35	(chain F and resid 167:191)
36	X-RAY DIFFRACTION	36	(chain F and resid 192:258)
37	X-RAY DIFFRACTION	37	(chain G and resid 79:84)
38	X-RAY DIFFRACTION	38	(chain G and resid 85:90)
39	X-RAY DIFFRACTION	39	(chain H and resid -4:4)
40	X-RAY DIFFRACTION	40	(chain H and resid 5:72)
41	X-RAY DIFFRACTION	41	(chain H and resid 73:109)
42	X-RAY DIFFRACTION	42	(chain H and resid 110:124)
43	X-RAY DIFFRACTION	43	(chain H and resid 125:139)
44	X-RAY DIFFRACTION	44	(chain H and resid 140:169)
45	X-RAY DIFFRACTION	45	(chain H and resid 170:194)
46	X-RAY DIFFRACTION	46	(chain H and resid 195:256)
47	X-RAY DIFFRACTION	47	(chain I and resid 78:83)
48	X-RAY DIFFRACTION	48	(chain I and resid 84:91)
49	X-RAY DIFFRACTION	49	(chain J and resid 78:83)
50	X-RAY DIFFRACTION	50	(chain J and resid 84:91)
51	X-RAY DIFFRACTION	51	(chain K and resid -4:5)
52	X-RAY DIFFRACTION	52	(chain K and resid 6:24)
53	X-RAY DIFFRACTION	53	(chain K and resid 25:50)
54	X-RAY DIFFRACTION	54	(chain K and resid 51:70)
55	X-RAY DIFFRACTION	55	(chain K and resid 71:101)
56	X-RAY DIFFRACTION	56	(chain K and resid 102:124)
57	X-RAY DIFFRACTION	57	(chain K and resid 125:140)
58	X-RAY DIFFRACTION	58	(chain K and resid 141:256)
59	X-RAY DIFFRACTION	59	(chain L and resid 78:83)
60	X-RAY DIFFRACTION	60	(chain L and resid 84:90)

-
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://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