PDB-4ekx: Crystal Structure of YLDV 14L IL-18 Binding Protein in Complex wi...

ID or keywords:

Entry

Database: PDB / ID: 4ekx

Title

Crystal Structure of YLDV 14L IL-18 Binding Protein in Complex with Human IL-18

Components

14L protein
Interleukin-18Interleukin 18

Keywords

CYTOKINE/Viral protein /

Binding Protein / beta trefoil / Immunoglobulin fold / YLDV / Yaba /

yatapoxvirus / 14L / Cytokine Signaling / CYTOKINE-Viral protein complex

Function / homology

Function and homology information

interleukin-18 receptor binding / Interleukin-18 signaling / positive regulation of tissue remodeling / positive regulation of T-helper 2 cell differentiation / positive regulation of T-helper 1 cell cytokine production / positive regulation of macrophage derived foam cell differentiation /

neutrophil activation / positive regulation of neuroinflammatory response / interleukin-18-mediated signaling pathway / natural killer cell mediated cytotoxicity ...

interleukin-18 receptor binding / Interleukin-18 signaling / positive regulation of tissue remodeling / positive regulation of T-helper 2 cell differentiation / positive regulation of T-helper 1 cell cytokine production / positive regulation of macrophage derived foam cell differentiation /

neutrophil activation / positive regulation of neuroinflammatory response / interleukin-18-mediated signaling pathway / natural killer cell mediated cytotoxicity / triglyceride homeostasis / negative regulation of myoblast differentiation / type 2 immune response / natural killer cell activation /

sleep / Interleukin-1 processing / positive regulation of NK T cell proliferation / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of interleukin-13 production / T-helper 1 type immune response / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / Interleukin-10 signaling / positive regulation of natural killer cell proliferation / establishment of skin barrier /

Pyroptosis /

Purinergic signaling in leishmaniasis infection /

regulation of cell adhesion / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / cholesterol homeostasis /

cytokine activity / positive regulation of smooth muscle cell proliferation / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of type II interferon production / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / positive regulation of cold-induced thermogenesis /

peptidase activity /

angiogenesis / Interleukin-4 and Interleukin-13 signaling / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / defense response to Gram-positive bacterium /

inflammatory response / protein serine/threonine kinase activity / positive regulation of transcription by RNA polymerase II /

proteolysis /

extracellular space / extracellular region /

cytosol
Similarity search - Function

Biological species

Yaba-like disease virus

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

molecular replacement / Resolution: 1.75 Å

Authors

Krumm, B.E. / Xiang, Y. / Deng, J.

Citation

Journal: Plos Pathog. / Year: 2012
Title: A unique bivalent binding and inhibition mechanism by the yatapoxvirus interleukin 18 binding protein.
Authors: Krumm, B. / Meng, X. / Wang, Z. / Xiang, Y. / Deng, J.

History

Deposition	Apr 10, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 26, 2012	Provider: repository / Type: Initial release
Revision 1.1	Oct 3, 2012	Group: Data collection
Revision 1.2	Nov 15, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4ekx.cif.gz	219.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4ekx.ent.gz	188.2 KB	Display	PDB format
PDBx/mmJSON format	4ekx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ek/4ekx ftp://data.pdbj.org/pub/pdb/validation_reports/ek/4ekx	HTTPS FTP

-
Related structure data

Related structure data	4eeeC C: citing same article (ref.)
Similar structure data	4iod-d 4muk-2 1y4h-3 4lvq-d 5j39-d 2h02-d 2fcw-2 5l7n-d 4ndk-d 5iit-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) 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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (7) #56 - Aug 2004 Caspases similarity (3) #122 - Feb 2010 Enhanceosome similarity (3) #224 - Aug 2018 Legumain similarity (3) #79 - Jul 2006 Amyloid-beta Precursor Protein similarity (1) #189 - Sep 2015 Amyloids similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #267 - Mar 2022 Vascular Endothelial Growth Factor (VegF similarity (1) #202 - Oct 2016 Dipeptidyl Peptidase 4 similarity (1) #213 - Sep 2017 Sirtuins similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#21 - Sep 2001
Antibodies
similarity (1)
#256 - Apr 2021
SARS-CoV-2 Spike and Antibodies
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (7)
#56 - Aug 2004
Caspases
similarity (3)
#122 - Feb 2010
Enhanceosome
similarity (3)
#224 - Aug 2018
Legumain
similarity (3)
#79 - Jul 2006
Amyloid-beta Precursor Protein
similarity (1)
#189 - Sep 2015
Amyloids
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#267 - Mar 2022
Vascular Endothelial Growth Factor (VegF
similarity (1)
#202 - Oct 2016
Dipeptidyl Peptidase 4
similarity (1)
#213 - Sep 2017
Sirtuins
similarity (1)
#221 - May 2018
Human Papillomavirus and Vaccines
similarity (1)
#234 - Jun 2019
MDM2 and Cancer
similarity (1)
#233 - May 2019
S-Nitrosylated Hemoglobin
similarity (1)
#261 - Sep 2021
DNA-Sequencing Nanopores
similarity (1)

Deposited unit

C: 14L protein

B: Interleukin-18

D: Interleukin-18

A: 14L protein

63.4 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

2

C: 14L protein

D: Interleukin-18

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

3

B: Interleukin-18

A: 14L protein

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

Unit cell

Length a, b, c (Å)	75.363, 41.156, 100.843
Angle α, β, γ (deg.)	90.000, 97.900, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	14L protein Mass: 13732.985 Da / Num. of mol.: 2 / Fragment: UNP residues 22-136 / Mutation: C67S, C112S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yaba-like disease virus / Gene: 14L / Plasmid: pSKB3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-Gami 2 / References: UniProt: Q9DHU8
#2: Protein	Interleukin-18 / Interleukin 18 / IL-18 / Iboctadekin / Interferon gamma-inducing factor / IFN-gamma-inducing factor / Interleukin-1 ...IL-18 / Iboctadekin / Interferon gamma-inducing factor / IFN-gamma-inducing factor / Interleukin-1 gamma / IL-1 gamma Mass: 17959.145 Da / Num. of mol.: 2 / Mutation: C38S, K67A, C68S, E69A, K70A, I71A, C76S, C127S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGIF, IL-18, IL18, IL1F4 / Plasmid: pSKB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q14116
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.44 Å³/Da / Density % sol: 49.67 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 8 Details: 12% PEG 3350, pH 8.0, vapor diffusion, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.075 Å / Relative weight: 1
Reflection	Resolution: 1.75→50 Å / Num. all: 61263 / Num. obs: 61221 / B_iso Wilson estimate: 30.1 Å²

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
PHASER		phasing
PHENIX	1.7.1_743	refinement
PDB_EXTRACT	3.11	data extraction
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Resolution: 1.75→33.21 Å / SU ML: 0.53 / σ(F): 1.34 / Phase error: 26.1 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.231	3083	5.04 %
R_work	0.19	-	-
obs	0.192	61221	98 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 60.16 Å² / k_sol: 0.39 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.1612 Å²	0 Å²	-0.0894 Å²
2-	-	16.1153 Å²	0 Å²
3-	-	-	-10.9541 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→33.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4047	0	0	240	4287

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4188
X-RAY DIFFRACTION	f_angle_d	1.035	5641
X-RAY DIFFRACTION	f_dihedral_angle_d	12.202	1617
X-RAY DIFFRACTION	f_chiral_restr	0.068	627
X-RAY DIFFRACTION	f_plane_restr	0.005	724

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 (%)
1.75-1.7773	0.3657	107	0.3214	2479	X-RAY DIFFRACTION	92
1.7773-1.8064	0.3423	139	0.2882	2538	X-RAY DIFFRACTION	95
1.8064-1.8376	0.3323	141	0.2712	2622	X-RAY DIFFRACTION	98
1.8376-1.871	0.347	131	0.2533	2588	X-RAY DIFFRACTION	96
1.871-1.907	0.2763	147	0.2317	2643	X-RAY DIFFRACTION	100
1.907-1.9459	0.3188	130	0.215	2651	X-RAY DIFFRACTION	98
1.9459-1.9882	0.2458	139	0.2096	2606	X-RAY DIFFRACTION	98
1.9882-2.0345	0.2134	131	0.1912	2680	X-RAY DIFFRACTION	99
2.0345-2.0853	0.2035	140	0.1917	2594	X-RAY DIFFRACTION	98
2.0853-2.1417	0.2624	149	0.1918	2700	X-RAY DIFFRACTION	100
2.1417-2.2047	0.2457	136	0.1985	2625	X-RAY DIFFRACTION	99
2.2047-2.2758	0.2445	143	0.1996	2682	X-RAY DIFFRACTION	99
2.2758-2.3572	0.2287	125	0.1861	2661	X-RAY DIFFRACTION	99
2.3572-2.4515	0.2445	173	0.2007	2645	X-RAY DIFFRACTION	99
2.4515-2.5631	0.2315	131	0.2012	2694	X-RAY DIFFRACTION	100
2.5631-2.6981	0.223	151	0.2048	2682	X-RAY DIFFRACTION	100
2.6981-2.8671	0.2592	163	0.2071	2671	X-RAY DIFFRACTION	100
2.8671-3.0883	0.2344	148	0.195	2693	X-RAY DIFFRACTION	100
3.0883-3.3988	0.2224	156	0.1886	2700	X-RAY DIFFRACTION	100
3.3988-3.89	0.2219	148	0.18	2726	X-RAY DIFFRACTION	100
3.89-4.8984	0.1764	128	0.1405	2699	X-RAY DIFFRACTION	98
4.8984-33.206	0.2371	127	0.1992	2559	X-RAY DIFFRACTION	89

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	4.7194	1.4673	1.7175	2.2017	-0.355	4.9122	0.1074	-1.4034	0.6543	-0.0237	-0.2878	0.21	-0.9317	-1.6667	0.3161	0.3581	0.1296	0.0064	0.5671	-0.0919	0.3735	19.9753	-6.7013	-10.4704
2	3.3462	-0.4802	-0.8544	3.0153	1.2286	4.2336	-0.032	0.3415	-0.0469	-0.1424	0.1177	0.315	0.1913	-0.145	-0.0865	0.3258	0.0272	-0.0822	0.3664	-0.0034	0.3592	12.2758	-16.0925	-28.7503
3	3.1172	1.0144	3.224	1.3306	2.8695	7.4359	-0.0247	-0.5491	0.4802	0.1139	0.1326	-0.1025	-0.2441	-0.4936	-0.0004	0.318	0.0831	-0.0357	0.3583	-0.0818	0.3504	20.0987	-5.9507	-17.3477
4	5.5071	-3.2708	0.5141	1.9296	-0.2044	4.0115	-0.6713	0.065	2.0783	0.0393	-0.1112	-0.3281	-2.4857	-0.3786	0.7136	0.5692	0.1661	-0.1723	0.3734	-0.0495	0.682	29.2175	2.7073	-12.1814
5	2.5667	-0.827	-0.4339	4.4441	0.7662	2.2963	-0.0812	-0.1935	0.1004	-0.2377	0.1647	-0.5574	0.1056	0.1449	-0.081	0.2541	0.0818	-0.0055	0.2738	-0.0038	0.2963	28.8088	-15.0628	-19.1743
6	6.8043	-0.1131	-0.5199	4.3063	2.2649	1.9771	-0.0006	0.8315	0.4805	0.0268	0.3089	-0.0507	-0.7769	-0.2071	-0.1539	0.3166	0.0849	0.0055	0.2873	-0.0393	0.3512	33.1159	-18.9411	-27.3159
7	3.147	-0.7435	-0.2244	4.165	2.2016	3.4442	0.3812	0.7197	0.0625	-0.611	-0.3122	-0.1261	-0.2539	-0.0976	0.0074	0.3626	0.1334	-0.0239	0.3531	-0.0149	0.3038	25.8125	-12.2907	-29.8612
8	4.8416	2.5128	2.5869	6.2732	1.4892	5.773	-0.5967	0.1455	0.9531	-0.2068	0.606	-0.9636	-0.5097	0.9877	-0.5611	0.3498	0.0793	-0.089	0.2922	-0.0419	0.4835	23.0957	-0.5698	-21.2275
9	3.0612	0.3931	0.8983	2.1631	0.8493	3.4057	0.0782	0.0555	-0.3118	-0.2963	0.017	-0.2579	0.226	-0.1485	-0.0824	0.328	0.0227	-0.0357	0.2654	-0.0421	0.3404	20.9362	-20.2091	-29.8376
10	2.8109	2.1185	2.2709	3.837	3.5232	3.4114	0.0617	-0.2798	-0.253	-0.0572	0.0739	-0.0655	0.017	0.0064	-0.1066	0.3311	0.0253	-0.0418	0.2699	0.0014	0.3082	25.5925	-14.7542	-15.4694
11	9.3603	7.7684	7.1168	6.9555	6.2143	5.5092	0.3255	-1.0281	-0.0088	0.4734	-0.586	0.4514	0.4653	-0.5032	0.3515	0.3365	0.0097	0.0139	0.3262	0.0145	0.3298	20.9352	-16.9093	-14.4414
12	7.8384	-1.7412	0.1861	6.819	-1.2651	8.3828	-0.1364	-0.1999	-1.0342	0.4618	0.22	0.9322	0.6644	-0.737	-0.2941	0.3427	-0.0492	-0.0856	0.2705	0.064	0.496	10.982	-23.5274	-22.2775
13	0.7283	-0.8956	0.2235	1.6352	-0.9846	2.9155	-0.2664	-0.0583	0.0314	0.1094	0.2159	-0.2573	-0.4331	0.5068	-0.0142	0.3407	-0.0923	0.0096	0.4574	0.0162	0.3545	-5.5904	6.8284	-35.6785
14	1.4083	1.2036	0.883	2.6976	0.0492	4.8313	-0.1363	0.5196	0.3349	0.0671	0.2122	-0.0522	-0.7544	0.5462	-0.0754	0.427	-0.0537	-0.0067	0.37	0.083	0.3274	-9.0676	8.7261	-56.6596
15	2.6046	0.2372	0.0766	8.7657	0.3362	3.051	-0.4869	-0.0594	1.8789	0.9627	1.0696	1.4102	-1.4431	-0.9073	-0.7704	1.0146	0.2431	0.0936	0.5336	0.0693	0.9087	-18.4382	19.527	-51.7079
16	5.0097	2.4829	-2.4785	3.697	-0.5223	3.8717	0.3846	1.0803	1.4056	-0.2939	0.6833	-0.4498	-0.8477	0.7887	-0.9084	0.6559	-0.0207	0.0431	0.4265	0.0443	0.4487	-11.7121	13.4393	-57.5425
17	2.3286	-1.1163	-0.0152	4.6861	-4.1201	5.1806	-0.1994	0.1138	0.1106	-0.3693	0.2674	-0.1645	0.0082	-0.0081	-0.1159	0.3489	-0.0799	-0.0067	0.2922	-0.0277	0.3054	-8.2193	6.9886	-39.0342
18	2.4004	0.701	-0.5381	3.3345	-2.7123	4.7286	-0.0664	0.1679	0.2713	0.3115	0.0773	-0.0074	-0.6124	-0.2228	-0.0175	0.3813	0.0221	-0.0146	0.3192	-0.0145	0.3309	-13.1523	8.3863	-39.6382
19	3.8613	1.9581	0.5349	8.9448	5.2343	4.2834	0.0257	0.0732	0.4101	-0.8597	0.2047	0.6206	-1.5079	-1.794	-0.061	0.5255	0.2443	0.0359	0.4751	0.122	0.4974	-21.9428	11.2174	-41.9048
20	4.2256	-0.0168	-0.5381	2.5259	-1.5611	6.2705	-0.035	0.2972	-0.1313	0.0025	0.0927	0.155	0.2198	-0.1401	-0.0685	0.2227	0.0078	-0.0174	0.2162	0.048	0.2622	-11.6182	0.9239	-40.517
21	3.9843	-0.9003	-0.9937	3.3364	-0.1219	6.752	-0.0414	-0.0324	0.1204	-0.3899	0.4176	0.6426	0.7107	-1.2664	-0.3039	0.2842	-0.0713	-0.0389	0.3653	0.0939	0.3348	-19.7883	-1.0921	-44.902
22	3.8408	-1.2126	4.6183	6.9691	2.0322	7.3609	-0.0988	0.0999	2.6534	-0.5176	0.4753	0.4033	-1.4929	-2.0101	-0.0606	0.6169	0.14	-0.1365	0.7439	0.4036	0.7252	-21.64	10.4483	-62.3281
23	2.0926	0.1979	-1.2589	0.0308	-0.3232	3.0604	0.3615	0.6495	-0.4632	-0.4332	0.1284	0.2287	0.6979	-0.5375	-0.5438	0.3892	-0.0599	-0.1801	0.5038	0.0582	0.3854	-19.2504	0.495	-54.3976
24	7.8346	1.7237	2.3711	6.3932	0.9437	6.275	0.3825	0.0727	-0.1698	-0.3545	-0.1908	-0.4201	-0.1842	0.688	-0.1823	0.4398	0.0095	0.0416	0.4106	0.064	0.2985	-6.3785	3.1101	-52.2947
25	1.419	-0.2921	0.2474	8.349	1.6599	1.942	-0.1453	0.0987	0.0467	-0.2407	-0.3264	0.761	-0.4492	-0.8008	0.3964	0.3839	0.1443	-0.0515	0.3184	-0.045	0.3328	37.1408	-5.7873	-21.5393
26	9.1645	-1.0763	5.8919	3.6478	-2.676	4.8946	0.452	-0.438	-0.3578	-0.4219	0.0469	0.6322	-1.3792	-1.1266	-0.3894	0.4845	0.1527	0.0525	0.2553	0.0327	0.3589	41.4965	8.8345	-11.8901
27	4.4113	-0.2625	-0.2329	3.6466	0.9867	6.0702	0.3118	0.2755	0.7084	-0.3906	0.1645	-0.8488	-1.0927	0.1279	-0.2674	0.4288	-0.0027	0.1158	0.3579	-0.0003	0.4233	51.3534	10.5398	-8.1057
28	7.2933	0.2553	1.7643	9.7727	1.564	1.961	-0.0443	-0.1999	0.583	-0.5114	-1.1476	0.103	-0.839	0.6886	1.1403	0.7483	0.0875	-0.0153	0.6256	0.1018	0.4932	48.1214	17.6368	-15.8469
29	4.5357	3.5007	0.8894	2.9364	0.701	1.3853	0.2841	-0.1975	0.2814	0.3171	-0.458	0.5347	-0.1362	-0.1678	0.0948	0.3675	0.1421	0.0549	0.2333	0.0025	0.2392	39.713	-3.1835	-17.6072
30	1.895	2.7499	-1.2284	5.6321	0.3357	2.8564	0.0736	0.5819	0.3156	-0.2722	0.2956	0.0644	-0.5967	-0.4191	-0.3181	0.3366	0.1186	0.0372	0.2527	0.0452	0.3016	41.9723	-2.7871	-16.1728
31	4.4974	-1.1949	0.9235	7.2761	-1.1499	6.9468	0.289	-0.0393	0.1755	-0.9886	-0.2215	-1.8831	0.2057	0.8687	0.156	0.2768	0.0885	0.0997	0.3177	0.0026	0.5315	53.7639	-4.7134	-14.5664
32	1.9072	-0.4157	1.9772	4.7367	-4.3813	6.1985	-0.4876	1.0496	-0.2499	-0.1111	-0.8115	-0.877	0.0304	-0.6539	1.07	0.2297	-0.013	0.1152	0.5365	-0.04	0.4171	54.9387	-1.711	-17.0755
33	5.942	3.536	0.6922	8.5435	1.5768	2.5031	-0.1515	0.6904	-0.1669	-0.8927	0.4311	-0.6194	-0.3519	0.0413	-0.3358	0.4606	0.1007	0.119	0.2881	-0.0085	0.3213	45.2058	-9.3368	-23.8579
34	1.9876	0.6193	-0.3157	3.1749	1.4551	2.9524	0.1558	-0.4065	-0.2744	0.1103	-0.1512	-0.2628	0.0912	0.0211	0.0648	0.2937	0.0384	0.0028	0.2577	0.0397	0.3147	42.4764	-7.6607	-10.1526
35	3.9864	-0.5556	-3.8895	1.4952	0.7201	7.3752	0.2033	-1.4268	0.5428	0.4838	-0.8082	0.9253	-0.026	-1.9825	0.5604	0.3426	0.0031	0.0554	0.6425	-0.1781	0.4132	34.3355	2.905	-0.9489
36	2.9767	1.2123	0.644	1.8473	0.8783	2.8556	0.0982	-0.255	-0.5162	0.5837	-0.0194	-0.0834	0.5072	0.1263	-0.0713	0.3385	0.0771	-0.0002	0.2082	0.0587	0.3621	46.6003	-7.0368	-5.3698
37	2.5244	1.9356	-0.6336	1.7894	-1.3958	2.8734	0.8618	-0.2946	-0.4802	1.0424	-0.1711	-1.4694	-0.127	1.6338	-0.6544	0.3716	-0.1002	-0.0909	0.7565	-0.0664	0.7102	58.5685	7.7612	-1.1444
38	3.8647	-2.2636	-0.967	5.2855	2.8789	1.5668	-0.4044	-1.5846	0.056	1.3981	0.4747	-0.0882	0.6125	-1.0676	-0.0885	0.4545	0.0635	-0.0013	0.8487	0.1332	0.385	47.9471	-4.0971	2.1443
39	4.5594	1.2303	0.2995	4.7167	1.6301	6.3686	0.4506	0.4028	0.4212	-0.1265	-0.1899	0.1657	-0.9749	-0.2193	-0.2975	0.3621	0.0609	0.0697	0.3801	0.0021	0.3064	40.64	5.9366	-5.4276
40	2.4574	-0.2006	2.9729	3.1716	-0.4877	5.0292	0.5487	0.9091	-1.0158	-0.4113	0.2051	0.0065	0.5806	2.2705	-0.6896	0.3848	0.1367	-0.0274	0.6368	-0.086	0.3899	4.7978	-11.0548	-34.9249
41	2.1248	-1.4654	-0.5893	2.4244	-0.3839	3.5421	-0.2972	-0.7302	-0.0027	0.377	0.2475	-0.2192	-0.2357	-0.2865	0.0078	0.3062	0.1041	-0.0569	0.506	0.0018	0.3114	9.4383	-8.8804	-16.1694
42	0.8586	-0.1202	1.7278	4.3202	-1.8205	4.1367	0.1753	1.5477	-0.3123	-0.2307	-0.3874	-0.7323	0.0179	0.2983	0.4656	0.3004	0.1615	0.0512	0.7418	-0.004	0.2657	6.0638	-6.5223	-36.1872
43	7.1467	-3.4855	0.5288	2.696	0.7037	3.0211	0.155	1.5251	0.9113	-1.026	-0.8421	-1.4598	0.4565	1.9895	0.6184	0.4332	0.1061	0.0928	0.882	0.1796	0.527	2.132	0.7726	-43.4742
44	3.8988	-0.2285	-1.5937	2.2852	-0.427	3.5085	-0.1814	0.293	-0.1503	0.1457	0.3395	0.2943	-0.0425	-0.9581	-0.1891	0.2586	0.0328	0.0065	0.412	0.0353	0.3125	-5.2367	-5.5278	-26.1375
45	2.689	-1.0892	-0.3887	2.4525	-0.7623	9.3591	-0.4867	-1.6446	0.9382	0.6396	0.3136	-0.2466	-1.0345	-0.4488	0.1628	0.4876	0.1824	0.0228	0.7861	-0.0499	0.3398	-7.6267	0.3124	-15.7304
46	7.7829	0.0174	-2.8356	5.6992	-2.7163	2.4419	-0.0734	-0.3221	1.4263	0.0026	0.6453	-0.1654	-0.418	-0.4243	-0.2853	0.3899	0.0474	-0.0326	0.4512	-0.0631	0.4089	2.8136	1.2232	-22.0579
47	8.5136	-0.8379	-0.6982	7.8371	1.1105	2.0342	-0.2118	1.701	0.0618	-1.3458	-0.1123	-0.9359	1.129	0.5448	0.3877	0.4322	0.0227	0.0919	0.5355	0.0695	0.3956	7.4826	-2.5748	-32.5269
48	3.0286	-0.3316	-0.1627	3.4378	-0.8448	4.0996	-0.1974	-1.1789	0.0802	0.8125	0.4548	0.2432	-0.1816	-0.7414	-0.2395	0.379	0.1884	0.0156	0.7819	0.046	0.3217	0.7043	-6.8264	-12.3569
49	3.3534	-1.2251	-0.3421	1.6072	-1.0411	4.6992	-0.0614	-0.2626	-0.5046	0.0149	0.1191	0.2079	0.3931	-0.1848	-0.0527	0.2985	0.0153	-0.0184	0.3377	0.0802	0.3434	-2.4428	-9.9153	-26.9683
50	2.5055	-1.3031	1.5989	3.1126	-3.1097	3.1747	0.3979	-0.0325	-0.6004	-0.3328	0.0868	0.3849	1.5635	-0.1172	-0.2598	0.3781	0.0564	-0.0329	0.3805	0.0785	0.3866	-1.0482	-13.9161	-26.9126
51	5.0851	-3.6661	-0.7983	6.6949	-3.3585	7.8346	-0.5312	-1.4459	-1.5442	-0.1021	-0.0016	0.026	2.2729	0.1495	0.1	0.401	0.0688	-0.0353	0.5507	0.233	0.5758	6.3231	-19.2542	-14.5796

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain C and resid 24:29)
2	X-RAY DIFFRACTION	2	(chain C and resid 30:39)
3	X-RAY DIFFRACTION	3	(chain C and resid 40:48)
4	X-RAY DIFFRACTION	4	(chain C and resid 49:53)
5	X-RAY DIFFRACTION	5	(chain C and resid 54:62)
6	X-RAY DIFFRACTION	6	(chain C and resid 63:70)
7	X-RAY DIFFRACTION	7	(chain C and resid 71:79)
8	X-RAY DIFFRACTION	8	(chain C and resid 80:92)
9	X-RAY DIFFRACTION	9	(chain C and resid 93:104)
10	X-RAY DIFFRACTION	10	(chain C and resid 105:119)
11	X-RAY DIFFRACTION	11	(chain C and resid 120:125)
12	X-RAY DIFFRACTION	12	(chain C and resid 126:132)
13	X-RAY DIFFRACTION	13	(chain B and resid 1:11)
14	X-RAY DIFFRACTION	14	(chain B and resid 12:21)
15	X-RAY DIFFRACTION	15	(chain B and resid 22:27)
16	X-RAY DIFFRACTION	16	(chain B and resid 28:33)
17	X-RAY DIFFRACTION	17	(chain B and resid 44:56)
18	X-RAY DIFFRACTION	18	(chain B and resid 57:77)
19	X-RAY DIFFRACTION	19	(chain B and resid 78:86)
20	X-RAY DIFFRACTION	20	(chain B and resid 87:115)
21	X-RAY DIFFRACTION	21	(chain B and resid 116:127)
22	X-RAY DIFFRACTION	22	(chain B and resid 128:133)
23	X-RAY DIFFRACTION	23	(chain B and resid 134:146)
24	X-RAY DIFFRACTION	24	(chain B and resid 147:155)
25	X-RAY DIFFRACTION	25	(chain D and resid 1:8)
26	X-RAY DIFFRACTION	26	(chain D and resid 9:13)
27	X-RAY DIFFRACTION	27	(chain D and resid 14:33)
28	X-RAY DIFFRACTION	28	(chain D and resid 34:44)
29	X-RAY DIFFRACTION	29	(chain D and resid 45:56)
30	X-RAY DIFFRACTION	30	(chain D and resid 57:69)
31	X-RAY DIFFRACTION	31	(chain D and resid 70:80)
32	X-RAY DIFFRACTION	32	(chain D and resid 81:85)
33	X-RAY DIFFRACTION	33	(chain D and resid 86:94)
34	X-RAY DIFFRACTION	34	(chain D and resid 95:107)
35	X-RAY DIFFRACTION	35	(chain D and resid 108:113)
36	X-RAY DIFFRACTION	36	(chain D and resid 114:127)
37	X-RAY DIFFRACTION	37	(chain D and resid 128:135)
38	X-RAY DIFFRACTION	38	(chain D and resid 136:146)
39	X-RAY DIFFRACTION	39	(chain D and resid 147:156)
40	X-RAY DIFFRACTION	40	(chain A and resid 24:29)
41	X-RAY DIFFRACTION	41	(chain A and resid 30:42)
42	X-RAY DIFFRACTION	42	(chain A and resid 43:48)
43	X-RAY DIFFRACTION	43	(chain A and resid 49:52)
44	X-RAY DIFFRACTION	44	(chain A and resid 53:64)
45	X-RAY DIFFRACTION	45	(chain A and resid 65:72)
46	X-RAY DIFFRACTION	46	(chain A and resid 73:80)
47	X-RAY DIFFRACTION	47	(chain A and resid 89:93)
48	X-RAY DIFFRACTION	48	(chain A and resid 94:104)
49	X-RAY DIFFRACTION	49	(chain A and resid 105:117)
50	X-RAY DIFFRACTION	50	(chain A and resid 118:127)
51	X-RAY DIFFRACTION	51	(chain A and resid 128:132)

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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