PDB-3r2w: Crystal Structure of UDP-glucose Pyrophosphorylase of Homo Sapiens

ID or keywords:

Entry

Database: PDB / ID: 3r2w

Title

Crystal Structure of UDP-glucose Pyrophosphorylase of Homo Sapiens

Components

UTP--glucose-1-phosphate uridylyltransferase

Keywords

TRANSFERASE / Homo sapiens / Rossmann Fold Beta Barrel / Nucleotidyltransferase

Function / homology

Function and homology information

glucose 1-phosphate metabolic process / pyrimidine ribonucleotide binding / Formation of the active cofactor, UDP-glucuronate / UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-alpha-D-glucose metabolic process / D-glucose binding / glycogen biosynthetic process / glycogen metabolic process / Glycogen synthesis ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 3.6 Å

Authors

Zheng, X. / Yu, Q.

Citation

Journal: Biochem.J. / Year: 2012
Title: The crystal structure of human UDP-glucose pyrophosphorylase reveals a latch effect that influences enzymatic activity.
Authors: Yu, Q. / Zheng, X.

History

Deposition	Mar 14, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 8, 2012	Provider: repository / Type: Initial release
Revision 1.1	Feb 29, 2012	Group: Database references
Revision 1.2	Sep 9, 2020	Group: Database references / Structure summary / Category: struct / struct_ref_seq_dif / Item: _struct.title / _struct_ref_seq_dif.details
Revision 1.3	Feb 21, 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	3r2w.cif.gz	695.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3r2w.ent.gz	584.8 KB	Display	PDB format
PDBx/mmJSON format	3r2w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3r2w_validation.pdf.gz	468.9 KB	Display	wwPDB validaton report
Full document	3r2w_full_validation.pdf.gz	531.2 KB	Display
Data in XML	3r2w_validation.xml.gz	69 KB	Display
Data in CIF	3r2w_validation.cif.gz	92.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r2/3r2w ftp://data.pdbj.org/pub/pdb/validation_reports/r2/3r2w	HTTPS FTP

-
Related structure data

Similar structure data	4r7p-1 2i5k-1 0488 4ln3-d 20605 4ln4-d 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	#254 - Feb 2021 Cellulose Synthase similarity (5) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: UTP--glucose-1-phosphate uridylyltransferase

B: UTP--glucose-1-phosphate uridylyltransferase

C: UTP--glucose-1-phosphate uridylyltransferase

D: UTP--glucose-1-phosphate uridylyltransferase

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

1

A: UTP--glucose-1-phosphate uridylyltransferase

B: UTP--glucose-1-phosphate uridylyltransferase

C: UTP--glucose-1-phosphate uridylyltransferase

D: UTP--glucose-1-phosphate uridylyltransferase

A: UTP--glucose-1-phosphate uridylyltransferase

B: UTP--glucose-1-phosphate uridylyltransferase

C: UTP--glucose-1-phosphate uridylyltransferase

D: UTP--glucose-1-phosphate uridylyltransferase

defined by author&software
473 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	140.445, 140.445, 311.724
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	UTP--glucose-1-phosphate uridylyltransferase / UDP-glucose pyrophosphorylase / UDPGP / UGPase Mass: 59184.402 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UGP2, UGP1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) References: UniProt: Q16851, UTP-glucose-1-phosphate uridylyltransferase

#1: Protein

UTP--glucose-1-phosphate uridylyltransferase / UDP-glucose pyrophosphorylase / UDPGP / UGPase

Mass: 59184.402 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: UGP2, UGP1 / Plasmid: pET28 / Production host:

Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
References: UniProt: Q16851, UTP-glucose-1-phosphate uridylyltransferase

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.75 Å³/Da / Density % sol: 67.19 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MgSO4, 35.8% PEG3350, glycerol, HEPES, pH 6.5, vapor diffusion, hanging drop, temperature 290K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
Detector	Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 15, 2009
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.6→120 Å / Num. all: 39283 / Num. obs: 39283 / % possible obs: 96.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell	Resolution: 3.6→3.69 Å / % possible all: 64.1

-
Processing

Software

Name	Version	Classification
REFMAC	5.5.0102	refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Resolution: 3.6→20 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.891 / Occupancy max: 1 / Occupancy min: 1 / SU B: 79.886 / SU ML: 0.542 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.695 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.3038	1985	5.1 %	RANDOM
R_work	0.2475	37298	-	-
obs	0.2502	39283	93.97 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 119.77 Å² / B_iso mean: 144.356 Å² / B_iso min: 20 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.72 Å²	2.36 Å²	0 Å²
2-	-	4.72 Å²	0 Å²
3-	-	-	-7.08 Å²

Refinement step

Cycle: LAST / Resolution: 3.6→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13938	0	0	0	13938

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	14181
X-RAY DIFFRACTION	r_angle_refined_deg	1.558	1.968	19301
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.032	5	1837
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.341	24.828	582
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.049	15	2291
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.929	15	64
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	2318
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	10601
X-RAY DIFFRACTION	r_mcbond_it	0.468	1.5	9193
X-RAY DIFFRACTION	r_mcangle_it	0.9	2	14783
X-RAY DIFFRACTION	r_scbond_it	1.071	3	4988
X-RAY DIFFRACTION	r_scangle_it	1.946	4.5	4518

LS refinement shell

Resolution: 3.6→3.69 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.386	80	-
R_work	0.368	1558	-
all	-	1638	-
obs	-	-	55.19 %

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	0.7885	-0.3832	0.1593	0.8853	0.3376	0.538	-0.0468	-0.237	0.108	0.3278	0.0664	0.2411	-0.1427	-0.374	-0.0195	0.9006	0.1432	-0.0101	1.1487	-0.0569	1.0677	-75.9602	24.9223	2.2724
2	4.3669	-0.2437	0.8482	2.2398	0.8639	4.0348	-0.3383	-0.1448	-0.0615	0.3668	0.3074	-0.1339	0.1639	-0.2512	0.0309	0.5462	0.1413	-0.1258	0.8005	-0.0144	0.4996	-55.5917	20.4421	-4.1011
3	0.1993	0.661	-0.5182	38.6744	-32.1476	26.7359	-0.1837	0.2414	-0.8079	3.0566	0.2365	-0.1704	-2.6003	-0.2647	-0.0528	0.9053	-0.5992	0.5378	1.6321	-0.6726	3.5629	-81.0701	3.6834	-1.0702
4	4.106	2.4855	-0.8264	5.8281	-1.7863	4.1794	-0.0367	-0.3711	0.5477	0.3916	0.0383	0.1624	-0.5577	-0.8536	-0.0016	0.4665	0.3063	-0.1438	0.8252	-0.1152	0.737	-63.5995	28.9473	0.7872
5	2.5188	-1.1299	-2.0341	1.726	-1.6427	7.3825	0.1544	0.4055	0.4772	0.0405	0.1559	-0.0387	-0.1468	-0.8039	-0.3103	0.7192	0.3283	-0.1292	0.8842	-0.0077	1.0278	-74.0842	38.3612	-8.5678
6	2.3834	1.3424	0.4514	2.8179	-1.0975	1.1296	-0.2368	-0.1298	0.059	-0.3026	0.2832	0.3951	-0.0471	-0.6485	-0.0464	0.7141	0.3123	-0.1319	1.1427	-0.1171	0.9361	-76.7416	29.6251	-6.3441
7	6.7227	0.2583	-0.1215	1.1318	1.093	5.2124	0.0313	0.1329	0.3172	0.1351	-0.1211	-0.3107	-0.5901	0.1046	0.0898	0.4155	0.0593	-0.1729	0.8455	-0.008	0.4484	-56.4685	23.1425	-25.6704
8	5.1489	-1.5347	3.8779	4.93	2.9188	6.7385	-0.2842	-0.2142	0.4534	0.0964	0.0431	-0.465	-0.1729	-0.1752	0.2411	0.3354	0.0133	-0.0092	0.8274	0.0131	0.4448	-56.6129	19.777	-36.3942
9	12.6762	2.0398	2.5575	3.6199	-2.0924	4.2954	0.0433	0.4737	-0.5161	-0.2223	0.0631	-0.4314	0.3991	0.0712	-0.1064	0.3958	0.0808	0.0872	0.7804	-0.1223	0.6316	-55.1233	12.7857	-41.0361
10	8.2687	-7.31	1.8058	16.8053	-0.8025	1.556	-0.3707	-0.0053	-0.204	0.6912	0.0992	-0.2259	0.2004	-0.1011	0.2714	0.4822	0.0179	0.0962	0.6823	-0.0049	0.5681	-54.2198	10.2505	-43.6731
11	4.6764	0.454	0.791	4.9871	1.7985	2.5653	-0.1738	0.056	0.0352	-0.5375	0.2844	-0.0655	-0.1102	-0.3232	-0.1106	0.8746	-0.1382	-0.0477	1.3621	0.0314	0.7879	-32.0823	0.1865	-102.2818
12	2.5654	-0.1285	0.2444	2.9549	-0.3381	2.0502	0.0316	0.0372	0.2271	-0.0507	0.0268	-0.1302	-0.0344	-0.0271	-0.0585	0.2233	-0.0829	-0.0002	0.9006	0.1331	0.6446	-20.2957	16.2033	-73.1976
13	6.9391	2.7113	2.6235	4.1344	1.8135	2.1909	-0.2234	0.481	-0.2059	-0.3892	0.1841	-0.0212	-0.1577	-0.0166	0.0392	0.6261	-0.0247	0.0072	0.9536	0.2024	0.4893	-27.3036	15.172	-88.4027
14	3.7223	2.3571	-0.5551	3.8135	-1.1058	3.3014	0.0708	0.0905	-0.1431	-0.2145	-0.0107	-0.0574	-0.0079	0.1669	-0.0601	0.1436	-0.0394	0.003	0.9876	0.0351	0.646	-12.3877	11.0079	-73.6235
15	0.9941	0.0586	1.0555	2.3683	0.3578	1.5215	0.1764	0.1656	-0.4782	-0.4059	-0.0395	0.4716	0.5843	0.0898	-0.1369	0.6487	-0.0677	0.1565	1.0644	0.0294	1.0345	-20.7452	-3.4121	-78.2479
16	3.0048	-2.6419	1.4172	3.5194	0.4071	3.2183	0.2632	0.1799	-0.2885	-0.259	0.0291	0.076	0.267	-0.0833	-0.2923	0.3182	-0.1959	0.0845	1.0445	0.2597	0.725	-24.9442	1.6924	-80.0525
17	5.9009	-0.1473	-0.7869	5.0534	0.5826	3.7347	-0.1936	-0.202	-0.0742	0.2878	-0.0165	-0.1492	-0.253	0.2525	0.2102	0.2426	-0.0136	-0.0055	0.8282	0.1309	0.6386	-35.2453	14.2296	-59.1529
18	5.8571	0.3879	0.6839	7.2631	1.876	7.2526	-0.3264	0.0221	0.381	-0.3973	0.0852	-0.0115	0.1956	-0.0485	0.2413	0.2481	0.0109	0.1501	0.7394	0.1363	0.5219	-45.7833	10.5363	-51.9011
19	10.9168	4.9654	8.2567	2.2604	3.7617	6.268	-0.24	0.3138	0.4127	-0.0765	0.0312	0.1648	-0.1412	0.0752	0.2088	0.502	0.0857	0.1412	1.1557	0.1375	0.98	-43.2919	13.3618	-44.091
20	9.3857	-9.3521	0.3952	9.4567	0.0913	4.3313	0.4101	0.7265	0.4651	-0.6362	-0.5654	-0.499	-0.3423	0.4768	0.1553	0.4922	-0.1217	0.0505	0.72	0.0335	0.7944	-56.22	13.9174	-48.8632
21	0.9197	2.555	0.0059	7.1692	0.0168	0.0029	-0.2809	-0.0297	0.1353	-0.561	0.2194	0.4044	-0.0091	0.0068	0.0615	1.5921	0.0669	0.0691	2.0733	0.0555	1.6108	-52.7245	56.8263	-80.5816
22	1.68	0.5561	0.589	1.1167	0.1016	1.0186	-0.0511	-0.1901	0.5012	-0.1933	0.2014	-0.2289	-0.6878	0.0175	-0.1504	1.0383	0.0026	-0.0194	0.9801	0.1598	1.2388	-70.9167	54.3741	-53.0073
23	0.2365	0.2727	0.5236	1.8717	1.1387	2.132	0.1034	0.2072	0.2525	-0.3917	-0.3057	-0.259	-0.2893	-0.2477	0.2023	1.1983	0.1307	-0.0075	1.0566	0.3159	1.2938	-73.5959	53.3587	-65.7439
24	6.4907	0.838	0.557	0.215	0.1559	0.1557	0.0747	0.598	0.5484	-0.1458	0.0465	-0.2706	-0.3318	0.0969	-0.1211	1.4415	-0.0032	-0.03	1.2196	0.1946	1.3679	-67.8585	60.6219	-59.7831
25	0.7482	1.642	0.2793	4.0633	0.3907	2.3075	0.1431	-0.1089	0.0485	-0.2715	-0.3405	-0.2222	-0.7348	0.3178	0.1974	1.3093	-0.022	0.0612	1.0344	-0.0353	1.3451	-64.8684	57.7776	-42.6365
26	1.6581	0.5644	-1.0973	0.912	0.0742	1.2221	0.1729	-0.0857	0.0146	-0.2077	-0.0999	-0.0166	-0.0728	0.439	-0.073	1.1468	-0.0435	-0.0974	1.1172	0.0512	1.4261	-54.6811	52.4977	-52.7675
27	0.3281	0.0352	-0.2046	3.808	0.0947	0.2322	0.4523	-0.2127	0.3346	0.439	-0.4828	-0.0019	-0.523	0.1325	0.0305	1.3316	-0.204	-0.0953	1.0658	0.0701	0.9687	-73.1342	46.2586	-43.5024
28	2.8556	0.5367	-1.3494	9.0797	-1.1766	3.5708	-0.1558	0.2496	0.4676	-0.1896	0.265	-0.0391	-0.0429	-0.2192	-0.1092	0.2686	-0.0024	-0.0979	0.7869	0.0294	0.6864	-76.2469	25.8903	-47.0172
29	15.7493	0.3864	-2.5296	0.3682	0.3686	1.7773	0.266	0.1212	0.1537	-0.3789	-0.2592	-0.2734	-0.6032	-0.4262	-0.0068	0.5739	0.0394	0.1188	0.8131	0.154	0.8575	-78.7228	15.6434	-48.115
30	9.5246	4.5057	3.4406	7.2538	6.2133	5.3552	-0.1743	-0.007	-0.1931	-0.0412	0.1489	0.01	-0.0378	0.0702	0.0254	0.5123	0.0119	-0.0135	0.5792	0.1843	0.7377	-79.5455	13.259	-46.4036
31	4.425	-0.2749	1.4382	3.2334	0.4395	8.0738	0.027	0.3818	-0.5406	-0.2513	0.1593	0.2432	1.1019	-0.0181	-0.1863	0.737	0.1373	0.0291	0.9907	0.1695	0.7782	-102.3758	-41.9469	-23.6493
32	4.031	-0.2772	0.5368	1.7072	0.4985	2.1924	-0.0981	-0.3132	0.1549	-0.1456	0.0214	0.1949	0.018	-0.1166	0.0766	0.2716	0.0077	0.076	0.8255	0.2078	0.5487	-113.9598	-9.2593	-30.1108
33	3.4968	-1.1237	0.4455	4.4818	1.0424	1.0157	0.1402	-0.1398	0.3141	0.0963	-0.0419	-0.5731	0.2503	0.0821	-0.0983	0.3713	0.1055	0.0189	0.9519	0.2573	0.4927	-106.3096	-16.2984	-19.0418
34	1.3227	-0.674	0.2537	1.5941	0.508	1.1342	-0.1933	-0.0253	-0.1495	0.2918	-0.1048	0.3861	0.2535	-0.089	0.2981	0.2984	0.0342	0.1008	0.9709	0.2381	0.5854	-117.5667	-17.4292	-27.2424
35	4.1677	-4.3632	-1.6096	4.7202	1.7982	1.0276	0.2481	0.3231	-0.1468	-0.351	-0.1641	-0.1467	0.3906	0.1174	-0.0841	1.0434	-0.0577	0.2399	1.2052	0.0692	0.792	-111.193	-23.3611	-48.5211
36	3.0856	-2.0587	2.2217	3.1296	-0.292	2.466	0.1887	0.4595	-0.0521	-0.0315	-0.1113	-0.1089	0.3388	0.345	-0.0774	0.4434	0.0258	0.1746	0.9966	0.1731	0.5855	-109.9487	-26.2154	-33.2391
37	3.1354	2.1092	0.1894	3.4168	0.6427	1.1	-0.0463	-0.0637	0.27	-0.1448	0.1236	0.2408	-0.0316	-0.1748	-0.0773	0.3273	0.0428	-0.0212	0.8939	0.1802	0.4849	-104.0716	-3.021	-36.5677
38	7.1113	-1.7121	-0.6853	5.7296	0.1587	5.6739	-0.22	-0.1432	0.4946	0.066	0.2112	-0.361	0.102	-0.1141	0.0088	0.2412	-0.0905	0.0573	0.6976	0.1157	0.5086	-88.8323	5.8732	-41.9922
39	3.6474	-2.7606	-2.5522	7.8477	1.7943	1.8036	-0.2122	0.1423	-0.1546	-0.8623	0.0435	0.2364	0.092	-0.0915	0.1687	0.7113	-0.0648	-0.1402	0.7975	0.184	0.8098	-89.1974	13.4328	-44.043
40	7.5764	1.0238	-0.6212	2.9644	0.5388	0.1939	0.0486	-0.1682	-0.3625	0.1715	-0.0052	-0.3122	0.0802	0	-0.0435	0.5044	0.0219	0.0511	0.6059	0.0944	0.7663	-77.847	9.9675	-42.0059

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	24 - 106
2	X-RAY DIFFRACTION	2	A	107 - 193
3	X-RAY DIFFRACTION	3	A	207 - 210
4	X-RAY DIFFRACTION	4	A	218 - 266
5	X-RAY DIFFRACTION	5	A	267 - 308
6	X-RAY DIFFRACTION	6	A	309 - 391
7	X-RAY DIFFRACTION	7	A	392 - 448
8	X-RAY DIFFRACTION	8	A	449 - 481
9	X-RAY DIFFRACTION	9	A	482 - 495
10	X-RAY DIFFRACTION	10	A	496 - 497
11	X-RAY DIFFRACTION	11	B	18 - 67
12	X-RAY DIFFRACTION	12	B	76 - 169
13	X-RAY DIFFRACTION	13	B	170 - 241
14	X-RAY DIFFRACTION	14	B	242 - 286
15	X-RAY DIFFRACTION	15	B	287 - 357
16	X-RAY DIFFRACTION	16	B	358 - 391
17	X-RAY DIFFRACTION	17	B	392 - 451
18	X-RAY DIFFRACTION	18	B	452 - 489
19	X-RAY DIFFRACTION	19	B	490 - 496
20	X-RAY DIFFRACTION	20	B	497 - 498
21	X-RAY DIFFRACTION	21	C	26 - 50
22	X-RAY DIFFRACTION	22	C	51 - 153
23	X-RAY DIFFRACTION	23	C	154 - 189
24	X-RAY DIFFRACTION	24	C	219 - 254
25	X-RAY DIFFRACTION	25	C	255 - 299
26	X-RAY DIFFRACTION	26	C	300 - 373
27	X-RAY DIFFRACTION	27	C	374 - 424
28	X-RAY DIFFRACTION	28	C	425 - 481
29	X-RAY DIFFRACTION	29	C	482 - 494
30	X-RAY DIFFRACTION	30	C	495 - 497
31	X-RAY DIFFRACTION	31	D	22 - 68
32	X-RAY DIFFRACTION	32	D	76 - 144
33	X-RAY DIFFRACTION	33	D	145 - 193
34	X-RAY DIFFRACTION	34	D	216 - 285
35	X-RAY DIFFRACTION	35	D	286 - 322
36	X-RAY DIFFRACTION	36	D	323 - 376
37	X-RAY DIFFRACTION	37	D	377 - 445
38	X-RAY DIFFRACTION	38	D	446 - 487
39	X-RAY DIFFRACTION	39	D	488 - 496
40	X-RAY DIFFRACTION	40	D	497 - 498

-
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