PDB-5u0c: Structure of Zika virus NS5 RNA polymerase domain

ID or keywords:

Entry

Database: PDB / ID: 5u0c

Title

Structure of Zika virus NS5 RNA polymerase domain

Components

NS5 RNA polymerase domain

Keywords

TRANSFERASE /

RNA polymerase

Function / homology

Function and homology information

symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity /

flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity /

viral capsid / nucleoside-triphosphate phosphatase /

double-stranded RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA (guanine-N7)-methyltransferase ...
Similarity search - Function

Flavivirus RNA-directed RNA polymerase, thumb domain /

: / Flavivirus envelope glycoprotein E, stem/anchor domain /

RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus ...Flavivirus RNA-directed RNA polymerase, thumb domain /

: / Flavivirus envelope glycoprotein E, stem/anchor domain /

RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M /

RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain /

DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily /

Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain /

RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology

Biological species

Zika virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Zhao, B. / Du, F.

Citation

Journal: Nat Commun / Year: 2017
Title: Structure and function of the Zika virus full-length NS5 protein.
Authors: Zhao, B. / Yi, G. / Du, F. / Chuang, Y.C. / Vaughan, R.C. / Sankaran, B. / Kao, C.C. / Li, P.

History

Deposition	Nov 23, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 29, 2017	Provider: repository / Type: Initial release
Revision 1.1	Apr 12, 2017	Group: Database references
Revision 1.2	Oct 4, 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	5u0c.cif.gz	1.9 MB	Display	PDBx/mmCIF format
PDB format	pdb5u0c.ent.gz	1.6 MB	Display	PDB format
PDBx/mmJSON format	5u0c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u0/5u0c ftp://data.pdbj.org/pub/pdb/validation_reports/u0/5u0c	HTTPS FTP

-
Related structure data

Related structure data	5u0bC 4k6mS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6izx-d 6ld3-d 4mtp-2 5f3t-d 5iq6-d 5f3z-d 6izz-d 4mtp-3 6ld1-d 4hdg-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) 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

5u0bC

4k6mS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#103 - Jul 2008 Dengue Virus similarity (43) #40 - Apr 2003 RNA Polymerase similarity (1) #197 - May 2016 Zika Virus similarity (43) #145 - Jan 2012 Messenger RNA Capping similarity (1)

Deposited unit

A: NS5 RNA polymerase domain

B: NS5 RNA polymerase domain

C: NS5 RNA polymerase domain

D: NS5 RNA polymerase domain

E: NS5 RNA polymerase domain

F: NS5 RNA polymerase domain

G: NS5 RNA polymerase domain

H: NS5 RNA polymerase domain

hetero molecules

592 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: NS5 RNA polymerase domain

hetero molecules

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

2

B: NS5 RNA polymerase domain

hetero molecules

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

3

C: NS5 RNA polymerase domain

hetero molecules

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

4

D: NS5 RNA polymerase domain

hetero molecules

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

5

E: NS5 RNA polymerase domain

hetero molecules

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

6

F: NS5 RNA polymerase domain

hetero molecules

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

7

G: NS5 RNA polymerase domain

hetero molecules

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

8

H: NS5 RNA polymerase domain

hetero molecules

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

Unit cell

Length a, b, c (Å)	121.520, 188.710, 192.539
Angle α, β, γ (deg.)	90.00, 91.99, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	NS5 RNA polymerase domain Mass: 73863.078 Da / Num. of mol.: 8 / Fragment: residues 2781-3419 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zika virus (strain Mr 766) / Strain: Mr 766 / Production host: Escherichia coli (E. coli) References: UniProt: Q32ZE1, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn

#1: Protein

NS5 RNA polymerase domain

Mass: 73863.078 Da / Num. of mol.: 8 / Fragment: residues 2781-3419
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Zika virus (strain Mr 766) / Strain: Mr 766 / Production host:

Escherichia coli (E. coli)
References: UniProt: Q32ZE1, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1,

RNA-directed RNA polymerase

#2: Chemical

ChemComp-ZN / ZINC ION

Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.73 Å³/Da / Density % sol: 67.06 %
Crystal grow	Temperature: 277 K / Method: evaporation / pH: 7.5 Details: 0.1 M Tris pH 7.5, 0.2 M sodium citrate, and 17% PEG 3350

-
Data collection

Diffraction	Mean temperature: 120 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3→89.14 Å / Num. obs: 169594 / % possible obs: 98 % / Redundancy: 2.6 % / CC_1/2: 0.984 / R_merge(I) obs: 0.144 / Net I/σ(I): 6
Reflection shell	Resolution: 3→3.05 Å / Redundancy: 2.6 % / R_merge(I) obs: 0.698 / CC_1/2: 0.665 / % possible all: 97.9

-
Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4k6m

4k6m

Resolution: 3→89.137 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.42 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2599	8546	5.05 %
R_work	0.2263	-	-
obs	0.228	169314	97.76 %

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→89.137 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	40549	0	16	0	40565

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	41541
X-RAY DIFFRACTION	f_angle_d	0.477	56181
X-RAY DIFFRACTION	f_dihedral_angle_d	22.019	24709
X-RAY DIFFRACTION	f_chiral_restr	0.039	5856
X-RAY DIFFRACTION	f_plane_restr	0.003	7224

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 (%)
3-3.0341	0.3987	279	0.3386	5387	X-RAY DIFFRACTION	98
3.0341-3.0698	0.3459	303	0.3194	5287	X-RAY DIFFRACTION	98
3.0698-3.1072	0.3599	300	0.3239	5333	X-RAY DIFFRACTION	98
3.1072-3.1466	0.3523	276	0.3218	5341	X-RAY DIFFRACTION	98
3.1466-3.188	0.3549	291	0.3074	5300	X-RAY DIFFRACTION	98
3.188-3.2317	0.3531	257	0.3164	5327	X-RAY DIFFRACTION	97
3.2317-3.2778	0.334	267	0.3001	5377	X-RAY DIFFRACTION	97
3.2778-3.3268	0.3544	276	0.2988	5345	X-RAY DIFFRACTION	98
3.3268-3.3787	0.3063	291	0.2876	5392	X-RAY DIFFRACTION	99
3.3787-3.4341	0.2798	263	0.2646	5387	X-RAY DIFFRACTION	99
3.4341-3.4934	0.3081	247	0.2637	5443	X-RAY DIFFRACTION	99
3.4934-3.5569	0.2996	272	0.2524	5414	X-RAY DIFFRACTION	98
3.5569-3.6253	0.2849	310	0.2441	5342	X-RAY DIFFRACTION	98
3.6253-3.6993	0.2841	330	0.2458	5364	X-RAY DIFFRACTION	99
3.6993-3.7797	0.247	352	0.2332	5351	X-RAY DIFFRACTION	99
3.7797-3.8677	0.251	285	0.2214	5356	X-RAY DIFFRACTION	98
3.8677-3.9644	0.2441	308	0.2135	5333	X-RAY DIFFRACTION	98
3.9644-4.0716	0.2428	289	0.205	5399	X-RAY DIFFRACTION	98
4.0716-4.1914	0.2332	234	0.2084	5438	X-RAY DIFFRACTION	98
4.1914-4.3267	0.2456	250	0.1983	5417	X-RAY DIFFRACTION	98
4.3267-4.4813	0.2273	297	0.1912	5399	X-RAY DIFFRACTION	99
4.4813-4.6607	0.2259	310	0.1851	5365	X-RAY DIFFRACTION	98
4.6607-4.8728	0.2419	295	0.1875	5329	X-RAY DIFFRACTION	98
4.8728-5.1297	0.2127	322	0.1963	5254	X-RAY DIFFRACTION	97
5.1297-5.451	0.2412	266	0.1984	5367	X-RAY DIFFRACTION	97
5.451-5.8718	0.2381	292	0.2031	5354	X-RAY DIFFRACTION	97
5.8718-6.4626	0.231	271	0.2043	5389	X-RAY DIFFRACTION	98
6.4626-7.3974	0.2358	290	0.2017	5380	X-RAY DIFFRACTION	98
7.3974-9.3183	0.1767	271	0.1541	5325	X-RAY DIFFRACTION	95
9.3183-89.1759	0.1744	252	0.1684	5273	X-RAY DIFFRACTION	94

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	0.5725	-0.9891	0.1733	3.1364	0.8323	0.7908	-0.0181	-0.2071	0.4863	0.3213	-0.1304	-0.1435	-0.3322	0.0036	0.1278	0.6068	-0.0004	0.0847	0.5412	-0.0984	0.6372	2.9755	22.138	96.0644
2	2.7064	-0.2324	0.4034	3.2631	0.9431	2.5151	0.2784	-0.1359	0.5449	-0.0705	-0.6289	0.4967	-0.278	-0.714	0.3461	0.7425	0.179	0.0775	0.5993	-0.1462	0.6717	-12.0836	26.4561	80.3889
3	1.0714	1.2445	-0.2196	3.0035	2.0494	3.982	0.1846	-0.1633	0.0925	-0.2417	-0.4113	0.0441	0.0362	-0.0494	0.1515	0.6491	0.1931	0.1457	0.5359	0.0325	0.4299	-3.1042	15.8495	77.7307
4	0.859	-0.4663	0.0937	2.88	0.1524	0.5029	0.2817	0.2158	0.3446	-0.5285	-0.3126	-0.256	-0.382	-0.0586	0.04	0.6038	0.1816	0.19	0.5078	0.083	0.4034	3.074	10.6876	73.9515
5	4.1873	0.8192	-1.6457	2.4724	-0.2824	2.5654	-0.0008	0.2882	-0.2511	0.0267	0.0773	-0.09	0.0573	-0.066	-0.1	0.261	0.0163	-0.0083	0.2863	-0.04	0.1971	-0.812	-17.3327	87.8511
6	0.3354	0.0975	-0.1068	1.9644	-1.0186	0.6141	0.0426	0.2064	0.2962	-0.1069	0.1058	0.3037	-0.1886	-0.0092	-0.1035	0.3686	-0.0045	0.0908	0.3845	0.1596	0.5037	53.9239	-8.8185	5.3939
7	2.5464	-0.8741	1.0547	2.5804	-0.4023	4.0141	0.2391	0.3346	0.0054	-0.1027	-0.2822	-0.3034	0.1643	0.3394	0.1194	0.3197	0.0017	0.0772	0.3686	0.0956	0.3674	68.7911	-9.7492	10.1496
8	0.5819	0.3189	-0.1062	2.4786	-0.4919	0.876	0.0711	0.0569	0.285	0.4689	0.1372	0.4278	-0.3255	-0.1149	-0.1173	0.295	0.0461	0.1367	0.2998	0.0751	0.3825	51.8082	-14.1913	23.6938
9	1.5837	-0.1724	-1.0358	2.2462	0.4927	3.3656	-0.008	0.0546	-0.0333	0.0007	0.0432	-0.1859	-0.1116	0.1608	-0.0216	0.1438	-0.0123	0.0183	0.1982	0.0098	0.2338	62.6486	-42.5968	15.4583
10	0.8722	0.4737	0.2388	0.389	0.0809	0.3592	0.2472	-0.3996	0.3007	0.26	-0.1377	0.0699	-0.6867	0.4273	0.0694	0.8349	-0.4897	0.0307	0.7722	-0.1932	0.4126	35.4117	93.2282	90.4369
11	1.4218	0.4869	-0.5811	0.5561	-0.3325	0.3579	0.1256	-0.4616	0.1155	0.1702	-0.1306	-0.124	-0.6123	0.4164	-0.026	0.5867	-0.3013	0.0705	0.4337	-0.0651	0.3411	38.4203	86.6354	73.5457
12	3.1856	0.6937	0.7384	0.5494	-0.6533	1.855	0.2236	-0.9884	0.6745	0.3943	-0.229	0.259	-0.382	-0.37	-0.3318	1.4648	-0.0029	0.1747	0.4867	-0.002	0.7066	23.7111	107.1884	75.6275
13	2.3939	0.2185	0.2154	0.9845	-0.6889	1.5807	0.4208	-0.3792	0.2913	-0.2156	-0.2562	0.2506	-0.9262	0.0544	-0.0833	1.1247	-0.2272	0.1387	0.5043	-0.1689	0.4621	31.6172	98.7819	80.4935
14	1.0965	0.1182	-0.3302	0.8027	0.1411	2.3817	0.1548	-0.0196	0.1652	-0.0106	-0.0577	-0.0335	-0.6434	0.3322	-0.0331	0.5146	-0.1696	0.0853	0.2823	-0.0173	0.2575	35.983	88.4618	62.4815
15	1.8939	-0.4342	-0.8627	1.6103	-0.033	4.2722	0.0204	0.2374	-0.0765	-0.0733	-0.0989	0.2681	-0.401	-0.5782	0.0455	0.2608	0.0259	0.0737	0.4107	-0.0044	0.3381	5.5061	80.5009	70.3188
16	4.0267	-2.5804	0.0066	3.2872	-0.2006	4.169	-0.0172	0.3374	-0.0059	-0.2332	-0.138	0.1357	-0.2087	-0.2886	0.0355	0.4467	-0.0032	-0.0967	0.2256	-0.0047	0.2421	11.5154	65.7295	4.5257
17	0.8277	-0.4509	-0.0288	0.7127	-0.695	1.1033	0.0156	0.1369	-0.0545	-0.0318	-0.0688	0.0578	-0.1815	-0.0221	0.0372	0.2621	-0.0595	-0.0751	0.2754	-0.0691	0.1876	26.2972	56.8384	20.8007
18	4.1843	1.441	0.9039	2.4517	0.223	0.4074	-0.1244	0.3808	0.5509	-0.5516	0.0123	-0.1238	-0.3002	0.078	0.0764	0.6538	-0.0777	-0.0322	0.2992	0.0373	0.2956	28.4889	75.67	13.1712
19	2.2698	0.1079	-0.1123	0.0648	0.4105	2.7163	0.0223	-0.0683	-0.2648	0.5702	-0.2313	-0.067	0.7059	0.2729	0.0593	0.5148	0.0324	-0.1279	0.3477	0.077	0.2993	27.7149	60.3176	20.2502
20	0.6101	-0.026	-0.1403	0.7056	-0.319	1.8411	-0.0648	-0.1732	-0.0011	0.1505	-0.0491	0.0355	-0.19	-0.057	0.1044	0.3071	-0.0335	-0.0463	0.2616	-0.0548	0.1941	22.4265	54.3856	32.7118
21	1.5439	0.0067	-0.5701	1.8484	-0.325	3.1606	0.0346	-0.2795	0.0129	0.1099	-0.0529	-0.194	-0.0709	0.5682	0.0427	0.185	-0.0129	-0.0234	0.4781	0.0035	0.2851	52.761	48.5329	26.1467
22	0.5975	-0.3128	-0.2117	1.6081	-0.7452	0.5748	-0.0592	-0.4515	-0.5001	0.3464	-0.0452	0.3697	0.462	0.1763	-0.0518	0.6153	0.0915	-0.0203	0.7024	0.2864	0.7157	51.0599	30.9017	91.0935
23	1.8568	0.5276	0.0245	2.4469	-1.0979	2.113	0.1466	-0.7653	-0.3734	0.7047	-0.3546	-0.4236	0.0334	0.745	0.1722	0.6501	0.002	-0.0856	1.0866	0.3419	0.6272	65.9079	32.0351	86.2685
24	0.96	0.0472	-0.4501	3.1963	-0.1653	1.0993	-0.0803	-0.2009	-0.3761	-0.2109	0.029	0.4449	0.4012	0.0805	0.0352	0.3564	-0.0087	-0.0774	0.4666	0.1104	0.481	48.7429	36.3319	72.8451
25	1.5916	0.2363	0.586	2.0301	0.2122	2.8948	0.0814	-0.0673	-0.0109	0.1013	0.1033	-0.1101	-0.0237	0.2701	-0.1906	0.2014	-0.0485	-0.0019	0.5297	0.009	0.2782	59.0619	64.9928	81.0481
26	0.7158	0.8541	0.1241	1.9472	0.7697	0.4059	0.1291	0.1253	-0.4193	0.3673	0.0608	-0.5148	0.2755	0.0615	-0.1726	0.4999	0.0052	-0.1639	0.2804	0.0043	0.4711	6.3897	-1.5693	5.5148
27	2.14	-0.4327	-1.0118	2.6942	0.7532	3.737	0.4421	0.1175	-0.0031	0.2029	-0.4735	0.4266	-0.2416	-0.6069	0.1355	0.4731	-0.0368	-0.1126	0.4006	-0.1299	0.4724	-8.5203	-0.6454	10.8582
28	0.9599	0.5817	-0.0257	2.156	0.6195	1.1631	0.3395	-0.1323	-0.367	0.801	-0.1938	-0.4664	0.6878	-0.0419	-0.1242	0.686	-0.1086	-0.3321	0.3412	0.1094	0.4344	8.2495	3.9802	24.2837
29	1.1684	-0.3056	0.7826	1.636	-0.1403	2.998	0.1701	-0.1799	0.0614	0.1969	-0.0767	0.1326	0.1505	-0.3808	-0.064	0.1976	-0.0987	-0.0046	0.3005	0.0385	0.2881	-2.0831	32.4537	15.218
30	3.5027	1.8996	-1.2745	1.9595	-0.248	3.2933	0.1611	-0.0887	-0.3969	0.3449	-0.2299	0.1811	0.5594	-0.4487	0.0651	0.8811	-0.1597	0.0379	0.4775	0.0275	0.3652	8.2903	-43.6949	91.4668
31	2.9325	1.0204	-0.3161	0.7078	-0.2578	1.3839	0.2648	-0.542	-0.2716	0.3894	-0.2344	-0.0388	0.0605	-0.0525	-0.0221	0.5053	-0.0093	0.0265	0.3393	-0.0106	0.27	27.4007	-26.8172	85.3895
32	2.7124	-2.5137	-0.5687	2.6127	-0.032	1.5447	-0.0356	0.1049	-0.3473	-0.1487	0.0128	-0.0157	0.5275	-0.0047	0.0272	0.6158	0.0107	-0.1132	0.3297	-0.1626	0.4912	19.0448	-47.5089	61.2484
33	3.7391	-0.46	0.6882	1.278	1.6609	2.6118	0.4621	-0.2953	-0.5995	0.0795	-0.2838	-0.4191	0.7969	0.2393	-0.1357	0.8508	0.038	-0.0385	0.4762	0.1496	0.4243	24.5455	-47.6392	82.537
34	0.7949	-0.06	0.1547	0.7143	0.3483	1.5981	0.0899	0.1199	-0.1389	-0.0321	-0.1069	0.0694	0.1843	0.0036	0.0085	0.5146	0.0416	-0.0028	0.368	-0.0358	0.2748	19.5538	-33.8442	64.3679
35	1.6885	-0.8183	0.4395	2.1828	0.3355	3.266	0.1056	0.1479	0.0725	-0.16	0.0713	-0.2591	0.0121	0.5932	-0.1477	0.3168	0.0223	0.0236	0.6089	-0.0213	0.2981	49.5051	-26.8152	69.6498
36	4.2332	-3.1725	-1.5573	2.4111	1.334	1.1895	0.2083	0.572	-0.265	-0.1856	-0.3269	0.1274	0.0593	-0.0721	0.1276	0.3568	-0.0052	0.0964	0.3261	-0.0537	0.2936	39.8099	-70.7283	6.1473
37	1.1248	-0.0289	0.7831	0.5742	-0.023	2.552	-0.0984	0.2987	-0.08	0.0671	-0.1166	-0.0686	0.0648	0.3116	0.1441	0.1887	-0.0304	0.051	0.2604	-0.0657	0.2579	42.7947	-65.7485	24.378
38	3.2812	-0.648	1.372	2.8601	1.2681	3.9446	0.1397	0.8487	-0.2892	-0.642	-0.0963	0.265	-0.1422	-0.5627	0.0697	0.4771	-0.0519	0.1365	0.5655	-0.0724	0.4861	27.7956	-85.8863	18.9119
39	2.6552	-0.3535	0.0011	0.6914	-0.9871	2.767	0.13	0.3381	-0.2412	-0.0469	-0.1616	0.3597	0.1534	-0.2849	0.0624	0.3195	-0.0767	0.1186	0.3726	-0.1082	0.3391	35.4906	-78.5339	18.2065
40	0.972	-0.2795	0.0727	0.781	0.0214	0.9997	-0.0894	-0.0654	-0.0707	0.1177	-0.0754	0.0085	0.0714	0.0119	0.1663	0.2454	-0.0581	0.0517	0.216	-0.0097	0.1927	38.544	-64.8735	33.2252
41	1.7623	0.1181	0.6282	1.9223	-0.9738	3.7899	0.0439	-0.0878	-0.0041	0.0765	-0.0372	0.2799	0.1175	-0.4089	-0.0266	0.1729	-0.043	0.0301	0.3113	-0.1023	0.3324	8.1721	-59.7665	26.5946

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 268 through 368 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 369 through 458 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 459 through 515 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 516 through 842 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 843 through 891 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 268 through 388 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 389 through 479 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 480 through 749 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 750 through 888 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 268 through 334 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 335 through 386 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 387 through 429 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 430 through 479 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 480 through 724 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 725 through 888 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 266 through 311 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 312 through 401 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 402 through 458 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 459 through 495 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 496 through 749 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 750 through 888 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 268 through 388 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 389 through 479 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 480 through 749 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 750 through 889 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 269 through 386 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 387 through 479 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 480 through 749 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 750 through 890 )
30	X-RAY DIFFRACTION	30	chain 'G' and (resid 265 through 311 )
31	X-RAY DIFFRACTION	31	chain 'G' and (resid 312 through 368 )
32	X-RAY DIFFRACTION	32	chain 'G' and (resid 369 through 406 )
33	X-RAY DIFFRACTION	33	chain 'G' and (resid 407 through 472 )
34	X-RAY DIFFRACTION	34	chain 'G' and (resid 473 through 749 )
35	X-RAY DIFFRACTION	35	chain 'G' and (resid 750 through 888 )
36	X-RAY DIFFRACTION	36	chain 'H' and (resid 265 through 335 )
37	X-RAY DIFFRACTION	37	chain 'H' and (resid 336 through 389 )
38	X-RAY DIFFRACTION	38	chain 'H' and (resid 390 through 429 )
39	X-RAY DIFFRACTION	39	chain 'H' and (resid 430 through 495 )
40	X-RAY DIFFRACTION	40	chain 'H' and (resid 496 through 749 )
41	X-RAY DIFFRACTION	41	chain 'H' and (resid 750 through 887 )

-
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