PDB-3aev: Crystal structure of a/eIF2alpha-aDim2p-rRNA complex from Pyrococ...

ID or keywords:

Entry

Database: PDB / ID: 3aev

Title

Crystal structure of a/eIF2alpha-aDim2p-rRNA complex from Pyrococcus horikoshii OT3

Components

Putative uncharacterized protein PH1566
RNA (5'-R(*GP*GP*AP*UP*CP*AP*CP*CP*UP*CP*C)-3')
Translation initiation factor 2 subunit alpha

Keywords

TRANSLATION/RNA BINDING PROTEIN/RNA / Proteins-rRNA complex / 16S rRNA / RNA-binding / RNA processing / Initiation factor / Protein biosynthesis / TRANSLATION-RNA BINDING PROTEIN-RNA complex

Function / homology

Function and homology information

translation initiation factor activity / RNA binding
Similarity search - Function

Biological species

Pyrococcus horikoshii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Tanokura, M. / Jia, M.Z. / Nagata, K.

Citation

Journal: J.Mol.Biol. / Year: 2010
Title: An archaeal Dim2-like protein, aDim2p, forms a ternary complex with a/eIF2 alpha and the 3' end fragment of 16S rRNA
Authors: Jia, M.Z. / Horita, S. / Nagata, K. / Tanokura, M.

History

Deposition	Feb 10, 2010	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 21, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Jan 29, 2014	Group: Database references
Revision 1.3	Nov 1, 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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3aev.cif.gz	94 KB	Display	PDBx/mmCIF format
PDB format	pdb3aev.ent.gz	70.6 KB	Display	PDB format
PDBx/mmJSON format	3aev.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3aev_validation.pdf.gz	466.8 KB	Display	wwPDB validaton report
Full document	3aev_full_validation.pdf.gz	473.6 KB	Display
Data in XML	3aev_validation.xml.gz	14.4 KB	Display
Data in CIF	3aev_validation.cif.gz	19.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ae/3aev ftp://data.pdbj.org/pub/pdb/validation_reports/ae/3aev	HTTPS FTP

-
Related structure data

Related structure data	1yz6S 2e3uS S: Starting model for refinement
Similar structure data	3bqq-d 3tjz-1 3wo3-6 3t4b-d 5c23-2 6ley-1 5y04-d 6iu3-1 5ziz-2 6uie-d 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	#121 - Jan 2010 70S Ribosomes similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #253 - Jan 2021 Expressome similarity (6) #260 - Aug 2021 Ribonuclease P similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #10 - Oct 2000 Ribosome similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #65 - May 2005 Self-splicing RNA similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (2) #245 - May 2020 Spliceosomes similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #227 - Nov 2018 Telomerase similarity (1) #161 - May 2013 Ricin similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (4) #86 - Feb 2007 Exosomes similarity (4) #255 - Mar 2021 Cisplatin and DNA similarity (4)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#130 - Oct 2010
Riboswitches
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#253 - Jan 2021
Expressome
similarity (6)
#260 - Aug 2021
Ribonuclease P
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#15 - Mar 2001
Transfer RNA
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#10 - Oct 2000
Ribosome
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#65 - May 2005
Self-splicing RNA
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (2)
#245 - May 2020
Spliceosomes
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#161 - May 2013
Ricin
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (4)
#86 - Feb 2007
Exosomes
similarity (4)
#255 - Mar 2021
Cisplatin and DNA
similarity (4)

Deposited unit

A: Translation initiation factor 2 subunit alpha

B: Putative uncharacterized protein PH1566

C: RNA (5'-R(*GP*GP*AP*UP*CP*AP*CP*CP*UP*CP*C)-3')

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	86.998, 93.600, 116.704
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Translation initiation factor 2 subunit alpha / eIF-2-alpha / aIF2-alpha Mass: 32036.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH0961 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / References: UniProt: O58655
#2: Protein	Putative uncharacterized protein PH1566 / aDim2p Mass: 25189.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1566 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / References: UniProt: O59282
#3: RNA chain	RNA (5'-R(GPGPAPUPCPAPCPCPUPCPC)-3') Mass: 3442.106 Da / Num. of mol.: 1 / Source method*: obtained synthetically

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.92 Å³/Da / Density % sol: 68.59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 12% PEG 8000, 0.1M citrate buffer, 0.2M Sodium Chloride, 6% 1,5-Diaminopentane di-HCl, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 19, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.8→50 Å / Num. obs: 24090 / B_iso Wilson estimate: 48 Å²

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
MOLREP		phasing
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2E3U AND 1YZ6

2e3u

1yz6

Resolution: 2.8→50 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.908 / SU B: 19.359 / SU ML: 0.177 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.246	1226	5.1 %	RANDOM
R_work	0.212	-	-	-
obs	0.214	22819	99.8 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 28.96 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.65 Å²	0 Å²	0 Å²
2-	-	-0.61 Å²	0 Å²
3-	-	-	-0.04 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2808	227	0	0	3035

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	3112
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1
X-RAY DIFFRACTION	r_angle_refined_deg	1.613	2.061	4242
X-RAY DIFFRACTION	r_angle_other_deg	0.336	3	2
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.634	5	342
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.416	23.577	137
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.111	15	548
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.785	15	27
X-RAY DIFFRACTION	r_chiral_restr	0.108	0.2	475
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2239
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1
X-RAY DIFFRACTION	r_nbd_refined	0.228	0.2	1209
X-RAY DIFFRACTION	r_nbd_other	0.145	0.2	1
X-RAY DIFFRACTION	r_nbtor_refined	0.32	0.2	2083
X-RAY DIFFRACTION	r_nbtor_other	0.288	0.2	2
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.139	0.2	79
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.237	0.2	35
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.159	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	0.749	1.5	1756
X-RAY DIFFRACTION	r_mcbond_other	0.035	1.5	1
X-RAY DIFFRACTION	r_mcangle_it	1.282	2	2768
X-RAY DIFFRACTION	r_scbond_it	1.813	3	1595
X-RAY DIFFRACTION	r_scangle_it	2.946	4.5	1474

LS refinement shell

Resolution: 2.8→2.87 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.413	94	-
R_work	0.336	1623	-
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	8.6567	-2.0235	-0.0152	20.0258	-16.6854	29.1432	0.4685	-0.0748	0.6973	-0.3443	0.4129	1.6502	-2.0356	-0.0814	-0.8814	0.4911	0.1687	-0.1426	0.219	-0.1041	0.3588	-12.9135	24.8093	4.4658
2	9.5216	2.1587	1.1478	2.164	2.198	4.3713	0.0699	0.4543	-0.0347	-0.4447	0.2685	-0.008	-0.5276	0.3532	-0.3384	0.329	-0.0449	0.0183	0.2953	-0.0168	0.2514	0.8471	16.7174	3.6109
3	18.5938	4.7817	6.1395	3.8005	0.581	7.7528	-0.7109	1.2821	0.5769	-0.8056	0.3224	0.1596	-0.73	0.5349	0.3885	0.4667	-0.0374	-0.0555	0.3398	0.0167	0.2197	-5.4887	19.8718	-2.1609
4	2.3238	-1.1798	3.5427	4.3077	-3.2152	7.0701	-0.093	0.14	0.1158	-0.0941	0.1016	-0.2222	0.0437	0.0134	-0.0085	0.3295	-0.0298	0.0273	0.3228	-0.0359	0.3188	1.0671	15.8878	10.7038
5	5.5333	0.2115	1.9016	7.9936	4.9783	24.6971	0.9716	0.7944	-0.8835	0.2399	-0.0749	-0.8972	0.2165	1.6229	-0.8967	0.2656	0.0265	-0.0264	0.4684	-0.1113	0.3675	9.6062	9.4608	9.9181
6	3.0286	0.1962	1.5302	1.666	-0.0563	3.5103	-0.0659	0.2121	-0.0027	-0.144	0.1047	0.0764	0.0003	0.0441	-0.0388	0.2852	-0.0208	-0.0164	0.3119	-0.036	0.2728	-3.0523	15.7774	4.9692
7	4.3542	-3.5827	1.0114	4.8904	2.69	6.6215	0.1224	-0.3808	0.4385	-0.0204	-0.1206	-0.2726	-0.6375	-0.0585	-0.0018	0.2972	-0.0025	-0.0139	0.3337	-0.0728	0.3116	-5.269	22.3064	8.9197
8	22.5411	24.6998	-3.5333	38.641	12.4599	23.5952	0.31	-1.1061	-1.037	0.6712	-0.6812	0.0146	1.4298	-0.7382	0.3713	0.3398	-0.0976	-0.0719	0.3274	0.0852	0.3005	-12.4095	6.116	10.1801
9	24.6311	3.3487	5.3144	4.7049	-0.6463	19.9293	1.0974	-0.1887	-1.2386	-0.0429	-0.5678	-0.177	1.0312	-0.2817	-0.5296	0.3505	-0.0523	-0.1357	0.266	0.0237	0.2667	-13.3085	6.1714	3.0313
10	17.9712	-1.8986	9.9244	9.144	-5.1569	7.3679	0.3845	-0.5189	-0.1383	-0.1577	-0.4231	-0.3053	0.1435	-0.1415	0.0386	0.3982	0.0409	-0.1187	0.3528	-0.081	0.2526	-16.972	8.6253	-4.2481
11	5.6514	-3.7958	-2.2126	2.8577	-0.2779	10.962	-0.4283	0.1754	-0.01	-0.4528	-0.0175	-1.1247	0.6741	0.8373	0.4457	0.3035	0.0624	-0.0289	0.359	-0.0142	0.2985	-20.8047	12.9166	-15.7889
12	16.0077	7.2224	2.8188	12.9668	13.0646	34.595	0.8158	0.3851	0.4208	-0.4892	0.0182	-0.6973	-0.5941	1.4257	-0.834	0.207	0.0903	0.0552	0.3299	0.0648	0.2079	-21.4235	21.6566	-19.0986
13	3.3893	-3.3813	0.5744	3.4994	-1.5529	7.7056	0.039	-0.1661	0.0345	0.5214	0.0378	-0.6131	-0.3123	0.2536	-0.0768	0.2877	0.0345	-0.0359	0.3545	-0.0535	0.3232	-25.558	18.7575	-6.218
14	6.7644	1.6733	-1.1919	13.7592	-3.044	4.1879	-0.0816	-0.4914	-0.148	0.2891	-0.0066	0.5724	-0.056	-0.4491	0.0882	0.3049	0.0302	-0.0397	0.4207	-0.0552	0.2093	-34.5914	12.401	-8.2609
15	1.5497	-3.1988	-0.9297	6.9977	1.4066	1.2227	-0.1683	-0.1229	-0.0684	-0.3695	0.2014	0.3305	-0.0729	-0.0399	-0.0331	0.335	0.0499	-0.0374	0.3827	-0.0238	0.2993	-32.4526	17.8098	-16.1928
16	13.382	12.4333	-4.9193	13.0773	-12.0144	38.1323	0.4626	-0.476	-0.2158	0	0.093	0.5276	1.1518	0.3165	-0.5556	0.2697	0.1158	-0.037	0.1883	-0.0207	0.2893	-30.1332	4.1982	-11.3999
17	91.836	-32.7572	-28.6175	43.4294	4.7214	37.3848	1.1876	1.1186	2.124	-0.4912	0.2142	-3.956	-0.6433	2.465	-1.4018	0.6563	0.3111	-0.0946	0.6269	-0.1355	0.5503	-5.6159	1.1991	-6.3535
18	23.8324	8.2379	13.2972	19.3253	18.6957	19.4834	1.2396	-0.8951	-0.7435	0.7666	-1.0091	-0.2346	1.5914	-0.8044	-0.2305	0.3559	0.0244	-0.1731	0.3018	0.0049	0.2691	-11.2969	2.6639	-6.5275
19	8.1826	0.7695	3.1766	6.7791	2.5039	4.6413	0.7034	-0.256	-1.1559	0.7305	-0.2001	-0.2033	1.1128	-0.0946	-0.5032	0.3727	0.0856	-0.2288	0.1863	-0.0217	0.4271	-23.4291	-15.9613	-16.2677
20	4.5769	-3.0714	-2.5502	38.7588	-6.9917	3.4849	0.2545	1.3905	-0.2186	-2.2284	0.0138	-2.6718	0.0739	1.3373	-0.2683	0.2133	0.1837	-0.1397	0.4459	-0.4604	0.5805	-14.0264	-14.0797	-24.3656
21	8.2764	4.9849	-0.6376	5.12	1.8228	2.4165	0.6042	-0.1679	-0.8611	0.5841	-0.226	-1.0863	0.2312	0.8038	-0.3782	0.2469	0.1588	-0.1912	0.3135	-0.2042	0.4351	-16.3424	-10.6538	-15.0871
22	26.8879	11.1246	-2.758	23.5126	-4.5106	19.7988	-0.4493	0.4567	0.7398	-0.4044	0.6664	-1.429	-0.6316	0.8553	-0.2171	0.1078	-0.0437	0.0263	0.3574	-0.2334	0.3547	-11.1192	2.6003	-18.2933
23	9.2895	8.6229	-1.1052	12.0558	2.8427	3.8254	0.3712	-0.2892	0.2104	-0.1077	0.0072	0.4013	0.3308	0.1782	-0.3784	0.3313	0.0527	-0.1425	0.3089	-0.054	0.3431	-23.3848	-4.7094	-18.2009
24	8.0297	-0.7341	1.4392	0.8976	2.3059	7.4118	0.0769	0.6849	-0.6741	-0.567	0.2434	-0.2213	0.5861	0.4137	-0.3202	0.3536	0.0521	-0.0246	0.2705	-0.1527	0.3454	-27.4327	-9.7915	-26.9081
25	13.7223	-19.2754	13.2466	39.7059	-8.8472	20.3296	0.1457	-0.0939	0.9376	-0.7884	-0.0507	-1.0926	-1.5446	0.6457	-0.095	0.3039	-0.0954	-0.0106	0.2791	-0.1903	0.3338	-25.3002	1.6857	-26.9543
26	17.1651	8.5885	-1.0355	4.469	0.204	3.0983	0.7142	-1.2942	1.0041	0.5202	-0.3978	0.5391	0.1669	-0.2671	-0.3165	0.391	-0.0139	-0.063	0.3463	-0.0405	0.3247	-41.0706	-8.5066	-17.1441
27	2.3374	0.3818	4.213	2.5131	1.2973	7.7449	0.0643	-0.0483	0.0113	0.0957	0.0585	-0.1565	0.3439	-0.2574	-0.1227	0.332	-0.0476	0.0021	0.3318	-0.0255	0.282	-44.9589	-14.8129	-29.9046
28	4.0282	2.4645	-0.2945	11.086	7.739	14.4011	-0.2401	0.525	0.084	-0.4132	0.0106	-0.092	-0.63	0.2452	0.2295	0.3107	-0.0808	0.0153	0.3484	-0.0302	0.28	-40.2651	-4.3152	-34.0565
29	3.5303	1.7599	1.8157	9.5074	-1.7415	4.3557	-0.1977	-0.1933	0.2285	-0.0225	0.0485	0.1136	-0.0723	-0.2025	0.1492	0.3281	0.0164	-0.0354	0.2887	-0.0771	0.2519	-37.0643	-4.9008	-24.6125
30	29.3263	15.9069	6.3065	18.8504	0.6297	2.1182	0.3879	-1.093	1.0609	2.0325	-0.4221	0.7955	-0.5914	-0.7611	0.0342	0.3532	-0.0258	0.1078	0.4334	-0.1159	0.2826	-48.1116	-4.796	-22.7295
31	3.7787	2.3934	-0.66	6.7527	-0.6358	10.7825	-0.4612	0.2666	0.3308	0.1194	0.4104	0.4918	-0.0476	-0.8827	0.0508	0.1833	-0.0324	-0.0095	0.4401	-0.0803	0.3552	-51.9667	-5.2331	-31.0939
32	10.656	0.4755	-6.5992	34.0998	-30.5334	30.9187	-0.4694	1.2588	0.344	-1.5131	0.068	1.7144	-2.0071	0.314	0.4014	0.4068	0.0277	-0.1569	0.2942	-0.0035	0.3537	-46.8146	5.4493	-35.8863
33	4.5099	-0.7214	3.8651	3.4361	0.5593	4.5639	0.3113	0.1393	-0.1393	0.1753	-0.0404	0.0296	0.4078	-0.1484	-0.271	0.3524	-0.0595	0.0105	0.3409	-0.0172	0.2307	-45.7732	-18.2574	-33.0486
34	8.718	0.1181	10.2149	7.9317	0.5868	15.1684	0.4277	0.7789	-1.7379	0.6401	0.5845	-0.5669	0.4444	0.8467	-1.0122	0.3566	0.1666	-0.2111	0.2526	-0.2236	0.6265	-21.9019	-21.0407	-24.9459

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 12
2	X-RAY DIFFRACTION	2	A	13 - 27
3	X-RAY DIFFRACTION	3	A	28 - 36
4	X-RAY DIFFRACTION	4	A	37 - 50
5	X-RAY DIFFRACTION	5	A	51 - 56
6	X-RAY DIFFRACTION	6	A	57 - 73
7	X-RAY DIFFRACTION	7	A	74 - 84
8	X-RAY DIFFRACTION	8	A	85 - 89
9	X-RAY DIFFRACTION	9	A	90 - 94
10	X-RAY DIFFRACTION	10	A	95 - 101
11	X-RAY DIFFRACTION	11	A	102 - 111
12	X-RAY DIFFRACTION	12	A	112 - 123
13	X-RAY DIFFRACTION	13	A	124 - 139
14	X-RAY DIFFRACTION	14	A	140 - 151
15	X-RAY DIFFRACTION	15	A	152 - 167
16	X-RAY DIFFRACTION	16	A	168 - 174
17	X-RAY DIFFRACTION	17	B	26 - 29
18	X-RAY DIFFRACTION	18	B	30 - 35
19	X-RAY DIFFRACTION	19	B	36 - 51
20	X-RAY DIFFRACTION	20	B	52 - 59
21	X-RAY DIFFRACTION	21	B	60 - 79
22	X-RAY DIFFRACTION	22	B	80 - 88
23	X-RAY DIFFRACTION	23	B	89 - 101
24	X-RAY DIFFRACTION	24	B	102 - 111
25	X-RAY DIFFRACTION	25	B	112 - 117
26	X-RAY DIFFRACTION	26	B	118 - 137
27	X-RAY DIFFRACTION	27	B	138 - 153
28	X-RAY DIFFRACTION	28	B	154 - 158
29	X-RAY DIFFRACTION	29	B	159 - 181
30	X-RAY DIFFRACTION	30	B	182 - 190
31	X-RAY DIFFRACTION	31	B	191 - 201
32	X-RAY DIFFRACTION	32	B	202 - 208
33	X-RAY DIFFRACTION	33	C	1 - 6
34	X-RAY DIFFRACTION	34	C	7 - 11

-
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