PDB-2he9: Structure of the peptidylprolyl isomerase domain of the human NK-...

ID or keywords:

Entry

Database: PDB / ID: 2he9

Title

Structure of the peptidylprolyl isomerase domain of the human NK-tumour recognition protein

Components

NK-tumor recognition protein

Keywords

ISOMERASE /

Cyclosporin /

Membrane / Rotamase /

Peptidylprolyl isomerase /

Structural Genomics /

Structural Genomics Consortium / SGC

Function / homology

Function and homology information

cyclosporin A binding / protein peptidyl-prolyl isomerization /

peptidylprolyl isomerase /

peptidyl-prolyl cis-trans isomerase activity /

protein folding / intracellular membrane-bounded organelle /

nucleus /

plasma membrane /

cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Walker, J.R. / Davis, T. / Newman, E.M. / MacKenzie, F. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. ...

Citation

Journal: PLoS Biol. / Year: 2010
Title: Structural and biochemical characterization of the human cyclophilin family of peptidyl-prolyl isomerases.
Authors: Davis, T.L. / Walker, J.R. / Campagna-Slater, V. / Finerty, P.J. / Paramanathan, R. / Bernstein, G. / MacKenzie, F. / Tempel, W. / Ouyang, H. / Lee, W.H. / Eisenmesser, E.Z. / Dhe-Paganon, S.

History

Deposition	Jun 21, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 18, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Feb 7, 2018	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.4	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2he9.cif.gz	154.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2he9.ent.gz	123.7 KB	Display	PDB format
PDBx/mmJSON format	2he9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/he/2he9 ftp://data.pdbj.org/pub/pdb/validation_reports/he/2he9	HTTPS FTP

-
Related structure data

Related structure data	1zkcC 2eslC 2gw2C 2hq6C 2r99C 1zcx PDB Unreleased entryS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4dlw-d 1a33-d 1dyw-d 6w8y-1 4dls-d 3l8z-d 4l9w-d 6quu-1 5fad-d 4m1t-1 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	#163 - Jul 2013 HIV Capsid similarity (7) #245 - May 2020 Spliceosomes similarity (7)

Deposited unit

A: NK-tumor recognition protein

B: NK-tumor recognition protein

hetero molecules

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

1

A: NK-tumor recognition protein

hetero molecules

defined by author
21.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: NK-tumor recognition protein

defined by author
21.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	64.753, 72.786, 73.014
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-231- HOH
2	1	A-315- HOH

#1: Protein	NK-tumor recognition protein / Natural-killer cells cyclophilin-related protein / NK-TR protein Mass: 21219.324 Da / Num. of mol.: 2 Fragment: peptidylprolyl isomerase cyclophilin-type domain (residues 7-179) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NKTR / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30414, peptidylprolyl isomerase
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.03 Å³/Da / Density % sol: 39.3 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: Well solution: 21% Peg 3350, 0.25M potassium sulfate; Protein solution: 50 mM Tris pH 7.5, 100 mM NaCl, 1 mM DTT, 15 mg/mL protein, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 10, 2006
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2→20 Å / Num. all: 23807 / Num. obs: 23807 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / R_sym value: 0.146 / Net I/σ(I): 15.2
Reflection shell	Resolution: 2→2.07 Å / Redundancy: 6.5 % / Num. unique all: 2317 / R_sym value: 0.769 / % possible all: 98.7

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 1ZCX

1zcx
PDB Unreleased entry

Resolution: 2→19.91 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.946 / SU B: 6.955 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19752	1215	5.1 %	RANDOM
R_work	0.14631	-	-	-
obs	0.14889	22557	99.9 %	-
all	-	23772	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 20.605 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.82 Å²	0 Å²	0 Å²
2-	-	1.59 Å²	0 Å²
3-	-	-	-0.77 Å²

Refinement step

Cycle: LAST / Resolution: 2→19.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2708	0	5	275	2988

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	2775
X-RAY DIFFRACTION	r_angle_refined_deg	1.515	1.951	3731
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.306	5	350
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.13	23.937	127
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.663	15	483
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.046	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.111	0.2	395
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2113
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	1215
X-RAY DIFFRACTION	r_nbtor_refined	0.315	0.2	1893
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.122	0.2	220
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.175	0.2	37
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.128	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	2.12	3	1767
X-RAY DIFFRACTION	r_mcangle_it	2.503	4	2758
X-RAY DIFFRACTION	r_scbond_it	4.025	5	1123
X-RAY DIFFRACTION	r_scangle_it	5.543	7	972

LS refinement shell

Resolution: 2.004→2.056 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.289	84	-
R_work	0.19	1602	-
obs	-	-	98.71 %

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	4.0805	-0.2072	1.3572	1.9228	1.7784	3.1097	-0.0356	0.2094	0.0446	-0.2309	0.0012	0.0593	-0.1176	-0.2154	0.0344	0.0856	0	0.0252	0.072	0.0118	0.0824	39.2715	5.6559	37.6847
2	1.727	-0.8663	2.3784	1.428	-3.5092	12.9402	-0.1876	-0.1003	0.1305	0.0329	0.2106	0.0356	-0.5073	-0.3603	-0.0229	0.0578	0.0125	0.0138	0.0824	-0.0279	0.0686	42.1922	9.9853	51.8122
3	1.87	1.4357	2.9632	9.0464	9.8097	19.3553	0.0497	0.1556	0.1558	-0.0409	-0.1277	0.1645	-0.0563	-0.3382	0.078	0.0645	-0.0043	-0.0116	0.0623	0.0176	0.0948	42.135	7.2452	34.0818
4	2.2424	-5.1309	-0.2004	14.2426	1.8301	0.7696	0.239	0.1362	-0.0539	-0.1545	-0.1534	0.1165	-0.0662	0.262	-0.0856	0.0712	-0.044	0.003	0.0957	-0.002	0.0245	44.0819	0.4971	23.2194
5	2.791	0.9858	-1.1175	2.0675	-0.1597	2.6992	-0.0584	0.0182	-0.2777	-0.1587	-0.0266	0.059	0.1267	-0.1396	0.085	0.0584	-0.0017	-0.0123	0.0456	-0.0148	0.1065	40.667	-5.7652	34.4882
6	8.9662	-3.1184	0.075	8.4385	-1.446	3.1793	-0.1616	-0.5916	-0.1867	0.7996	0.2988	0.2688	-0.0536	-0.0738	-0.1373	0.0971	0.0069	0.041	0.0162	0.0531	0.1267	43.6681	-14.8077	43.6034
7	0.7476	-0.8705	0.1134	2.4249	0.8207	0.6602	-0.1254	-0.2338	-0.2024	-0.1187	-0.0582	0.1036	0.005	0.0431	0.1836	0.0926	-0.0016	0.0219	0.0558	-0.002	0.0483	45.5316	-1.7638	45.1728
8	11.4633	4.0967	-2.1788	7.6056	-8.3472	9.7413	-0.0247	-0.3037	0.1452	-0.0428	-0.1431	-0.2061	-0.2475	0.5429	0.1678	0.069	-0.0243	0.022	0.1278	-0.0564	0.1016	59.5598	8.8261	42.7328
9	2.1547	-0.9128	-0.767	1.0919	0.4896	1.3354	0.0746	-0.181	-0.2145	0.0312	-0.1888	-0.17	0.088	0.0618	0.1142	0.1013	0.016	-0.0173	0.0863	0.0025	0.0699	51.4873	-1.3898	43.4098
10	3.1438	6.8657	-0.0919	18.5974	7.9496	18.4365	0.1713	-0.4063	-0.6221	0.4669	-0.1845	-0.63	0.3288	0.0458	0.0132	0.051	0.0416	-0.0387	0.0639	0.0215	0.0816	54.4443	-7.8228	46.9901
11	4.1111	0.0363	-2.8934	0.3922	0.1804	2.1447	0.2168	0.0652	-0.4074	0.0038	-0.1698	0.0773	0.3288	-0.03	-0.047	0.0841	-0.0011	-0.0013	0.0023	-0.0143	0.0872	45.9624	-12.5136	35.2487
12	8.2501	3.4248	-5.9438	11.0617	-6.6798	12.115	-0.1869	0.28	-0.389	-0.1978	-0.0146	-0.3428	0.8028	0.185	0.2015	0.0844	0.0086	0.0076	0.0347	-0.0286	0.0951	52.9603	-10.5928	30.7333
13	0.8709	0.2585	0.0883	2.4678	0.9053	1.7211	-0.0193	0.1542	0.0674	-0.2534	0.0621	0.0339	-0.0926	-0.0084	-0.0429	0.0701	-0.0066	-0.0027	0.0641	-0.0053	0.0638	53.3038	5.4121	27.2482
14	15.4045	-9.5977	-3.6881	11.4474	4.0468	2.5912	-0.1949	-0.4482	-0.4721	0.297	0.1495	-0.121	0.2513	0.1494	0.0454	0.1277	-0.0064	-0.0024	0.1022	0.0215	0.103	57.4001	-5.5279	34.0874
15	0.8279	-0.6106	-0.0941	2.599	-0.0605	2.1815	-0.0734	-0.0027	0.0386	0.0093	0.0938	-0.1962	0.0008	0.1307	-0.0205	0.0537	0.0018	0.0053	0.0968	-0.0089	0.0898	53.8341	0.2698	35.8971
16	0.5415	-0.1015	-0.4946	1.2977	0.3638	1.5768	-0.0897	0.0592	0.0278	0.1092	0.0892	-0.0214	-0.0085	0.1007	0.0005	0.0648	0.0016	-0.0044	0.0552	0.0021	0.0674	54.1868	5.6883	30.7909
17	5.3049	0.1574	4.5943	4.4807	-1.4911	10.8349	-0.0774	-0.3313	0.6531	0.0787	0.0352	0.0935	-0.2863	-0.2514	0.0422	0.0403	-0.0204	0.0403	0.0533	-0.0202	0.1279	48.3104	14.6308	43.4269
18	7.5299	-2.2832	-2.6442	7.0959	-0.9865	1.4279	-0.2595	-0.2655	0.3525	0.3258	0.159	-0.2204	-0.1461	0.2465	0.1006	0.0992	-0.0172	-0.013	0.0953	-0.0463	0.0907	58.3759	9.7956	50.3243
19	13.6834	-3.4	-3.0822	1.3476	0.4593	0.8812	-0.2155	-0.2184	-0.5333	0.0164	0.0556	0.1929	0.0843	0.2123	0.1599	0.0728	-0.0165	0.0107	0.086	-0.0231	0.0701	55.2375	4.2305	52.6871
20	4.4834	0.3201	3.3451	2.0015	0.6672	4.8369	-0.016	-0.2018	0.2648	-0.0251	-0.1119	0.0923	-0.0825	-0.3025	0.1279	0.0606	-0.0038	0.0149	0.0817	-0.0067	0.0917	37.9275	2.7714	43.002
21	3.0323	-0.2213	-0.6472	3.3956	0.3766	13.3374	0.0179	-0.2272	-0.1089	0.3394	0.0935	0.0669	0.4068	-0.3263	-0.1114	0.078	-0.0149	-0.01	0.0712	0.0309	0.1071	40.6342	-0.4339	6.079
22	4.2646	2.0974	1.1686	3.1149	-2.1614	9.957	0.1633	0.2895	-0.2597	-0.1897	0.0048	-0.0705	0.4119	0.12	-0.168	0.0683	0.0105	-0.0048	0.0677	-0.0482	0.0789	46.4259	-0.0497	-11.7732
23	1.3883	-1.2792	-3.266	2.5135	5.2475	14.5099	-0.0504	0.0555	-0.223	0.2126	-0.0826	0.1124	0.5358	-0.2492	0.133	0.0794	0.0019	-0.004	0.0752	0.0224	0.0821	44.2361	-0.3845	6.6909
24	1.7898	0.4567	-0.2812	0.8441	-0.2726	9.7601	0.093	-0.2088	-0.0015	0.058	-0.0765	0.1393	-0.1176	-0.055	-0.0165	0.0533	-0.0045	0.017	0.0576	0.0157	0.0739	39.6503	9.0222	14.6677
25	1.2093	-0.5413	1.1352	6.6934	-2.3165	1.834	0.0265	0.0547	0.1272	-0.1053	0.0288	0.2247	-0.1015	-0.1628	-0.0553	0.0475	0.0298	0.0004	0.0881	0.0037	0.0638	32.5115	14.3984	1.9519
26	1.4218	-1.8149	-1.5765	4.4876	2.4537	6.3545	-0.0318	0.3309	0.0597	-0.0356	-0.1244	0.4493	0.1579	-0.369	0.1562	0.0634	-0.017	0.0143	0.0667	-0.016	0.0862	36.7845	9.4685	-1.9058
27	9.6127	-3.7307	-1.3281	5.5081	-0.7883	8.8594	-0.0503	0.1744	0.2628	0.1135	0.1151	-0.3527	-0.364	0.1651	-0.0649	0.0964	-0.0088	0.0188	0.0841	0.0151	0.0447	51.0081	10.9131	-3.6119
28	46.6398	11.1964	11.6804	7.3259	-3.1693	10.6183	0.1785	1.287	-1.3508	-0.1849	0.1816	-0.337	0.2237	0.4875	-0.36	0.0435	-0.0209	-0.0051	0.13	-0.0303	0.1232	60.7926	8.3638	0.9573
29	2.5161	-1.4005	-1.5471	3.1803	2.0446	1.5347	0.007	0.1355	0.288	0.1407	-0.0829	0.0289	-0.1502	-0.0147	0.0758	0.0676	-0.0234	0.0238	0.0775	0.0208	0.0603	45.2154	13.191	-1.4012
30	17.4166	-2.7369	-10.4569	1.7771	2.0533	12.4981	0.5305	0.4015	0.5081	-0.4767	-0.1263	-0.2539	-0.7149	0.1073	-0.4042	0.1027	0.0153	0.0434	-0.0062	0.0437	0.072	43.797	19.5492	-3.1904
31	6.9943	0.1459	4.3058	3.9761	0.7129	3.2198	-0.0885	0.1097	0.496	0.1193	-0.1159	0.0842	-0.1648	0.0484	0.2043	0.1028	0.0115	0.0311	0.0619	-0.0131	0.0526	39.1237	19.4151	10.3809
32	1.944	-0.3141	0.2141	1.5795	0.7968	2.3595	0.052	-0.1508	-0.0092	0.1085	0.0725	-0.0589	0.0102	0.1601	-0.1244	0.0526	-0.0181	-0.0001	0.0757	0.0132	0.0532	51.8065	8.8508	14.1655
33	17.5017	-3.4948	-7.3939	13.7741	6.1805	23.2811	0.4589	-0.016	1.2668	-0.6434	0.2101	-0.4	-1.4989	0.5292	-0.669	0.1228	-0.0681	0.013	-0.0217	0.0104	0.1107	48.4589	23.4606	10.022
34	0.1269	-0.7765	-0.0729	5.067	-0.1464	1.1523	0.0462	-0.0218	0.0342	0.0157	0.0447	-0.1233	-0.2118	0.0775	-0.0908	0.0722	-0.0142	0.0121	0.0454	0.0072	0.0602	44.8292	15.6971	5.3746
35	1.4157	0.0371	0.6552	12.0611	-2.1356	10.7384	-0.0787	-0.1272	-0.1308	0.3005	0.0303	-0.3675	0.1628	0.7723	0.0484	0.0562	-0.02	-0.0106	0.1385	0.01	0.0737	55.7163	6.8606	6.04
36	1.0341	-0.1652	0.1421	0.0558	0.1932	1.6081	-0.0481	-0.0094	0.0984	-0.0621	0.0468	0.021	-0.0422	0.2129	0.0013	0.0727	-0.0139	0.0002	0.102	0.0059	0.0639	53.1242	8.5426	11.6145
37	8.5674	1.9117	-9.4384	5.4052	-6.2933	31.0383	-0.05	0.0157	-0.8797	-0.3168	-0.5526	-0.1989	0.9861	0.3663	0.6026	0.0292	0.0382	-0.005	0.0595	-0.0039	0.1245	53.6084	-2.9816	0.8732
38	2.9623	3.0816	-1.3682	6.9291	-1.925	6.0479	0.0875	-0.056	-0.0429	-0.1042	-0.1695	0.023	-0.1227	0.2715	0.082	0.033	-0.0269	0.0035	0.1501	-0.0354	0.0615	57.2236	8.0459	-7.3615
39	2.3179	0.6546	-0.2624	0.7914	1.2165	2.776	0.0436	-0.0298	0.035	-0.1129	0.1125	0.1404	-0.1706	0.1238	-0.1561	0.065	-0.0047	0.0176	0.0643	0.0016	0.057	49.1892	7.2391	-10.1971
40	5.8301	2.8666	-4.8376	3.331	-1.0898	10.6547	-0.1475	0.0204	-0.2001	-0.1223	0.0421	-0.0802	0.3871	0.3037	0.1054	0.108	0.0207	-0.0046	0.0757	-0.0078	0.0855	36.7376	-0.4123	1.9888

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	6 - 13	19 - 26
2	X-RAY DIFFRACTION	2	A	A	14 - 22	27 - 35
3	X-RAY DIFFRACTION	3	A	A	23 - 27	36 - 40
4	X-RAY DIFFRACTION	4	A	A	28 - 33	41 - 46
5	X-RAY DIFFRACTION	5	A	A	34 - 48	47 - 61
6	X-RAY DIFFRACTION	6	A	A	49 - 56	62 - 69
7	X-RAY DIFFRACTION	7	A	A	57 - 65	70 - 78
8	X-RAY DIFFRACTION	8	A	A	66 - 71	79 - 84
9	X-RAY DIFFRACTION	9	A	A	72 - 79	85 - 92
10	X-RAY DIFFRACTION	10	A	A	80 - 86	93 - 99
11	X-RAY DIFFRACTION	11	A	A	87 - 92	100 - 105
12	X-RAY DIFFRACTION	12	A	A	93 - 96	106 - 109
13	X-RAY DIFFRACTION	13	A	A	97 - 109	110 - 122
14	X-RAY DIFFRACTION	14	A	A	110 - 116	123 - 129
15	X-RAY DIFFRACTION	15	A	A	117 - 128	130 - 141
16	X-RAY DIFFRACTION	16	A	A	129 - 146	142 - 159
17	X-RAY DIFFRACTION	17	A	A	147 - 153	160 - 166
18	X-RAY DIFFRACTION	18	A	A	154 - 160	167 - 173
19	X-RAY DIFFRACTION	19	A	A	161 - 168	174 - 181
20	X-RAY DIFFRACTION	20	A	A	169 - 177	182 - 190
21	X-RAY DIFFRACTION	21	B	B	6 - 12	19 - 25
22	X-RAY DIFFRACTION	22	B	B	13 - 18	26 - 31
23	X-RAY DIFFRACTION	23	B	B	19 - 29	32 - 42
24	X-RAY DIFFRACTION	24	B	B	30 - 40	43 - 53
25	X-RAY DIFFRACTION	25	B	B	41 - 55	54 - 68
26	X-RAY DIFFRACTION	26	B	B	56 - 62	69 - 75
27	X-RAY DIFFRACTION	27	B	B	63 - 67	76 - 80
28	X-RAY DIFFRACTION	28	B	B	68 - 72	81 - 85
29	X-RAY DIFFRACTION	29	B	B	73 - 79	86 - 92
30	X-RAY DIFFRACTION	30	B	B	80 - 87	93 - 100
31	X-RAY DIFFRACTION	31	B	B	88 - 96	101 - 109
32	X-RAY DIFFRACTION	32	B	B	97 - 112	110 - 125
33	X-RAY DIFFRACTION	33	B	B	113 - 117	126 - 130
34	X-RAY DIFFRACTION	34	B	B	118 - 123	131 - 136
35	X-RAY DIFFRACTION	35	B	B	124 - 128	137 - 141
36	X-RAY DIFFRACTION	36	B	B	129 - 146	142 - 159
37	X-RAY DIFFRACTION	37	B	B	147 - 151	160 - 164
38	X-RAY DIFFRACTION	38	B	B	152 - 163	165 - 176
39	X-RAY DIFFRACTION	39	B	B	164 - 170	177 - 183
40	X-RAY DIFFRACTION	40	B	B	171 - 177	184 - 190

-
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