PDB-2huz: Crystal structure of GNPNAT1

ID or keywords:

Entry

Database: PDB / ID: 2huz

Title

Crystal structure of GNPNAT1

Components

Glucosamine 6-phosphate N-acetyltransferase

Keywords

Structural Genomics / transferase / acetyltransferase / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

glucosamine-phosphate N-acetyltransferase / glucosamine 6-phosphate N-acetyltransferase activity / Synthesis of UDP-N-acetyl-glucosamine / UDP-N-acetylglucosamine biosynthetic process / endoplasmic reticulum-Golgi intermediate compartment / cellular response to leukemia inhibitory factor / late endosome / endosome membrane / Golgi membrane / identical protein binding / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.67 Å

Authors

Min, J. / Wu, H. / Zeng, H. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)

Citation

Journal: To be Published
Title: Crystal structure of glucosamine-phosphate N-acetyltransferase 1
Authors: Wu, H. / Min, J. / Zeng, H. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N.

History

Deposition	Jul 27, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 8, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Feb 14, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2huz.cif.gz	84.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2huz.ent.gz	67 KB	Display	PDB format
PDBx/mmJSON format	2huz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2huz_validation.pdf.gz	432.7 KB	Display	wwPDB validaton report
Full document	2huz_full_validation.pdf.gz	439.3 KB	Display
Data in XML	2huz_validation.xml.gz	15.6 KB	Display
Data in CIF	2huz_validation.cif.gz	20.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hu/2huz ftp://data.pdbj.org/pub/pdb/validation_reports/hu/2huz	HTTPS FTP

-
Related structure data

Related structure data	2o28
Similar structure data	1ye3-d 4h2e-d 3cxs-1 7adh-d 6mww-d 1adf-d 5vjg-d 6d6m-1 8adh-d 5nv8-d 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	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (4) #97 - Jan 2008 Circadian Clock Proteins similarity (4)

Deposited unit

A: Glucosamine 6-phosphate N-acetyltransferase

B: Glucosamine 6-phosphate N-acetyltransferase

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	111.668, 47.645, 84.843
Angle α, β, γ (deg.)	90.00, 123.52, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-203- HOH

#1: Protein	Glucosamine 6-phosphate N-acetyltransferase / Phosphoglucosamine transacetylase / Phosphoglucosamine acetylase Mass: 20776.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GNPNAT1, GNA1 / Production host: Escherichia coli (E. coli) References: UniProt: Q96EK6, glucosamine-phosphate N-acetyltransferase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Glucosamine 6-phosphate N-acetyltransferase / Phosphoglucosamine transacetylase / Phosphoglucosamine acetylase

Mass: 20776.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: GNPNAT1, GNA1 / Production host:

Escherichia coli (E. coli)
References: UniProt: Q96EK6, glucosamine-phosphate N-acetyltransferase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.26 Å³/Da / Density % sol: 45.65 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% PEG4K, 0.2M NH4SO4, 0.1M Na Acetate pH4.6, 0.1M Yttrium Chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

-
Data collection

Diffraction source	Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
Detector	Type: RIGAKU / Detector: IMAGE PLATE / Date: Jul 23, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.67→70.71 Å / Num. obs: 10107 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 2.67→2.8 Å / % possible all: 94.7

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.67→70.71 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.879 / SU B: 35.443 / SU ML: 0.35 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.44 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29841	510	4.8 %	RANDOM
R_work	0.20011	-	-	-
obs	0.2048	10107	98.77 %	-
all	-	10107	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 29.419 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.51 Å²	0 Å²	1.77 Å²
2-	-	0.61 Å²	0 Å²
3-	-	-	-1.18 Å²

Refinement step

Cycle: LAST / Resolution: 2.67→70.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2876	0	0	41	2917

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	2936
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.313	1.978	3968
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.649	5	362
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.311	24.167	120
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.665	15	536
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.937	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	456
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	2150
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	1420
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.307	0.2	2053
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.171	0.2	112
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.29	0.2	40
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.3	0.2	3
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.436	1.5	1857
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.767	2	2954
X-RAY DIFFRACTION	r_scbond_it	0.956	3	1199
X-RAY DIFFRACTION	r_scangle_it	1.562	4.5	1014
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.67→2.742 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.381	37	-
R_work	0.309	659	-
obs	-	-	89.12 %

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	4.7088	-4.4663	-9.5679	4.2363	9.0752	19.4414	-0.1086	-0.4245	0.4611	0.6037	0.5438	0.0249	-0.5488	0.2531	-0.4353	0.3251	-0.049	0.0096	0.3174	0.013	0.2782	15.3454	12.4199	28.1342
2	7.8378	6.5479	2.7063	7.6671	0.0587	6.2053	-0.2626	0.249	0.1501	-1.1897	-0.3027	0.1817	-0.2618	-0.5599	0.5654	0.1828	0.1077	-0.0699	0.2696	-0.0664	0.4211	1.9993	4.0414	16.0815
3	4.6218	-3.496	6.1829	9.7915	4.9248	21.1708	0.0209	-0.0398	0.1967	-0.0225	-0.8946	0.3668	0.1728	-1.2735	0.8736	0.0924	0.0296	0.0593	0.2796	-0.0175	0.4324	-3.6376	4.4187	25.6551
4	0.8792	2.1018	0.3269	5.0246	0.7814	0.1215	-0.2526	-1.0061	0.3101	0.3621	0.3062	0.0143	-0.2932	-0.258	-0.0536	0.3132	0.0556	0.0632	0.3831	0.0091	0.2769	12.4625	5.7884	34.4135
5	37.5036	3.9441	7.1222	42.5557	9.0325	2.9808	0.9197	-0.3322	-3.2225	0.6108	0.3166	-1.4836	0.6651	-0.1392	-1.2363	0.3143	0.1755	0.0467	0.4314	0.0237	0.3336	14.4242	-7.8747	36.5626
6	4.8338	2.0779	-7.2021	28.9451	-19.445	33.0645	-0.0421	-1.2024	0.0802	0.2411	0.2842	-2.0738	0.6894	0.3634	-0.2421	0.1762	0.0562	-0.0964	0.6086	-0.0883	0.1494	24.6987	1.8913	38.6191
7	8.0984	-0.5385	-3.4292	4.1787	0.0807	6.8258	-0.1569	-0.6257	0.3522	0.2013	0.2468	0.2031	-0.1112	0.345	-0.0899	0.3019	0.0446	-0.0106	0.2552	-0.0111	0.2324	15.473	5.0475	29.8022
8	2.2419	0.7449	0.8673	0.2475	0.2882	0.3356	-0.1819	0.3317	-0.3888	0.0165	-0.0895	-0.0096	0.0168	-0.1191	0.2714	0.3524	0.0071	0.0313	0.3223	0.0665	0.4079	20.3761	-0.415	16.7382
9	4.7267	-1.5494	-5.2118	1.5377	3.7706	9.8764	-0.0517	0.2468	0.1302	-0.4296	0.3676	0.2875	-0.2505	-0.3645	-0.3159	0.2977	0.0551	-0.0031	0.3668	0.0702	0.2525	22.1738	-1.7019	9.2074
10	8.512	3.5301	6.8085	2.5231	2.7245	5.4551	-1.5617	0.0089	-0.4743	0.5537	0.5349	-0.1252	0.994	-1.0408	1.0268	0.5488	0.1468	0.0367	0.2389	0.0386	0.2323	9.1493	-6.2898	31.6403
11	33.2987	0.736	-19.6031	0.4444	2.3384	29.4832	-0.3672	-0.1237	-0.9793	0.7406	0.265	0.2252	1.5321	-0.4861	0.1022	0.3537	-0.0062	0.105	0.1469	0.0215	0.5814	0.3046	-4.3496	28.5135
12	4.2493	0.4062	-2.3657	4.6721	1.8598	3.173	0.0659	0.0959	0.0051	-0.2966	-0.1436	0.0141	-0.2346	0.1712	0.0777	0.2703	0.0135	-0.0645	0.3447	0.038	0.2557	11.9967	-1.5649	14.6809
13	4.732	1.1508	-0.3713	2.842	-3.0616	7.1426	0.0304	-0.4023	-0.5899	-0.1573	0.0483	1.2408	0.6048	-0.4921	-0.0786	0.2465	-0.0135	0.0534	0.3664	-0.0757	0.4072	6.0321	-13.2451	17.7572
14	20.1543	-4.0401	6.0467	5.3013	-1.5022	2.9138	-0.3435	0.0399	-0.6611	-0.1015	0.0817	0.6487	0.199	-0.0382	0.2618	0.3556	-0.0434	0.0724	0.2615	-0.0281	0.1963	20.6271	-18.1567	15.2383
15	19.9954	2.8494	13.2944	13.2526	9.5539	13.4058	2.9354	-1.1238	-1.3262	4.6254	-0.3431	2.9512	1.7249	-1.4476	-2.5923	0.9502	0.0781	0.2098	0.4299	0.2952	0.4446	28.6319	-17.3449	29.8855
16	7.6759	-0.1392	-3.3758	9.9878	-8.4596	16.5132	0.1281	0.7525	0.8135	0.2037	-0.594	-1.0593	-0.7363	0.5752	0.4658	0.1707	0.0243	0.0101	0.3187	-0.0237	0.3281	42.7392	2.5927	12.8824
17	5.0901	0.0404	-2.1304	33.8781	1.0758	4.081	0.2497	-0.7255	-0.2646	0.397	-0.2957	-1.2241	0.2573	0.6168	0.046	0.1513	0.1007	-0.0355	0.403	-0.0113	0.2841	43.904	-14.5871	21.0908
18	0.9264	-1.7053	0.0312	4.2884	-1.7695	2.5519	-0.4204	0.038	-0.0731	-0.2712	0.1516	-0.8315	0.417	0.5122	0.2688	0.2462	0.1062	0.0343	0.3733	-0.0012	0.4098	48.0735	-18.3285	10.4203
19	2.1497	-1.0727	-1.1834	4.4943	-2.7194	3.4187	-0.0013	0.2332	0.1082	-0.3132	0.0933	-0.4149	-0.209	0.4609	-0.092	0.2153	-0.0204	0.0747	0.3606	-0.0747	0.2874	38.7956	-3.0125	3.126
20	2.0302	-2.4905	1.7473	7.0734	2.5181	9.727	-0.1956	0.7359	0.747	-0.8152	-0.012	0.6719	-0.7487	-0.3277	0.2076	0.3476	0.057	0.0635	0.3657	0.1784	0.2873	28.5757	2.631	0.9332
21	6.5621	-0.6152	-3.539	4.7944	-1.3279	11.6026	-0.3529	0.0325	0.7698	0.4637	0.2562	-0.2089	-0.723	-0.2312	0.0967	0.2378	0.0144	-0.0715	0.2841	-0.0154	0.3046	33.2674	2.7474	14.2881
22	2.6155	-1.8796	-1.4445	4.025	1.1078	3.2157	-0.1599	0.314	0.6165	-0.9112	0.2842	-0.6246	0.2513	0.514	-0.1242	0.3074	0.0288	0.0474	0.4135	-0.0283	0.2947	41.0783	-7.1411	4.6016
23	24.055	-0.3822	-3.6941	0.0061	0.0587	0.5673	-0.3879	-0.4149	-1.9654	0.2526	-0.0429	0.3719	-0.0103	0.9557	0.4308	0.4588	0.1712	0.066	0.4295	0.0517	0.2556	24.3121	-3.3434	27.3713
24	5.9297	-2.8602	-2.4643	10.4513	11.817	21.4409	-0.4536	-0.8018	0.122	1.0387	0.3394	0.0364	0.6521	0.3221	0.1142	0.3414	0.0912	-0.0359	0.3065	0.0621	0.271	26.1008	-7.1661	27.6361
25	6.3395	-2.4645	-9.2731	7.0868	1.9913	23.0357	0.1016	0.6126	-0.1435	-0.9389	0.2412	-0.6065	-0.1844	0.1727	-0.3428	0.3423	-0.0854	0.0479	0.3777	-0.0758	0.2378	33.8438	-12.35	4.1133
26	9.9565	-3.0559	-0.2955	6.3117	-1.5356	0.501	-0.0607	1.0087	-0.7608	-0.6909	-0.1459	0.2399	0.1979	0.068	0.2066	0.3158	0.1176	0.0065	0.3392	-0.0701	0.3903	39.5563	-17.7147	7.9949
27	2.6346	-0.8523	0.2806	3.6961	1.785	4.2118	-0.3591	-0.5392	-0.0913	0.3139	0.1667	-0.3216	0.2599	-0.0477	0.1924	0.3387	0.0631	0.0089	0.3443	0.0126	0.2617	31.1823	-12.9413	20.7389
28	1.0671	-1.1126	-3.1986	2.4282	2.5973	10.0174	0.0489	0.1756	-0.5878	0.3626	0.3103	0.0408	0.9495	0.2962	-0.3592	0.2889	-0.0063	0.0071	0.3064	-0.0623	0.3152	29.935	-22.9565	12.8387
29	12.4479	-4.0044	4.557	2.3174	-0.6433	2.3257	-0.3732	0.206	-0.7794	0.2597	0.2028	0.3849	0.068	-0.1233	0.1704	0.2607	0.0023	0.1069	0.3502	0.0236	0.236	17.5402	-16.7942	16.9587
30	17.8434	2.9454	24.6382	1.1569	-0.2167	61.3794	-0.5828	2.6198	-1.0379	-3.4599	1.2537	0.0546	0.1935	1.469	-0.6709	0.7627	0.0125	-0.0275	0.2881	-0.0681	0.3025	12.7168	-4.0703	3.7936

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	3 - 12	3 - 12
2	X-RAY DIFFRACTION	2	A	A	13 - 26	13 - 26
3	X-RAY DIFFRACTION	3	A	A	27 - 38	27 - 38
4	X-RAY DIFFRACTION	4	A	A	39 - 54	39 - 54
5	X-RAY DIFFRACTION	5	A	A	55 - 62	55 - 62
6	X-RAY DIFFRACTION	6	A	A	63 - 72	63 - 72
7	X-RAY DIFFRACTION	7	A	A	73 - 100	73 - 100
8	X-RAY DIFFRACTION	8	A	A	101 - 108	101 - 108
9	X-RAY DIFFRACTION	9	A	A	109 - 119	109 - 119
10	X-RAY DIFFRACTION	10	A	A	120 - 127	120 - 127
11	X-RAY DIFFRACTION	11	A	A	128 - 136	128 - 136
12	X-RAY DIFFRACTION	12	A	A	137 - 157	137 - 157
13	X-RAY DIFFRACTION	13	A	A	158 - 171	158 - 171
14	X-RAY DIFFRACTION	14	A	A	172 - 180	172 - 180
15	X-RAY DIFFRACTION	15	A	A	181 - 184	181 - 184
16	X-RAY DIFFRACTION	16	B	B	3 - 12	3 - 12
17	X-RAY DIFFRACTION	17	B	B	13 - 24	13 - 24
18	X-RAY DIFFRACTION	18	B	B	25 - 38	25 - 38
19	X-RAY DIFFRACTION	19	B	B	39 - 59	39 - 59
20	X-RAY DIFFRACTION	20	B	B	60 - 72	60 - 72
21	X-RAY DIFFRACTION	21	B	B	73 - 88	73 - 88
22	X-RAY DIFFRACTION	22	B	B	89 - 104	89 - 104
23	X-RAY DIFFRACTION	23	B	B	105 - 110	105 - 110
24	X-RAY DIFFRACTION	24	B	B	111 - 118	111 - 118
25	X-RAY DIFFRACTION	25	B	B	119 - 128	119 - 128
26	X-RAY DIFFRACTION	26	B	B	129 - 139	129 - 139
27	X-RAY DIFFRACTION	27	B	B	140 - 159	140 - 159
28	X-RAY DIFFRACTION	28	B	B	160 - 169	160 - 169
29	X-RAY DIFFRACTION	29	B	B	170 - 180	170 - 180
30	X-RAY DIFFRACTION	30	B	B	181 - 184	181 - 184

-
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