PDB-3kik: Sgf11:Sus1 complex

ID or keywords:

Entry

Database: PDB / ID: 3kik

Title

Sgf11:Sus1 complex

Components

Protein SUS1
SAGA-associated factor 11

Keywords

TRANSCRIPTION / articulated hirpin fold / SAGA complex / Activator / Chromatin regulator / Metal-binding / Nucleus / Transcription regulation / Zinc / Zinc-finger / mRNA transport / Nuclear pore complex / Protein transport / Translocation / Transport

Function / homology

Function and homology information

DUBm complex / transcription export complex 2 / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / SLIK (SAGA-like) complex / SAGA complex / poly(A)+ mRNA export from nucleus / nuclear pore / mRNA export from nucleus / transcription elongation by RNA polymerase II ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Stewart, M. / Ellisdon, A.M.

Citation

Journal: J.Biol.Chem. / Year: 2010
Title: Structural basis for the interaction between yeast Spt-Ada-Gcn5 acetyltransferase (SAGA) complex components Sgf11 and Sus1
Authors: Ellisdon, A.M. / Jani, D. / Kohler, A. / Hurt, E. / Stewart, M.

History

Deposition	Nov 2, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 8, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 6, 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	3kik.cif.gz	209.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3kik.ent.gz	169 KB	Display	PDB format
PDBx/mmJSON format	3kik.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3kik_validation.pdf.gz	471.1 KB	Display	wwPDB validaton report
Full document	3kik_full_validation.pdf.gz	476.4 KB	Display
Data in XML	3kik_validation.xml.gz	21.5 KB	Display
Data in CIF	3kik_validation.cif.gz	30.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ki/3kik ftp://data.pdbj.org/pub/pdb/validation_reports/ki/3kik	HTTPS FTP

-
Related structure data

Related structure data	3kjlC 2fwbS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6y06-d 2bt2-4 6ut2-d 1qey-d 4npf-2 4esr-d 2dlv-d 1ls4-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

3kjlC

2fwbS

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	#205 - Jan 2017 Nuclear Pore Complex similarity (1)

Deposited unit

A: Protein SUS1

E: SAGA-associated factor 11

B: Protein SUS1

F: SAGA-associated factor 11

C: Protein SUS1

G: SAGA-associated factor 11

D: Protein SUS1

H: SAGA-associated factor 11

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

1

A: Protein SUS1

E: SAGA-associated factor 11

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

2

B: Protein SUS1

F: SAGA-associated factor 11

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

3

C: Protein SUS1

G: SAGA-associated factor 11

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

4

D: Protein SUS1

H: SAGA-associated factor 11

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

Unit cell

Length a, b, c (Å)	75.153, 75.153, 197.373
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

Details

SAGA complex

#1: Protein	Protein SUS1 Mass: 11094.497 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: see publication for details Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SUS1, YBR111W-A / Plasmid: pNMTK / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) / References: UniProt: Q6WNK7
#2: Protein/peptide	SAGA-associated factor 11 / 11 kDa SAGA-associated factor Mass: 3074.420 Da / Num. of mol.: 4 / Fragment: Sus1 binding region of Sgf11 Source method: isolated from a genetically manipulated source Details: see publication for details Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SGF11, YPL047W / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q03067
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.84 Å³/Da / Density % sol: 56.67 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 3.2 M Na formate. See publication for details, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54059 Å
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 4, 2009 / Details: osmic mirrors
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54059 Å / Relative weight: 1
Reflection	Resolution: 2.1→25 Å / Num. all: 36176 / Num. obs: 36176 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / R_merge(I) obs: 0.059 / Net I/σ(I): 26.2
Reflection shell	Resolution: 2.1→2.21 Å / Redundancy: 7.2 % / R_merge(I) obs: 0.757 / Mean I/σ(I) obs: 2.4 / Num. unique all: 5136 / % possible all: 95.3

-
Processing

Software

Name	Version	Classification
MAR345dtb		data collection
PHASER		phasing
PHENIX	(phenix.refine)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB 2FWB residues 21-90 of chain C

2fwb

Resolution: 2.1→19.86 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.39 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2306	1991	5.52 %	Random but accounting for merohedral symmetry using PHENIX
R_work	0.195	-	-	-
obs	0.197	36040	98.37 %	-
all	-	36167	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 52.407 Å² / k_sol: 0.413 e/Å³

Refinement step

Cycle: LAST / Resolution: 2.1→19.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3814	0	0	257	4071

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	7694
X-RAY DIFFRACTION	f_angle_d	0.517	13957
X-RAY DIFFRACTION	f_dihedral_angle_d	13.981	2027
X-RAY DIFFRACTION	f_chiral_restr	0.038	651
X-RAY DIFFRACTION	f_plane_restr	0.001	1193

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 (%)
2.1-2.1404	0.205	108	0.2414	1838	X-RAY DIFFRACTION	98
2.1404-2.184	0.2666	108	0.2461	1832	X-RAY DIFFRACTION	98
2.184-2.2314	0.2567	107	0.2405	1835	X-RAY DIFFRACTION	98
2.2314-2.2833	0.2555	104	0.248	1870	X-RAY DIFFRACTION	98
2.2833-2.3403	0.2147	111	0.2471	1869	X-RAY DIFFRACTION	98
2.3403-2.4035	0.2666	109	0.2304	1835	X-RAY DIFFRACTION	98
2.4035-2.474	0.2962	110	0.2386	1860	X-RAY DIFFRACTION	98
2.474-2.5537	0.2377	108	0.2412	1893	X-RAY DIFFRACTION	98
2.5537-2.6448	0.2771	112	0.2288	1888	X-RAY DIFFRACTION	98
2.6448-2.7505	0.267	111	0.2344	1925	X-RAY DIFFRACTION	98
2.7505-2.8753	0.3464	112	0.2279	1919	X-RAY DIFFRACTION	98
2.8753-3.0264	0.2605	103	0.2135	1930	X-RAY DIFFRACTION	98
3.0264-3.2152	0.276	113	0.203	1914	X-RAY DIFFRACTION	98
3.2152-3.4623	0.2021	111	0.198	1925	X-RAY DIFFRACTION	98
3.4623-3.8085	0.2177	116	0.1677	1925	X-RAY DIFFRACTION	98
3.8085-4.3545	0.1504	118	0.1382	1926	X-RAY DIFFRACTION	98
4.3545-5.4672	0.1846	115	0.1557	1924	X-RAY DIFFRACTION	98
5.4672-19.8609	0.2829	114	0.2095	1942	X-RAY DIFFRACTION	98

Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

ID	Method	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	refined	0.1549	0.6259	-0.2247	0.2457	0.0981	0.4284	-0.8659	-0.652	-0.5434	0.2474	-0.3646	-0.9958	-0.7186	-0.1906	0.0016	0.7269	0.0007	-0.1457	0.5336	0.1184	0.9202	25.7073	66.6696	-3.5298
2		0.1476	0.0468	-0.2868	0.1359	-0.044	0.2088	-0.4582	-0.7491	-0.7969	-0.4949	-0.4718	0.0867	0.6805	0.1544	-0.0011	0.5728	-0.1028	0.0924	0.4693	-0.1526	1.4494
3		0.1201	-0.0302	-0.2323	0.1529	0.0252	0.1947	-1.0813	-0.7708	-1.1049	-0.1334	0.5409	-0.731	-0.0377	-0.2646	0.0009	0.4933	0.0599	0.0197	0.357	-0.0828	0.8036
4		0.0356	0.0896	-0.1755	0.1258	-0.1023	0.0687	0.4356	-0.34	-0.5724	0.5641	-0.0579	0.0974	-0.769	-0.1328	0.001	0.7871	-0.0694	-0.1572	0.7331	-0.0475	0.4582
5		0.3899	0.1932	-0.3653	0.3608	-0.3087	0.3081	-0.3701	-0.5278	-0.5445	0.7918	0.2765	0.2717	0.0559	-1.12	-0.0002	0.4721	0.1516	0.0665	0.6981	-0.1434	0.3941
6		0.1265	0.0197	0.0468	0.1066	-0.1105	0.0946	0.3657	1.5679	-0.9199	0.2611	-0.9434	-0.0069	-1.1985	-1.7089	0.0027	0.7276	0.4358	0.0249	1.0726	-0.2217	0.5537
7		0.1623	0.1553	0.2786	0.8465	-0.0096	0.2088	-0.0527	-0.1899	0.3878	0.5623	0.0755	-0.1241	-0.6504	-0.7339	0.0002	0.4716	0.1309	-0.0846	0.5095	-0.1378	0.4068
8		0.3135	0.0645	-0.0393	0.0558	0.0179	0.2998	-0.7393	-1.3396	1.0791	1.2102	0.0075	-0.0355	-1.7552	-0.1226	0.0032	0.6115	0.1745	-0.2131	0.6971	-0.1115	0.5804
9		0.5325	0.4291	-0.4177	0.2141	0.2939	0.4546	-0.2683	-1.1335	-0.3742	-0.0295	0.1829	-0.0478	-0.8785	0.5543	0.0005	0.6419	0.0006	-0.1756	0.4661	0.0611	0.504
10		0.3752	-0.0334	-0.068	0.2886	0.4152	0.062	-0.6133	-1.0448	-0.5471	0.4171	-0.0514	-1.8675	0.3425	0.7281	-0.0029	0.4553	-0.11	-0.1372	0.4434	0.2996	0.7452
11		0.1289	-0.1319	0.064	0.1037	-0.2076	-0.0206	0.5038	0.3854	-0.0275	0.3695	-1.2389	-0.5059	0.6017	0.9723	0.0004	0.6542	-0.0492	0.0829	0.6916	0.0807	1.0761
12		0.1608	0.0426	-0.1676	0.0886	0.0151	0.1345	-0.8127	-0.6198	-0.3187	0.2752	-0.0915	-1.0088	1.8409	-0.8935	-0.0004	0.7159	-0.0947	0.0989	0.7911	-0.1013	0.8344
13		0.2474	-0.0433	0.2024	0.1395	0.1054	0.1767	0.2	-0.462	0.5105	1.0018	0.4979	0.0975	0.259	1.0219	-0.0004	0.4188	0.0717	-0.0277	0.5833	-0.1092	0.4593
14		0.5301	0.2577	0.2325	0.2011	0.8029	0.0828	-0.0534	0.3243	0.6075	-0.1295	0.0518	-0.1346	0.0421	0.3294	0.0001	0.4428	0.0274	0.0073	0.3806	0.0158	0.3718
15		0.2488	-0.011	0.1775	0.2411	-0.0451	0.1547	-0.9955	0.7667	0.538	-0.9882	0.6813	-0.3885	0.7514	-0.4095	0.001	0.5798	-0.086	0.0261	0.5093	-0.0361	0.4452
16		0.5037	0.335	0.1412	0.4791	0.0265	0.1763	0.4246	-0.0684	-0.0395	-0.9433	0.3862	0.5574	0.7048	-0.1474	-0.0006	0.7281	-0.1113	-0.0879	0.4469	-0.0471	0.4305
17		0.743	-0.079	0.105	-0.0773	0.1347	0.2486	0.5321	-0.1221	-0.3752	-0.4637	-0.1419	0.475	0.9161	0.2894	0	0.5584	0.0782	-0.0208	0.404	-0.1001	0.5047
18		0.7374	0.4711	-0.2609	0.4741	0.207	0.499	-0.0379	-0.0279	-0.2287	-0.6493	0.4691	-0.1215	0.6613	0.6039	-0.001	0.6504	0.1607	0.1555	0.6426	-0.0196	0.4827
19		0.6431	0.2474	0.09	0.0693	0.6109	0.3197	-0.1455	0.2872	0.3409	-0.1526	-0.0823	0.4589	0.7497	1.1443	-0.0001	0.5436	0.0982	0.0383	0.6786	0.0414	0.4984
20		-0.0759	-0.0739	0.0802	0.3154	0.0048	0.0978	1.0035	0.5103	1.8777	-1.2434	-1.3206	1.0008	-1.8713	0.9712	0.0004	0.6194	-0.0658	0.2338	0.8939	-0.0198	1.3542
21		-0.041	-0.0312	0.0482	-0.053	-0.0387	-0.029	0.4605	1.0531	0.5541	-0.0573	0.0457	-0.4691	-1.541	-0.8901	0.0005	0.9775	0.4883	-0.249	1.0198	-0.3667	1.2162
22		0.1529	-0.0205	-0.0334	0.2856	-0.0526	0.1351	0.1518	-0.1973	1.3974	-0.915	-0.1878	-0.0134	-0.9707	-0.0028	0.0001	0.8199	0.0923	-0.0543	0.4901	0.0031	0.6881
23		0.4022	-0.1017	0.1458	0.448	-0.7999	0.0781	0.4863	-0.1715	0.461	-0.1408	0.022	0.308	0.1273	-0.0561	0.0009	0.2982	0.0327	0.0845	0.2942	0.0253	0.3322
24		0.1794	-0.0125	0.2542	0.1951	-0.246	0.194	0.1647	-0.2554	-0.0034	0.9948	0.1722	-0.2811	-0.4433	0.7101	-0.0005	0.4637	-0.0114	-0.0446	0.4137	0.0359	0.4394
25		0.1584	0.919	0.5326	0.1833	-0.4907	0.4905	0.3816	-0.4332	-0.1118	0.3382	-0.312	-0.3898	0.9888	-0.3588	-0.0002	0.5248	-0.1258	0.0217	0.4902	0.0485	0.2031
26		-0.0106	-0.002	-0.1086	0.0494	0.0888	0.0918	1.2698	-1.6795	0.1462	-0.6073	0.0723	0.0109	0.2689	-0.224	-0.0008	0.9601	-0.3753	0.2493	1.0961	0.2695	0.901
27		0.077	-0.4052	-0.1513	0.4403	-0.1552	0.2297	0.3114	-0.4393	0.3042	0.177	-0.2412	-0.04	0.8498	-1.9757	-0.0017	0.3556	-0.1075	-0.0296	0.7641	0.0269	0.3561
28		0.4583	0.1983	-0.012	0.1253	-0.1586	0.3795	0.1647	-0.6415	0.3568	0.5792	0.1168	0.8511	-0.5335	-0.9112	-0.0018	0.4301	-0.0065	0.097	0.6471	-0.0443	0.4104
29		0.1045	-0.3949	-0.386	0.6234	-0.4251	0.6961	0.6382	0.0268	0.1017	1.3875	-0.8899	0.1847	0.0399	-0.2671	0.0003	0.4409	-0.0158	0.0871	0.6497	-0.0681	0.4569
30		0.0502	-0.04	0.0544	0.1453	-0.1226	-0.0736	-0.2244	-0.2461	0.2544	-0.0482	-0.0206	-1.1619	-0.0061	0.915	0.0006	0.5164	0.051	-0.0451	0.7099	0.0438	0.8713
31		0.1335	0.1159	0.0552	0.5644	-0.2149	0.2411	-0.6302	0.1312	0.022	-0.4291	0.1963	-0.0636	-0.933	-1.0868	-0.0002	0.5961	0.087	-0.0588	0.4126	-0.182	1.106
32		0.0396	0.0001	-0.2359	0.1821	-0.0195	0.1196	-0.6811	-0.3915	0.2139	-0.743	-0.7466	0.6028	0.705	-0.1072	-0.0035	0.7105	0.0038	0.0493	0.456	0.0042	0.8979
33		0.1309	0.0456	-0.2358	0.2004	-0.0938	0.2215	-0.4081	-0.1742	-0.66	-0.8489	-0.0534	0.677	-0.3751	0.1647	0.0005	0.5009	0.0461	-0.0154	0.3849	0.0187	0.7199
34		0.0719	0.0807	-0.1139	0.0876	0.0509	0.2663	-0.2012	0.9585	-1.0794	-0.9273	0.0682	0.5627	1.059	-0.4918	-0	0.6066	-0.1561	0.0065	0.4679	-0.0709	0.5509
35		0.7181	0.4632	0.0383	0.4127	0.2294	0.4949	-0.352	-0.0661	-0.2721	-0.98	0.6285	0.0195	0.3233	0.3697	-0.0007	0.6021	-0.2928	-0.057	0.8119	0.061	0.3767
36		0.0852	0.0062	0.0588	0.0754	-0.0248	-0.1321	-0.9575	-1.6717	0.8659	1.6703	1.7111	0.3958	-0.7156	-0.0826	-0.0029	1.4122	-0.5506	0.1498	1.5866	-0.0877	0.6068
37		0.3909	-0.2434	-0.1395	0.1157	0.124	0.1941	-0.5185	0.2943	0.4903	0.0686	0.2702	0.0283	-0.6959	0.2297	-0.0006	0.4412	-0.1536	-0.1217	0.3876	0.1634	0.4979
38		0.3323	-0.0742	0.0342	0.134	0.391	0.1069	-0.8883	0.4006	0.595	-0.5776	0.4247	0.4702	-0.9842	0.4595	0.0026	0.6001	-0.1354	-0.1258	0.4762	0.0637	0.431
39		0.7565	-0.6514	-0.047	0.2522	-0.092	0.6122	-0.4093	1.3133	-0.5085	-0.5813	0.3549	0.3724	0.1102	0.1791	0.0003	0.5444	0.0354	-0.1312	0.5789	-0.1182	0.4716
40		0.2334	0.325	-0.3582	0.3817	-0.1919	0.1214	-0.4162	1.1234	-1.9078	0.2986	-0.3849	-0.0528	-0.4037	-1.2898	-0.0013	0.5511	0.0358	-0.0165	0.638	-0.1685	0.6127
41		0.1404	0.2562	-0.3315	-0.0222	0.2332	0.153	-0.4586	-1.4241	-0.9603	-0.1293	0.0705	-0.09	-0.2601	0.369	0.0006	0.5132	0.0202	-0.1185	0.3813	-0.0278	0.4398
42		0.0869	-0.3159	0.078	0.0227	0.1111	0.3446	-0.0441	-0.0264	0.2965	0.1699	0.0905	-0.6748	0.1601	-0.0987	0.0004	0.4219	0.0622	-0.0812	0.3486	-0.0755	0.3974
43		0.2918	0.4167	0.1601	0.2112	-0.0922	0.3982	0.2536	0.4067	-0.9616	0.5975	-0.0998	0.4029	-0.1697	-0.7397	0.0004	0.5428	0.0706	0.0266	0.5686	-0.0318	0.3984
44		0.1381	0.0835	0.1072	-0.071	0.0569	0.2539	-0.8398	0.2383	-0.8895	-0.6467	0.2408	-0.1288	1.1572	0.2303	0.001	0.4537	0.0399	0.0778	0.5056	-0.0497	0.7565
45		0.0985	0.1248	0.0269	0.0605	-0.1219	-0.0634	0.0244	-1.1531	-0.8419	0.5384	0.1356	-1.3259	-0.4222	0.474	0.0011	0.4872	0.0368	-0.0153	0.6009	0.0769	0.5252
46		0.0935	0.1577	0.4183	0.2537	-0.5289	0.542	-0.0279	-0.1047	0.0862	0.0234	-0.2673	-0.4878	-0.2378	-0.5835	-0.0002	0.4353	0.0438	-0.0864	0.4593	-0.1036	0.4513
47		0.0783	-0.031	-0.1057	0.009	-0.0604	-0.034	0.799	-0.7471	0.5254	1.0524	-1.3239	1.0261	-1.3563	-1.3851	0.0008	0.8256	0.1376	0.1815	0.6806	-0.2407	0.72
48		0.0449	-0.1046	0.1803	0.2147	0.0853	0.0797	0.3337	0.2998	0.3714	-0.3968	-0.343	1.1143	0.0766	-0.0523	0.0011	0.5279	0.1539	-0.04	0.6054	0.1026	0.4559
49		-0.0785	0.5126	0.6014	0.3646	-0.064	0.6256	0.4146	-0.2388	-0.0301	0.4028	-0.2163	-0.7165	0.3092	0.0054	0.0005	0.4513	0.0477	0.0744	0.54	0.1196	0.4303
50		0.302	-0.0756	-0.1301	0.2405	-0.1345	0.6815	0.3629	0.123	0.0464	-0.3382	-0.1523	0.126	-0.5978	0.2237	-0.0003	0.4643	-0.0028	-0.1296	0.2475	-0.0095	0.4192
51		0.0863	0.2403	-0.2041	-0.1489	0.0616	0.0199	-0.1772	0.4444	-0.0081	0.0963	-0.0803	0.018	0.1315	0.4088	-0.0003	0.329	-0.0438	-0.0456	0.4037	0.121	0.478
52		0.2679	-0.1422	0.0983	0.0629	0.0072	0.2532	-0.1934	0.4456	0.0902	-0.4186	0.3991	1.0543	0.1107	0.9566	-0.0024	0.5118	-0.0142	0.0016	0.489	0.0748	0.3903

Refinement TLS group

Selection details: chain H and resid 26:32)

-
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