PDB-3wof: Crystal structure of P23-45 gp39 (6-132) bound to Thermus thermop...

ID or keywords:

Entry

Database: PDB / ID: 3wof

Title

Crystal structure of P23-45 gp39 (6-132) bound to Thermus thermophilus RNA polymerase beta-flap domain

Components

DNA-directed RNA polymerase subunit betaPolymerase
Putative uncharacterized protein

Keywords

TRANSFERASE/TRANSCRIPTION /

Transcription /

RNA polymerase / TRANSFERASE-TRANSCRIPTION complex

Function / homology

Function and homology information

DNA-directed RNA polymerase complex /

ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity /

DNA-directed RNA polymerase / DNA-templated transcription /

Biological species

Thermus thermophilus (bacteria)

Thermus phage P23-45 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.298 Å

Authors

Tagami, S. / Sekine, S. / Minakhin, L. / Esyunina, D. / Akasaka, R. / Shirouzu, M. / Kulbachinskiy, A. / Severinov, K. / Yokoyama, S.

Citation

Journal: Genes Dev. / Year: 2014
Title: Structural basis for promoter specificity switching of RNA polymerase by a phage factor.
Authors: Tagami, S. / Sekine, S. / Minakhin, L. / Esyunina, D. / Akasaka, R. / Shirouzu, M. / Kulbachinskiy, A. / Severinov, K. / Yokoyama, S.

History

Deposition	Dec 26, 2013	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 12, 2014	Provider: repository / Type: Initial release
Revision 1.1	Mar 25, 2015	Group: Database references / Derived calculations
Revision 1.2	Nov 8, 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 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3wof.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb3wof.ent.gz	917.3 KB	Display	PDB format
PDBx/mmJSON format	3wof.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wo/3wof ftp://data.pdbj.org/pub/pdb/validation_reports/wo/3wof	HTTPS FTP

-
Related structure data

Related structure data	3wodC 3woeSC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4s1k-d 6dcu-2 6dcu-1 5vsx-d 4o8s-d 4lnx-d 3a8t-d 1x11-3 1zoq-1 4s1l-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) 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

Related structure data

3wodC

3woeSC

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#48 - Dec 2003 Catabolite Activator Protein similarity (5) #40 - Apr 2003 RNA Polymerase similarity (1) #253 - Jan 2021 Expressome similarity (4)

Deposited unit

A: DNA-directed RNA polymerase subunit beta

B: Putative uncharacterized protein

C: DNA-directed RNA polymerase subunit beta

D: Putative uncharacterized protein

E: DNA-directed RNA polymerase subunit beta

F: Putative uncharacterized protein

G: DNA-directed RNA polymerase subunit beta

H: Putative uncharacterized protein

I: DNA-directed RNA polymerase subunit beta

J: Putative uncharacterized protein

K: DNA-directed RNA polymerase subunit beta

L: Putative uncharacterized protein

M: DNA-directed RNA polymerase subunit beta

N: Putative uncharacterized protein

O: DNA-directed RNA polymerase subunit beta

P: Putative uncharacterized protein

Q: DNA-directed RNA polymerase subunit beta

R: Putative uncharacterized protein

S: DNA-directed RNA polymerase subunit beta

T: Putative uncharacterized protein

U: DNA-directed RNA polymerase subunit beta

V: Putative uncharacterized protein

W: DNA-directed RNA polymerase subunit beta

X: Putative uncharacterized protein

352 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: DNA-directed RNA polymerase subunit beta

B: Putative uncharacterized protein

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

2

C: DNA-directed RNA polymerase subunit beta

D: Putative uncharacterized protein

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

3

E: DNA-directed RNA polymerase subunit beta

F: Putative uncharacterized protein

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

4

G: DNA-directed RNA polymerase subunit beta

H: Putative uncharacterized protein

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

5

I: DNA-directed RNA polymerase subunit beta

J: Putative uncharacterized protein

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

6

K: DNA-directed RNA polymerase subunit beta

L: Putative uncharacterized protein

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

7

M: DNA-directed RNA polymerase subunit beta

N: Putative uncharacterized protein

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

8

O: DNA-directed RNA polymerase subunit beta

P: Putative uncharacterized protein

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

9

Q: DNA-directed RNA polymerase subunit beta

R: Putative uncharacterized protein

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

10

S: DNA-directed RNA polymerase subunit beta

T: Putative uncharacterized protein

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

11

U: DNA-directed RNA polymerase subunit beta

V: Putative uncharacterized protein

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

12

W: DNA-directed RNA polymerase subunit beta

X: Putative uncharacterized protein

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

Unit cell

Length a, b, c (Å)	213.777, 213.777, 234.598
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	DNA-directed RNA polymerase subunit beta / Polymerase / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta Mass: 14481.525 Da / Num. of mol.: 12 / Fragment: beta-flap domain, UNP RESIDUES 703-830 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: rpoB, TTHA1813 / Plasmid: pGEX-6P / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RQE9, DNA-directed RNA polymerase
#2: Protein	Putative uncharacterized protein / gp39 Mass: 14854.996 Da / Num. of mol.: 12 / Fragment: UNP RESIDUES 6-132 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus phage P23-45 (virus) / Strain: Thermus phage P23-45 / Gene: gp39 (P23p39), P23p39 / Plasmid: pET-47b / Production host: Escherichia coli (E. coli) / References: UniProt: A7XX65

#1: Protein

DNA-directed RNA polymerase subunit beta /

Polymerase / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta

Mass: 14481.525 Da / Num. of mol.: 12 / Fragment: beta-flap domain, UNP RESIDUES 703-830
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thermus thermophilus (bacteria) / Strain: HB8 / Gene: rpoB, TTHA1813 / Plasmid: pGEX-6P / Production host:

Escherichia coli (E. coli) / References: UniProt: Q8RQE9,

DNA-directed RNA polymerase

#2: Protein

Putative uncharacterized protein / gp39

Mass: 14854.996 Da / Num. of mol.: 12 / Fragment: UNP RESIDUES 6-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thermus phage P23-45 (virus) / Strain: Thermus phage P23-45 / Gene: gp39 (P23p39), P23p39 / Plasmid: pET-47b / Production host:

Escherichia coli (E. coli) / References: UniProt: A7XX65

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.81 Å³/Da / Density % sol: 67.69 %
Crystal grow	Temperature: 293 K / pH: 5.6 Details: 50mM MES-NaOH (pH 5.6), 6% PEG 8000, 200mM KCl, 10mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 11, 2012
Radiation	Monochromator: NUMERICAL LINK TYPE SI(111) DOUBLE CRYSTAL MONOCHROMATOR, LIQUID NITROGEN COOLING Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.298→50 Å / Num. obs: 82014 / % possible obs: 99.9 % / Observed criterion σ(I): 5.2 / Redundancy: 10.6 % / R_sym value: 0.175 / Net I/σ(I): 14.2

-
Processing

Software

Name	Version	Classification
PHASER		phasing
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3WOE

3woe

Resolution: 3.298→34.549 Å / SU ML: 0.37 / σ(F): 1.41 / Phase error: 23.05 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2464	4107	5.01 %
R_work	0.2191	-	-
obs	0.2205	81938	99.9 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.298→34.549 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22026	0	0	0	22026

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	22516
X-RAY DIFFRACTION	f_angle_d	1.227	30539
X-RAY DIFFRACTION	f_dihedral_angle_d	17.251	8770
X-RAY DIFFRACTION	f_chiral_restr	0.076	3369
X-RAY DIFFRACTION	f_plane_restr	0.007	4020

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 (%)
3.2982-3.337	0.3033	158	0.2738	2592	X-RAY DIFFRACTION	99
3.337-3.3776	0.3262	112	0.2763	2678	X-RAY DIFFRACTION	100
3.3776-3.4203	0.3023	131	0.2776	2646	X-RAY DIFFRACTION	100
3.4203-3.4653	0.3423	148	0.2876	2638	X-RAY DIFFRACTION	100
3.4653-3.5127	0.2829	142	0.2672	2655	X-RAY DIFFRACTION	100
3.5127-3.5629	0.2981	117	0.2578	2717	X-RAY DIFFRACTION	100
3.5629-3.616	0.2781	130	0.25	2629	X-RAY DIFFRACTION	100
3.616-3.6724	0.3204	149	0.277	2644	X-RAY DIFFRACTION	100
3.6724-3.7326	0.2893	128	0.2539	2675	X-RAY DIFFRACTION	100
3.7326-3.7969	0.2415	136	0.2313	2643	X-RAY DIFFRACTION	100
3.7969-3.8658	0.2758	149	0.2413	2658	X-RAY DIFFRACTION	100
3.8658-3.9401	0.2846	159	0.2419	2632	X-RAY DIFFRACTION	100
3.9401-4.0204	0.2745	142	0.2253	2662	X-RAY DIFFRACTION	100
4.0204-4.1077	0.2541	138	0.2296	2668	X-RAY DIFFRACTION	100
4.1077-4.2031	0.2388	127	0.2152	2691	X-RAY DIFFRACTION	100
4.2031-4.308	0.2382	152	0.2015	2645	X-RAY DIFFRACTION	100
4.308-4.4242	0.2161	147	0.1915	2669	X-RAY DIFFRACTION	100
4.4242-4.5541	0.2164	149	0.1883	2685	X-RAY DIFFRACTION	100
4.5541-4.7008	0.2003	149	0.1889	2651	X-RAY DIFFRACTION	100
4.7008-4.8684	0.2163	140	0.1906	2693	X-RAY DIFFRACTION	100
4.8684-5.0627	0.2371	132	0.1947	2687	X-RAY DIFFRACTION	100
5.0627-5.2923	0.201	126	0.1951	2712	X-RAY DIFFRACTION	100
5.2923-5.5703	0.2399	155	0.1976	2682	X-RAY DIFFRACTION	100
5.5703-5.9177	0.219	146	0.2067	2713	X-RAY DIFFRACTION	100
5.9177-6.3719	0.274	128	0.219	2731	X-RAY DIFFRACTION	100
6.3719-7.0083	0.2534	156	0.213	2706	X-RAY DIFFRACTION	100
7.0083-8.0114	0.2453	156	0.2041	2744	X-RAY DIFFRACTION	100
8.0114-10.0522	0.1828	152	0.1644	2792	X-RAY DIFFRACTION	100
10.0522-34.5513	0.2132	153	0.2303	2893	X-RAY DIFFRACTION	99

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	0.0733	-0.0472	0.0714	0.1993	0.0799	0.0923	-0.0778	0.2609	-0.0174	-0.0131	0.0285	0.0956	-0.1622	0.2364	-0.0522	0.1855	-0.1587	-0.301	0.2511	0.03	0.2791	-17.9096	-32.1515	37.1021
2	0.0426	0.0474	-0.0145	0.1141	-0.0888	0.0821	-0.0028	-0.0965	-0.0524	0.0472	-0.0841	-0.012	-0.0223	0.0323	-0.1897	0.0963	-0.2062	-0.0122	-0.1959	0.0375	0.0796	-35.8321	-20.962	41.9259
3	0.1263	-0.0847	-0.1523	0.1871	-0.0295	0.3482	-0.0851	0.1015	0.1016	-0.2554	0.0911	0.1338	0.232	-0.359	0.0029	0.4081	-0.1257	-0.0386	0.421	0.0577	0.3652	-94.1297	-38.8725	8.6285
4	0.3241	0.0095	0.0692	0.1332	-0.0364	0.0205	0.0308	-0.1185	0.0178	0.2161	-0.0013	-0.0034	0.1591	-0.1404	0.0051	0.4045	-0.0787	-0.0111	0.2325	0.0965	0.3575	-81.7469	-31.2293	24.6909
5	0.0491	-0.0603	0.0147	0.2265	-0.1548	0.147	-0.1106	0.0347	0.273	-0.2207	-0.1866	-0.2396	-0.1134	0.0384	-0.226	0.5362	0.2612	-0.3624	-0.1304	-0.0368	0.7731	-60.0236	32.7689	19.1933
6	0.0853	-0.053	-0.0293	0.0339	0.0212	0.0159	-0.1866	-0.1011	0.1201	-0.0293	-0.0746	0.0247	-0.1113	-0.0741	-0.167	0.3176	0.3313	-0.2211	0.0064	-0.0361	0.4077	-66.7398	15.1258	28.9362
7	0.0275	-0.0025	0.0039	0.0183	-0.0007	0.0236	0.1784	0.031	0.1456	-0.1091	0.017	-0.0234	0.097	0.0975	0.3708	0.0623	-0.19	-0.3591	-0.0167	-0.3602	-0.2321	13.2559	-12.3677	49.1596
8	0.006	0.0082	-0.029	-0.0032	-0.0015	0.0807	0.0598	0.0481	-0.0375	-0.0432	0.0283	-0.0241	0.052	0.1217	0.0922	-0.1799	-0.293	-0.4084	0.198	-0.4094	-0.248	28.1747	-12.0832	33.469
9	0.0635	0.0661	0.0509	0.0929	0.0722	0.1672	-0.3461	-0.0127	0.2192	-0.2371	-0.0017	0.0653	-0.1492	-0.0083	-0.0216	0.2705	-0.1382	-0.0639	0.7154	-0.0628	0.348	76.8333	37.6902	37.6299
10	0.0466	0.0099	0.0233	0.0539	0.0142	0.0183	-0.0115	-0.0486	-0.0027	-0.0519	0.0333	-0.0143	-0.0031	0.0095	-0.0082	0.0194	-0.2509	0.0159	0.886	-0.2535	0.3102	67.5648	18.1461	34.8846
11	0.0489	0.0252	-0.0233	0.0034	0.0015	0.0349	0.1696	0.0983	0.0209	-0.1215	-0.1478	-0.0327	-0.0752	-0.0384	0.0056	0.5901	0.2044	0.0349	0.8753	-0.1437	0.3131	38.4389	6.4036	-25.6316
12	0.0232	0.0194	0.0315	0.0253	0.0326	0.0475	0.023	-0.0562	-0.1242	0.0112	-0.0751	0.0189	0.0965	0.05	0	0.2555	0.0462	0.0576	0.7834	-0.0627	0.3431	48.2339	1.7234	-7.1801
13	0.0859	-0.0512	0.1111	0.0331	-0.0516	0.1621	0.1212	-0.2212	0.2049	-0.1489	0.1112	0.022	-0.2728	-0.0483	0.0446	0.2765	-0.071	0.0776	0.1863	-0.0978	0.2852	-19.8938	9.708	33.0933
14	0.1241	0.0229	0.0006	0.099	-0.0665	0.0803	0.0249	0.0025	0.053	-0.1744	0.014	0.1377	-0.1013	-0.0607	0.0013	0.0648	0.2082	-0.0038	-0.1789	0.0821	0.0957	-32.9764	-5.2811	24.723
15	0.1133	-0.0225	0.0304	0.0301	-0.0359	0.0377	-0.0831	-0.0078	-0.1029	-0.063	0.1245	0.3196	-0.1329	-0.0974	-0.0033	0.7031	0.0246	-0.1993	0.3258	0.0949	0.7434	-91.8588	10.0156	3.3073
16	0.0126	0.0089	0.024	0.0857	-0.0104	0.0764	-0.0212	-0.0668	-0.1877	-0.0819	0.0634	-0.0005	-0.0393	0.0271	0.0909	0.3868	0.2051	-0.1884	-0.3146	0.1084	0.3588	-71.9343	3.8082	8.9889
17	0.08	0.0738	0.0016	0.0607	-0.0201	0.0988	0.236	0.1323	-0.2033	0.0564	-0.1317	-0.0687	0.1396	0.0914	0.0106	0.6736	0.0485	-0.2582	0.2332	-0.0371	0.993	-57.541	-57.0397	19.9159
18	0.0469	-0.0217	-0.0299	0.0208	0.0082	0.0472	0.0732	0.2151	0.0072	0.177	-0.034	-0.1156	0.0858	0.0088	0.0079	0.1875	0.0198	-0.2785	0.1529	-0.0399	0.3002	-61.0937	-36.8846	15.0313
19	0.1318	0.0581	-0.0444	0.0775	-0.0256	0.038	-0.0352	-0.0943	-0.1175	-0.0377	-0.0468	-0.1331	0.0333	0.188	-0.0901	0.161	-0.0227	0.0778	0.253	0.121	-0.0405	3.0756	-9.3464	8.3865
20	0.0075	-0.0035	0.0193	0.1041	0.0108	0.1761	0.1248	0.0236	0.0621	-0.0288	0.1169	-0.0779	-0.0856	0.1841	0.3168	0.1892	-0.1109	0.1395	0.4936	-0.1178	0.1731	17.2267	2.9374	19.0127
21	0.0472	-0.0134	0.0306	0.0061	0.0048	0.0475	-0.1844	-0.0764	0.0232	-0.0921	-0.008	-0.0044	-0.1211	0.154	-0.0148	0.8635	-0.4161	0.0645	0.804	0.0959	0.503	67.8567	30.9011	-8.9692
22	0.0415	0.009	0.0115	0.0287	-0.0038	0.0051	-0.0204	-0.1264	0.026	-0.1192	-0.0531	0.0345	-0.325	0.0326	-0	0.7245	-0.2341	-0.0677	0.7063	-0.0477	0.3218	50.5383	23.9743	-0.2075
23	0.0776	0.0254	0.0686	0.1078	-0.0612	0.1498	0.1026	-0.0931	0.1555	-0.0257	0.1573	-0.1347	0.1102	0.1385	0.2043	-0.0739	-0.0382	0.013	0.5465	-0.2842	0.3814	52.288	16.8016	65.0913
24	0.0394	0.0341	0.0287	0.0368	0.0499	0.0384	0.0399	0.1128	0.088	-0.1363	0.2775	0.0677	0.0203	0.0606	0.2713	-0.0393	-0.5656	-0.092	0.6684	-0.179	0.4329	46.9592	21.9242	44.7826

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A
2	X-RAY DIFFRACTION	2	CHAIN B
3	X-RAY DIFFRACTION	3	CHAIN C
4	X-RAY DIFFRACTION	4	CHAIN D
5	X-RAY DIFFRACTION	5	CHAIN E
6	X-RAY DIFFRACTION	6	CHAIN F
7	X-RAY DIFFRACTION	7	CHAIN G
8	X-RAY DIFFRACTION	8	CHAIN H
9	X-RAY DIFFRACTION	9	CHAIN I
10	X-RAY DIFFRACTION	10	CHAIN J
11	X-RAY DIFFRACTION	11	CHAIN K
12	X-RAY DIFFRACTION	12	CHAIN L
13	X-RAY DIFFRACTION	13	CHAIN M
14	X-RAY DIFFRACTION	14	CHAIN N
15	X-RAY DIFFRACTION	15	CHAIN O
16	X-RAY DIFFRACTION	16	CHAIN P
17	X-RAY DIFFRACTION	17	CHAIN Q
18	X-RAY DIFFRACTION	18	CHAIN R
19	X-RAY DIFFRACTION	19	CHAIN S
20	X-RAY DIFFRACTION	20	CHAIN T
21	X-RAY DIFFRACTION	21	CHAIN U
22	X-RAY DIFFRACTION	22	CHAIN V
23	X-RAY DIFFRACTION	23	CHAIN W
24	X-RAY DIFFRACTION	24	CHAIN X

-
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