PDB-8v06: Crystal structure of mouse PLD3 co-crystallized with 5'Pi-ssDNA f...

ID or keywords:

Entry

Database: PDB / ID: 8v06

Title

Crystal structure of mouse PLD3 co-crystallized with 5'Pi-ssDNA for 9 days

Components

(5'-3' exonuclease ...) x 2

Keywords

HYDROLASE / PLD3 / phospholipase / phosphohistidine / nuclease

Function / homology

Function and homology information

spleen exonuclease / single-stranded DNA 5'-3' DNA exonuclease activity / myotube differentiation / Role of phospholipids in phagocytosis / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phospholipase D activity / regulation of cytokine production involved in inflammatory response / lysosomal lumen / lipid metabolic process / late endosome membrane ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.73 Å

Authors

Yuan, M. / Wilson, I.A.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	AI142945	United States
National Institutes of Health/National Institute on Aging (NIH/NIA)	AG070775	United States

Citation

Journal: Structure / Year: 2024
Title: Structural and mechanistic insights into disease-associated endolysosomal exonucleases PLD3 and PLD4.
Authors: Yuan, M. / Peng, L. / Huang, D. / Gavin, A. / Luan, F. / Tran, J. / Feng, Z. / Zhu, X. / Matteson, J. / Wilson, I.A. / Nemazee, D.

History

Deposition	Nov 17, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 13, 2024	Provider: repository / Type: Initial release
Revision 1.1	Apr 17, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jun 19, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8v06.cif.gz	661.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8v06.ent.gz	544.4 KB	Display	PDB format
PDBx/mmJSON format	8v06.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v0/8v06 ftp://data.pdbj.org/pub/pdb/validation_reports/v0/8v06	HTTPS FTP

-
Related structure data

Related structure data	8v05C 8v07C 8v08C C: citing same article (ref.)
Similar structure data	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) #182 - Feb 2015 Insulin receptor similarity (1) #76 - Apr 2006 Hemagglutinin similarity (1)

Deposited unit

A: 5'-3' exonuclease PLD3

B: 5'-3' exonuclease PLD3

C: 5'-3' exonuclease PLD3

D: 5'-3' exonuclease PLD3

hetero molecules

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

1

A: 5'-3' exonuclease PLD3

B: 5'-3' exonuclease PLD3

hetero molecules

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

2

C: 5'-3' exonuclease PLD3

D: 5'-3' exonuclease PLD3

hetero molecules

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

Unit cell

Length a, b, c (Å)	54.155, 54.191, 202.774
Angle α, β, γ (deg.)	96.61, 89.16, 90.10
Int Tables number	1
Space group name H-M	P1

-
5'-3' exonuclease ... , 2 types, 4 molecules ACBD

#1: Protein	5'-3' exonuclease PLD3 Mass: 51935.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pld3 / Production host: Homo sapiens (human) / References: UniProt: O35405
#2: Protein	5'-3' exonuclease PLD3 Mass: 51856.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pld3 / Production host: Homo sapiens (human) / References: UniProt: O35405

-
Sugars , 4 types, 8 molecules

#3: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}	LINUCS	PDB-CARE

#4: Polysaccharide

beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...

Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}	LINUCS	PDB-CARE

#5: Polysaccharide

alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...

Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}	LINUCS	PDB-CARE

#6: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

-
Non-polymers , 2 types, 189 molecules

#7: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.85 Å³/Da / Density % sol: 56.84 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 1.6 M ammonium sulfate, 0.5 mM magnesium chloride, 0.1 M citric acid, pH 4.0

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 1.0332 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.0332 Å / Relative weight: 1

Reflection

Resolution: 2.73→60 Å / Num. obs: 57208 / % possible obs: 95.5 % / Redundancy: 3 % / CC_1/2: 0.967 / CC star: 0.992 / R_merge(I) obs: 0.121 / R_pim(I) all: 0.08 / R_rim(I) all: 0.146 / Χ²: 1.749 / Net I/σ(I): 7.6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.75-2.8	1.9	0.424	2215	0.592	0.862	0.34	0.546	0.844	75.9
2.8-2.85	2.1	0.373	2613	0.657	0.891	0.28	0.469	0.913	84.1
2.85-2.9	2.4	0.352	2596	0.711	0.912	0.252	0.435	0.885	88.9
2.9-2.96	2.6	0.333	2781	0.724	0.917	0.233	0.409	0.936	92.1
2.96-3.03	2.9	0.279	2918	0.83	0.952	0.19	0.339	1.001	95.6
3.03-3.1	3	0.262	2804	0.838	0.955	0.172	0.315	1.049	96.9
3.1-3.17	3.1	0.234	2997	0.884	0.969	0.153	0.281	1.114	97.4
3.17-3.26	3	0.219	2871	0.882	0.968	0.149	0.266	1.179	98.4
3.26-3.36	3.1	0.185	2988	0.909	0.976	0.125	0.225	1.323	97.6
3.36-3.46	3.2	0.164	2928	0.934	0.983	0.108	0.197	1.454	98.6
3.46-3.59	3.1	0.143	2961	0.944	0.985	0.097	0.173	1.714	98.1
3.59-3.73	3.4	0.13	2896	0.963	0.99	0.082	0.154	1.783	98.7
3.73-3.9	3.5	0.12	3050	0.97	0.992	0.075	0.142	1.848	98.6
3.9-4.11	3.4	0.105	2880	0.975	0.994	0.067	0.125	2.129	98.4
4.11-4.36	3.3	0.095	2926	0.978	0.994	0.061	0.113	2.265	98.5
4.36-4.7	3.1	0.086	2953	0.978	0.995	0.058	0.105	2.521	98.3
4.7-5.17	3.1	0.08	2942	0.979	0.995	0.055	0.098	2.584	98.1
5.17-5.92	3.2	0.087	2994	0.983	0.996	0.058	0.105	2.35	98.7
5.92-7.46	3.4	0.083	2939	0.986	0.996	0.052	0.099	2.237	98.6
7.46-60	3.3	0.056	2956	0.994	0.998	0.037	0.068	2.693	98.4

-
Processing

Software

Name	Version	Classification
PHENIX	(1.19.2_4158: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.73→49.92 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 32.55 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2954	2641	4.62 %
R_work	0.2552	-	-
obs	0.2572	57195	93.83 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.73→49.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12941	0	269	187	13397

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	13504
X-RAY DIFFRACTION	f_angle_d	0.639	18425
X-RAY DIFFRACTION	f_dihedral_angle_d	6.491	1946
X-RAY DIFFRACTION	f_chiral_restr	0.044	2102
X-RAY DIFFRACTION	f_plane_restr	0.005	2349

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 (%)
2.73-2.78	0.4098	74	0.3239	1420	X-RAY DIFFRACTION	48
2.78-2.83	0.3558	144	0.306	2608	X-RAY DIFFRACTION	82
2.83-2.89	0.4088	113	0.3027	2682	X-RAY DIFFRACTION	89
2.89-2.95	0.306	130	0.2861	2868	X-RAY DIFFRACTION	92
2.95-3.02	0.3474	119	0.2792	2948	X-RAY DIFFRACTION	96
3.02-3.1	0.3086	109	0.2725	2923	X-RAY DIFFRACTION	97
3.1-3.18	0.3495	138	0.2834	3110	X-RAY DIFFRACTION	98
3.18-3.27	0.3182	112	0.2814	2942	X-RAY DIFFRACTION	98
3.27-3.38	0.3222	145	0.2737	3047	X-RAY DIFFRACTION	98
3.38-3.5	0.2977	175	0.2571	2936	X-RAY DIFFRACTION	99
3.5-3.64	0.292	156	0.2441	3060	X-RAY DIFFRACTION	98
3.64-3.8	0.2853	147	0.2494	2976	X-RAY DIFFRACTION	98
3.8-4.01	0.2888	200	0.2324	2946	X-RAY DIFFRACTION	99
4.01-4.26	0.3227	121	0.231	3054	X-RAY DIFFRACTION	98
4.26-4.58	0.2356	161	0.2264	2996	X-RAY DIFFRACTION	98
4.58-5.05	0.2488	148	0.2105	3011	X-RAY DIFFRACTION	98
5.05-5.77	0.253	136	0.245	3007	X-RAY DIFFRACTION	99
5.77-7.27	0.2999	145	0.2693	3014	X-RAY DIFFRACTION	99
7.27-49.92	0.2915	168	0.2737	3006	X-RAY DIFFRACTION	98

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	0.0434	0.1093	-0.0537	0.2645	-0.1283	0.0981	-0.13	-0.008	0.0208	0.0998	0.0399	0.1094	0.0517	-0.0002	-0.2509	0.4173	0.032	-0.0066	-0.1116	0.0653	0.1822	9.0799	31.0024	-50.7224
2	0.1387	-0.2195	-0.096	0.3641	-0.0093	1.5154	-0.0137	0.0112	0.1065	0.1406	0.0618	-0.1726	-0.137	0.0376	0.6474	0.2476	-0.0393	-0.1704	0.0569	0.0352	0.2513	24.4684	34.9366	-52.7059
3	0.0061	-0.0582	-0.0006	0.2258	0.0382	0.0425	-0.0825	-0.0645	-0.1291	0.0753	-0.1158	-0.0933	0.2311	0.1132	-0.2665	0.2613	0.0273	0.0532	-0.0692	0.1545	0.1792	16.5839	21.5469	-60.6448
4	0.1721	-0.2426	0.0595	0.4012	0.0629	0.3649	0.0306	0.0537	0.1033	-0.1184	0.0282	-0.0795	-0.0282	0.022	0.748	0.2171	-0.037	0.0585	-0.0278	0.0893	0.0545	6.3059	25.8409	-77.4836
5	0.3209	0.0005	0.0764	0.1891	-0.1053	0.3085	-0.0296	-0.0317	0.0308	0.0764	-0.0458	-0.0234	-0.0781	-0.0184	-0.1052	0.1379	-0.0759	0.0172	-0.0578	0.0367	0.195	0.2606	31.5564	-74.2615
6	0.4762	-0.0717	0.0096	0.3688	0.3163	0.2763	-0.0393	0.0962	0.0864	-0.1276	0.035	0.0194	-0.0513	-0.0427	-0.0622	0.0605	-0.0356	0.0797	0.1072	0.0878	0.0175	-5.4323	30.4812	-67.2552
7	0.7965	-0.0991	-0.0522	0.2433	-0.0259	0.1557	-0.0277	-0.1019	-0.1598	0.0669	-0.1038	-0.0337	0.1068	0.0325	-0.1945	-0.1775	0.0412	-0.0513	0.2111	-0.0089	0.0939	3.7172	15.4559	-120.7204
8	1.5524	-0.9659	0.0458	2.2029	-1.1373	3.0517	0.0918	-0.1081	-0.3356	0.3388	-0.2017	-0.0686	0.0929	-0.0918	0.0329	0.1699	-0.0427	-0.0079	0.0666	-0.0082	0.1609	4.0438	23.4936	-99.6719
9	0.5839	0.0513	0.0943	0.2289	-0.0016	0.207	-0.0722	0.1587	-0.0526	0.0472	0.0015	0.0548	0.047	-0.0244	-0.1586	-0.0846	-0.006	-0.0211	0.069	-0.0149	0.18	-1.6797	29.6323	-102.8341
10	1.0165	0.1331	0.2327	0.3416	0.0561	0.2357	-0.0362	-0.2348	0.1435	0.0518	0.0122	0.004	-0.0074	-0.0504	0.1033	-0.0265	-0.052	-0.1028	0.2004	0.0465	0.0755	-0.6255	35.2313	-109.8754
11	1.6628	1.2326	-0.557	1.9148	0.3412	1.4992	0.2423	-0.1175	0.309	0.1541	-0.2484	0.0377	-0.0526	0.0022	-0.0343	0.2922	0.1162	-0.0395	0.566	-0.1918	0.3416	-5.1092	17.634	-151.3288
12	1.1557	0.1975	-0.5312	0.7658	0.2341	1.3966	-0.1533	-0.0558	0.1784	-0.2227	-0.0477	0.1888	-0.0533	0.096	0.1048	0.2493	0.0715	-0.0785	0.3654	-0.2139	0.4047	5.287	22.2652	-160.9061
13	2.063	0.2502	-0.9263	0.6298	-1.0704	4.938	0.0776	0.0161	0.311	-0.0339	-0.2705	0.2544	0.0981	-0.2847	-0.0855	0.255	-0.0615	0.102	0.4413	-0.281	0.4881	1.0028	12.2635	-177.9945
14	4.3009	0.2182	-1.1898	1.3741	0.4501	2.5818	0.5741	-0.367	-0.1104	-0.476	-0.3853	0.1023	-0.4766	0.1017	-0.221	0.4048	0.0852	-0.0136	0.4078	-0.132	0.3915	-2.8577	2.6383	-181.0271
15	1.7257	-1.2715	-0.769	2.9816	0.6855	2.5648	0.1441	0.1249	-0.0118	-0.2749	0.0953	0.0506	0.0017	-0.0932	-0.2253	0.3325	0.0969	-0.0773	0.561	-0.0666	0.1896	-6.9559	10.4551	-166.9034
16	2.9663	1.7819	0.9434	3.1986	1.2466	2.9264	0.1064	-0.011	-0.3849	0.1862	-0.0487	-0.1557	0.3739	0.1272	-0.0592	0.2964	0.0609	0.047	0.174	-0.0763	0.0847	-3.6768	0.3499	-167.8485
17	0.5517	-0.1883	-0.0601	0.0636	0.034	0.5474	-0.1146	0.06	-0.0368	-0.3994	0.1779	-0.1885	-0.1546	0.004	0.0336	0.7413	0.0523	0.0181	0.2935	-0.1642	0.4015	5.6712	4.7812	-227.0184
18	1.4793	0.6156	-0.5798	1.4163	-0.688	1.2776	0.0502	-0.2139	0.0707	-0.1214	-0.4341	-0.0221	-0.1902	0.0406	0.2077	0.5991	0.0497	-0.0374	0.3098	-0.1081	0.3853	14.5987	12.6003	-218.2386
19	2.5125	1.9539	0.3452	1.6396	0.9451	5.0066	-0.1135	0.309	-0.342	-0.231	-0.0213	0.2895	0.5105	0.6825	0.0983	0.5615	0.0051	0.016	0.422	-0.2383	0.4105	3.3346	10.2145	-200.1681
20	1.4065	-0.294	-0.3594	2.2708	-0.6171	1.2168	-0.1879	-0.0983	-0.1102	-0.003	0.0512	-0.0569	0.1055	-0.1216	0.1035	0.424	0.0252	-0.0606	0.3899	-0.148	0.2683	-3.7635	6.6769	-205.5605
21	4.7274	-1.6098	3.5228	2.7808	-0.6218	3.7732	0.2153	0.0277	-0.5321	0.7542	-0.3626	0.7316	0.8507	-0.1464	0.2613	1.0552	-0.1772	-0.1356	0.4653	-0.1498	0.5289	-10.364	-7.6861	-205.0863

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 72 through 157 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 158 through 180 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 181 through 304 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 305 through 341 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 342 through 440 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 441 through 488 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 72 through 304 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 305 through 341 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 342 through 440 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 441 through 488 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 73 through 180 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 181 through 304 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 305 through 341 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 342 through 396 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 397 through 440 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 441 through 488 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 73 through 157 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 158 through 304 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 305 through 341 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 342 through 467 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 468 through 488 )

-
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

-
5'-3' exonuclease ... , 2 types, 4 molecules ACBD

-
Sugars , 4 types, 8 molecules

-
Non-polymers , 2 types, 189 molecules

-
Details

-
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

-5'-3' exonuclease ... , 2 types, 4 molecules ACBD

-Sugars , 4 types, 8 molecules

-Non-polymers , 2 types, 189 molecules

-Details

-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

-
5'-3' exonuclease ... , 2 types, 4 molecules ACBD

-
Sugars , 4 types, 8 molecules

-
Non-polymers , 2 types, 189 molecules

-
Details

-
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