PDB-7e17: Structure of dimeric uPAR

ID or keywords:

Entry

Database: PDB / ID: 7.0E+17

Title

Structure of dimeric uPAR

Components

Urokinase plasminogen activator surface receptor

Keywords

CELL INVASION / GPI-anchored protein

Function / homology

Function and homology information

urokinase plasminogen activator receptor activity / Attachment of GPI anchor to uPAR / positive regulation of homotypic cell-cell adhesion / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / protein complex involved in cell-matrix adhesion / regulation of proteolysis / serine-type endopeptidase complex ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.96 Å

Authors

Cai, Y. / Huang, M.

Funding support

China, 1items

Citation

Journal: Nat Commun / Year: 2022
Title: Crystal structure and cellular functions of uPAR dimer
Authors: Yu, S. / Sui, Y. / Wang, J. / Li, Y. / Li, H. / Cao, Y. / Chen, L. / Jiang, L. / Yuan, C. / Huang, M.

History

Deposition	Feb 1, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 22, 2021	Provider: repository / Type: Initial release
Revision 1.1	Apr 6, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7e17.cif.gz	198.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7e17.ent.gz	160.1 KB	Display	PDB format
PDBx/mmJSON format	7e17.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7e17_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	7e17_full_validation.pdf.gz	1.7 MB	Display
Data in XML	7e17_validation.xml.gz	19.7 KB	Display
Data in CIF	7e17_validation.cif.gz	26 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e1/7e17 ftp://data.pdbj.org/pub/pdb/validation_reports/e1/7e17	HTTPS FTP

-
Related structure data

Related structure data	7v63C 2fd6S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5gyr-2 5h1l-d 5jsj-d 1ocy-1 4wvb-d 6ier-2 5ocs-2 3ban-d 3mr7-d 4qsf-1 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	#54 - Jun 2004 Acetylcholinesterase similarity (1)

Deposited unit

A: Urokinase plasminogen activator surface receptor

B: Urokinase plasminogen activator surface receptor

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	79.580, 79.580, 270.530
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein

Urokinase plasminogen activator surface receptor / uPAR / Monocyte activation antigen Mo3

Mass: 31053.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: PLAUR, MO3, UPAR / Plasmid: PMT/BIP / Production host:

Drosophila melanogaster (fruit fly) / Variant (production host): S2 Cells / References: UniProt: Q03405

#2: 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.: 6 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆ / Feature type: SUBJECT OF INVESTIGATION

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

Has ligand of interest

Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.5 Å³/Da / Density % sol: 64.91 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.8-2.2 M ammonium sulphate in 50 mM sodium acetate at pH 4.5oC5.2

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U / Wavelength: 0.979 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 3, 2013

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.96→56.27 Å / Num. obs: 37874 / % possible obs: 99.1 % / Redundancy: 6.74 % / B_iso Wilson estimate: 63.01 Å² / CC_1/2: 0.994 / R_merge(I) obs: 0.175 / R_rim(I) all: 0.191 / Χ²: 1.012 / Net I/σ(I): 10.25

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.96-3.04	7.272	1.312	2.05	9795	1348	1347	0.628	1.417	99.9
3.04-3.12	7.224	1.063	2.52	9630	1333	1333	0.7	1.15	100
3.12-3.21	7.184	0.815	3.29	9404	1310	1309	0.852	0.882	99.9
3.21-3.31	7.227	0.643	4.06	9251	1280	1280	0.815	0.696	100
3.31-3.42	6.838	0.597	4.62	8288	1219	1212	0.912	0.651	99.4
3.42-3.54	6.21	0.396	6.39	7278	1195	1172	0.96	0.437	98.1
3.54-3.67	6.295	0.338	7.46	7132	1153	1133	0.973	0.371	98.3
3.67-3.82	6.933	0.269	8.74	7723	1120	1114	0.981	0.292	99.5
3.82-3.99	5.865	0.227	9.41	6141	1083	1047	0.985	0.253	96.7
3.99-4.19	6.953	0.148	13.14	7162	1033	1030	0.991	0.161	99.7
4.19-4.41	6.903	0.106	16.13	6737	980	976	0.995	0.115	99.6
4.41-4.68	6.782	0.088	17.51	6389	946	942	0.997	0.095	99.6
4.68-5	6.786	0.093	16.7	5890	871	868	0.995	0.101	99.7
5-5.4	6.769	0.114	15.07	5598	831	827	0.994	0.124	99.5
5.4-5.92	6.712	0.102	15.76	5128	769	764	0.995	0.111	99.3
5.92-6.62	6.568	0.093	16.45	4683	719	713	0.995	0.101	99.2
6.62-7.64	6.17	0.079	18.3	3807	624	617	0.996	0.086	98.9
7.64-9.36	6.504	0.052	23.55	3538	551	544	0.998	0.056	98.7
9.36-13.24	6.068	0.046	24.64	2688	451	443	0.998	0.05	98.2
13.24-56.27	5.128	0.042	21.83	1364	291	266	0.996	0.048	91.4

-
Processing

Software

Name	Version	Classification
PHENIX	1.19_4092	refinement
xia2		data reduction
PDB_EXTRACT	3.15	data extraction
xia2		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2fd6

2fd6

Resolution: 2.96→56.27 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.77 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2993	1729	5.04 %
R_work	0.2479	32570	-
obs	0.2505	34299	99.26 %

Solvent computation

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

Displacement parameters

B_iso max: 131.02 Å² / B_iso mean: 61.3365 Å² / B_iso min: 29.27 Å²

Refinement step

Cycle: final / Resolution: 2.96→56.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3467	0	84	0	3551
B_iso mean	-	-	94.68	-	-
Num. residues	-	-	-	-	457

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 12

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.96-3.05	0.3286	159	0.3323	2685	2844	100
3.05-3.15	0.3271	163	0.2921	2720	2883	100
3.15-3.26	0.3081	154	0.2783	2699	2853	100
3.26-3.39	0.3765	137	0.2749	2747	2884	100
3.39-3.54	0.3607	139	0.2804	2674	2813	97
3.54-3.73	0.3276	145	0.2671	2715	2860	98
3.73-3.96	0.3305	123	0.2718	2657	2780	97
3.96-4.27	0.2966	138	0.2178	2723	2861	100
4.27-4.7	0.2078	160	0.182	2768	2928	100
4.7-5.38	0.2838	133	0.2194	2728	2861	100
5.38-6.77	0.2579	134	0.2623	2734	2868	100
6.77-56.27	0.3253	144	0.2505	2720	2864	99

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	2.4579	-1.1274	0.7449	2.4323	0.6012	3.6301	-0.1186	1.3724	-0.5821	-0.5671	0.691	0.0225	0.3105	1.332	-0.3966	0.3737	-0.0861	-0.0234	0.7912	-0.1656	0.5395	21.42	11.9171	286.907
2	0.9857	0.9928	1.2996	5.4547	2.1702	2.5697	0.0048	-0.4861	0.6767	1.3369	-0.1068	-0.2509	0.2211	-0.4534	0.0325	0.3403	0.0489	-0.0342	0.5318	-0.0547	0.5292	18.6458	14.7823	295.5049
3	4.5168	-1.9953	3.0332	2.8035	-0.77	6.4975	0.1291	0.0231	-0.37	-0.6803	-0.0228	0.6045	-0.0132	-0.5755	-0.1266	0.5027	0.1132	0.0386	0.4049	-0.0986	0.6909	7.1729	21.0371	273.0995
4	2.7866	-0.4039	0.1547	7.3944	4.808	7.9616	-0.5308	0.5508	0.1942	0.4408	0.5654	-0.9977	0.5319	1.5961	-0.0364	0.3542	0.0224	0.0066	0.4879	0.0532	0.4624	15.0158	17.3134	290.2234
5	4.1421	-0.7073	-0.6499	8.7273	-8.2998	8.9511	-1.3524	-0.3546	0.4383	0.1859	1.2165	-0.9941	-0.5271	-1.9799	0.0796	0.5002	-0.0608	0.0211	0.7572	-0.1986	0.413	13.1135	29.7077	296.7654
6	2.0509	0.3113	1.2882	6.9237	-1.0194	6.4127	-0.9883	-1.7171	-0.0638	-0.0468	-0.1972	1.4053	0.9041	1.368	-0.3696	0.5285	0.5353	0.3066	0.9805	-0.0007	0.5367	12.6378	40.0955	278.917
7	5.5343	-1.3774	-1.2292	4.3184	4.209	4.1601	0.8649	-0.7994	-0.5067	0.117	0.0107	0.107	1.3862	0.5892	-0.3456	0.7348	0.3318	-0.0493	0.3816	-0.0235	0.3872	23.5314	35.9942	254.5838
8	2.7883	2.9986	1.7279	9.1664	-0.3494	1.9049	0.6091	0.4416	-0.5463	-1.6394	-1.0281	-2.5571	-0.216	0.6839	0.2118	0.4774	0.0875	0.2499	1.1867	-0.142	0.8379	34.3466	28.5963	246.3597
9	2.217	-0.4444	3.5688	0.1102	-0.6362	6.4493	0.6488	1.3982	0.0147	0.4879	0.1639	0.2035	-0.4646	2.4069	-0.3348	0.8373	-0.1329	-0.0226	0.8501	0.1178	0.6422	39.5775	29.9926	257.4452
10	6.412	-4.0956	-6.1935	3.7768	4.1267	5.9133	0.5794	-1.1009	0.8273	0.2783	0.7684	-0.593	-0.1384	0.9514	-0.4852	0.7384	0.1785	-0.0193	0.6215	0.1468	0.4835	25.4285	34.3298	275.1123
11	1.7655	-0.7111	2.1417	0.6098	-0.4523	2.8613	-0.5119	0.1053	-0.6061	-0.5949	0.3186	0.5886	-0.682	-0.2789	0.0944	0.985	0.0729	-0.2878	0.6538	0.0053	1.3838	18.3118	47.4949	274.2927
12	4.9251	-0.1735	-1.2727	0.7741	-0.5649	2.7874	0.055	-1.2709	0.5855	-0.2464	0.3115	-0.0497	-0.4298	-0.2373	-0.0609	1.0425	0.3667	-0.1364	-0.3872	-0.2379	0.5491	19.2843	42.5173	254.1601
13	3.0441	1.3676	-3.7879	4.8709	0.1884	5.5032	-1.0903	-0.0182	-0.8461	-1.0075	0.3929	-0.9077	-0.683	-0.9014	0.9281	1.1399	0.3204	0.1367	0.7401	0.2251	0.9653	5.6056	37.7191	265.714
14	1.1221	-0.187	-0.2837	1.9891	-0.7169	1.2294	-0.3552	-0.3399	0.1022	0.0077	-0.0338	-0.2754	0.0964	-0.1957	0.3538	0.6461	0.0874	0.0577	0.4317	0.0943	0.5431	17.7797	41.2587	245.837
15	7.5807	1.2264	2.6442	3.7724	-0.2786	5.5854	-0.261	0.8036	-0.7363	-0.0065	0.0647	-0.9476	0.8679	1.4274	0.23	0.8568	0.1885	-0.0652	0.5124	-0.0225	0.4874	33.3773	48.8119	241.3837
16	1.6988	1.0013	-0.9117	3.9988	0.049	2.1553	-0.2429	-0.2163	0.0225	0.2716	0.2362	0.0246	-0.2681	0.2949	-0.0228	0.6534	0.0334	-0.0412	0.5091	0.0793	0.3102	22.9564	49.3168	249.0373
17	8.1647	-0.5484	0.6593	4.9988	2.4055	2.0045	-0.3209	0.6797	2.0048	3.5254	1.0257	-0.2101	-0.9685	-0.4757	-0.263	0.7449	0.1593	0.1197	0.7773	0.0182	0.6974	16.4263	52.6261	257.4625
18	7.0424	-4.5562	-2.0302	8.1199	5.1449	3.4267	-1.3182	-0.1803	-0.605	2.9224	0.5114	0.6072	-1.0924	1.7598	0.3487	1.1135	-0.1788	-0.2208	0.6833	0.1201	0.557	28.2258	48.3202	259.2441
19	3.2775	2.485	3.0102	4.6364	0.1351	4.5586	-0.9892	-0.5517	0.2315	2.3775	0.3668	0.3128	0.6087	0.9464	0.5458	0.7899	0.3639	-0.0748	0.8058	-0.122	0.678	22.6501	56.4044	252.8623
20	5.3705	3.6519	-1.8824	3.9733	-0.2697	3.8784	-0.916	-0.1534	2.7867	0.6308	0.6935	0.7622	-0.1192	-0.2859	-0.1412	0.8213	0.0329	-0.0469	0.2523	0.0514	0.8155	22.5983	56.6155	240.5955
21	3.2313	0.2217	-3.1471	0.4714	-0.0574	5.0553	0.6677	0.6136	-0.054	0.6923	0.473	-0.8667	0.7102	-0.2926	-0.6087	0.6779	0.0692	-0.0239	0.2866	-0.086	0.6869	31.2898	22.7034	248.2474
22	1.4529	-0.2944	1.2489	1.0108	0.3983	1.2735	0.1934	-0.0326	-0.0373	0.0319	-0.2754	0.1315	0.1951	0.0763	-0.0748	0.6146	-0.1093	-0.1163	0.3833	0.0371	0.6807	27.3832	21.1388	250.2273
23	6.0848	0.0206	-2.0757	3.5562	1.554	4.6902	-0.5802	-0.5289	-0.066	0.0142	0.7398	0.5358	-0.8768	-0.8444	-0.033	0.5998	0.0897	0.0167	0.3997	0.1528	0.5852	21.5745	34.4644	264.9788
24	5.9246	0.7088	-5.0644	2.7707	1.4021	5.8491	-0.2744	0.7588	-0.3931	-0.3914	0.2199	-0.3255	-0.8319	-0.6525	0.1921	0.5914	0.152	0.0363	0.5633	0.1125	0.4615	25.3669	29.7604	262.0935
25	4.6406	2.5247	-0.6154	2.6254	1.4421	2.8541	-1.1218	-0.236	-0.3839	-0.1472	1.1662	0.5933	0.5611	-0.086	-0.1599	0.5842	0.1313	-0.0355	0.4357	0.1396	0.5707	14.7739	28.9446	247.1054
26	0.2814	-0.0946	0.8101	0.8147	-1.1517	1.5293	-0.0048	-0.2214	0.5375	0.7133	-0.5996	-0.5519	-0.5722	-0.441	0.2732	0.2289	0.2715	0.1486	0.7613	0.0308	0.576	6.7095	19.6107	281.3532
27	1.9771	9.4897	-0.445	9.2894	3.0047	7.6414	-0.1882	-1.8499	-1.3234	0.4605	-1.8998	1.704	1.0458	0.5171	1.3155	0.7353	0.1259	-0.1154	0.6497	-0.3388	1.0704	11.4987	1.5789	283.4831
28	0.6861	0.1033	-0.1408	6.002	-3.7199	2.9018	-0.3064	0.2243	-1.5507	-0.4054	1.5104	0.3525	-0.4512	-1.4732	-0.6903	0.4884	0.1571	0.061	0.6763	0.0322	0.4487	11.6049	11.5542	273.7516
29	4.1287	-0.2672	0.9506	7.5931	-0.4132	5.4067	-0.4527	0.8552	-0.2599	-0.0641	1.0127	0.3931	-0.9714	-0.1807	-0.5699	0.4519	0.1604	-0.0059	0.8945	-0.1424	0.4562	3.0897	21.0905	258.0101
30	0.774	0.9147	1.0435	1.6891	-0.1599	4.6808	0.61	-1.2596	1.7801	0.3279	0.1679	0.3427	-0.0422	-2.2601	-0.5135	0.8422	0.2792	0.0698	1.1627	-0.0661	1.0757	-7.3791	22.3711	267.4005
31	1.9884	0.8416	0.3999	3.1172	-0.8796	4.6439	-0.1221	-0.0635	0.131	-0.3711	-0.3083	-0.4238	0.0622	-0.5847	0.2946	0.4228	0.1882	0.1193	0.6821	0.013	0.413	-0.1619	23.6498	285.9968
32	8.0259	1.9304	-2.7677	5.5681	-5.0073	7.9216	0.409	-2.1509	-0.6599	-0.311	-0.7332	-1.8361	-3.0654	-0.4159	0.2844	0.9679	0.1745	0.2202	0.5837	0.2949	1.1683	4.8373	37.0205	275.625
33	1.7333	-0.9002	0.4242	3.4923	0.6953	3.2269	0.6089	-0.2626	0.8831	-0.4321	-0.3221	-0.2871	-0.044	0.4938	-0.0263	0.4517	-0.0392	-0.035	0.5605	0.1096	0.4544	2.4494	26.6605	295.4174
34	2.7002	1.4658	0.7373	8.3024	2.7878	1.8253	0.6898	0.9442	-0.9308	1.9289	-1.1287	-0.4824	1.9294	0.6558	0.1901	0.8719	0.1358	-0.0544	0.6442	-0.1421	0.6733	-6.3787	7.2336	297.7985
35	0.4345	0.474	-0.5561	2.5399	-1.8513	4.3807	0.3517	0.4127	-0.1758	-0.0721	-0.2275	-0.2589	-0.8858	0.4469	-0.1726	0.2716	0.0999	0.067	0.6989	-0.0768	0.5668	-4.5002	23.8169	296.0814
36	1.9403	0.1377	-0.4458	0.2434	0.112	0.1566	-0.2886	1.9821	-1.8002	-0.2359	0.1552	-0.6734	-0.2025	0.0486	0.022	1.0461	0.0949	0.0419	1.2374	-0.2159	0.6836	-9.0556	6.0355	283.8886
37	3.17	1.5326	0.187	3.9561	0.6287	3.3225	-0.4177	0.2714	0.5855	0.0258	0.4425	0.9424	0.3708	-0.3085	0.0879	0.353	0.0624	-0.052	0.6578	0.037	0.4261	-8.542	20.5417	288.7765
38	1.6892	-0.6068	-0.0635	5.1538	1.1583	0.275	-1.3771	1.853	-0.2782	0.7558	0.4114	1.3989	-1.0182	1.4251	0.9537	1.543	0.2285	-0.1819	1.6164	-0.1947	0.777	-8.2938	15.068	280.1731
39	4.7663	-0.3951	-1.4424	2.1218	2.1655	2.5218	-0.4251	-0.1129	-0.2871	0.0436	-1.3124	1.7632	-0.9016	-2.2682	1.1361	0.6735	-0.0125	-0.0261	0.5849	-0.0741	0.6024	-13.9532	19.2187	288.7916
40	2.7891	-1.9652	0.3615	3.5708	-2.1903	4.92	0.9607	0.2123	0.0757	0.4076	-1.0181	0.4068	-0.3522	1.4884	-0.0976	0.2928	-0.09	0.0118	0.57	-0.0593	0.4846	-14.1107	19.1365	300.1647

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 0:13)	A	0 - 13
2	X-RAY DIFFRACTION	2	(chain A and resid 14:26)	A	14 - 26
3	X-RAY DIFFRACTION	3	(chain A and resid 27:40)	A	27 - 40
4	X-RAY DIFFRACTION	4	(chain A and resid 41:48)	A	41 - 48
5	X-RAY DIFFRACTION	5	(chain A and resid 49:53)	A	49 - 53
6	X-RAY DIFFRACTION	6	(chain A and resid 54:63)	A	54 - 63
7	X-RAY DIFFRACTION	7	(chain A and resid 64:71)	A	64 - 71
8	X-RAY DIFFRACTION	8	(chain A and resid 72:77)	A	72 - 77
9	X-RAY DIFFRACTION	9	(chain A and resid 78:84)	A	78 - 84
10	X-RAY DIFFRACTION	10	(chain A and resid 85:98)	A	85 - 98
11	X-RAY DIFFRACTION	11	(chain A and resid 99:154)	A	99 - 154
12	X-RAY DIFFRACTION	12	(chain A and resid 155:170)	A	155 - 170
13	X-RAY DIFFRACTION	13	(chain A and resid 171:179)	A	171 - 179
14	X-RAY DIFFRACTION	14	(chain A and resid 180:199)	A	180 - 199
15	X-RAY DIFFRACTION	15	(chain A and resid 200:213)	A	200 - 213
16	X-RAY DIFFRACTION	16	(chain A and resid 214:244)	A	214 - 244
17	X-RAY DIFFRACTION	17	(chain A and resid 245:250)	A	245 - 250
18	X-RAY DIFFRACTION	18	(chain A and resid 251:259)	A	251 - 259
19	X-RAY DIFFRACTION	19	(chain A and resid 260:267)	A	260 - 267
20	X-RAY DIFFRACTION	20	(chain A and resid 268:277)	A	268 - 277
21	X-RAY DIFFRACTION	21	(chain B and resid 0:6)	B	0 - 6
22	X-RAY DIFFRACTION	22	(chain B and resid 7:23)	B	7 - 23
23	X-RAY DIFFRACTION	23	(chain B and resid 24:37)	B	24 - 37
24	X-RAY DIFFRACTION	24	(chain B and resid 38:43)	B	38 - 43
25	X-RAY DIFFRACTION	25	(chain B and resid 44:56)	B	44 - 56
26	X-RAY DIFFRACTION	26	(chain B and resid 57:77)	B	57 - 77
27	X-RAY DIFFRACTION	27	(chain B and resid 78:83)	B	78 - 83
28	X-RAY DIFFRACTION	28	(chain B and resid 84:91)	B	84 - 91
29	X-RAY DIFFRACTION	29	(chain B and resid 92:99)	B	92 - 99
30	X-RAY DIFFRACTION	30	(chain B and resid 115:153)	B	115 - 153
31	X-RAY DIFFRACTION	31	(chain B and resid 154:171)	B	154 - 171
32	X-RAY DIFFRACTION	32	(chain B and resid 172:178)	B	172 - 178
33	X-RAY DIFFRACTION	33	(chain B and resid 179:195)	B	179 - 195
34	X-RAY DIFFRACTION	34	(chain B and resid 196:211)	B	196 - 211
35	X-RAY DIFFRACTION	35	(chain B and resid 212:225)	B	212 - 225
36	X-RAY DIFFRACTION	36	(chain B and resid 226:235)	B	226 - 235
37	X-RAY DIFFRACTION	37	(chain B and resid 236:249)	B	236 - 249
38	X-RAY DIFFRACTION	38	(chain B and resid 250:260)	B	250 - 260
39	X-RAY DIFFRACTION	39	(chain B and resid 261:266)	B	261 - 266
40	X-RAY DIFFRACTION	40	(chain B and resid 267:277)	B	267 - 277

-
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://pdbjlvh1.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