PDB-6wa6: Structure of the Chlamydia pneumoniae CdsV protein

ID or keywords:

Entry

Database: PDB / ID: 6wa6

Title

Structure of the Chlamydia pneumoniae CdsV protein

Components

Low calcium response locus protein D

Keywords

PROTEIN TRANSPORT / Type III secretion / protein secretion / effector secretion

Function / homology

Function and homology information

protein secretion / membrane => GO:0016020 / plasma membrane
Similarity search - Function

Biological species

Chlamydia pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIRAS / Resolution: 2.8 Å

Authors

Jensen, J.L. / Spiller, B.W.

Funding support

United States, 1items

Citation

Journal: Plos Pathog. / Year: 2020
Title: "The structure of the Type III secretion system export gate with CdsO, an ATPase lever arm".
Authors: Jensen, J.L. / Yamini, S. / Rietsch, A. / Spiller, B.W.

History

Deposition	Mar 24, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 30, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 28, 2020	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
Revision 1.2	Mar 6, 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	6wa6.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb6wa6.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	6wa6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6wa6_validation.pdf.gz	532.4 KB	Display	wwPDB validaton report
Full document	6wa6_full_validation.pdf.gz	584.7 KB	Display
Data in XML	6wa6_validation.xml.gz	105.1 KB	Display
Data in CIF	6wa6_validation.cif.gz	140.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wa/6wa6 ftp://data.pdbj.org/pub/pdb/validation_reports/wa/6wa6	HTTPS FTP

-
Related structure data

Related structure data	6wa9C C: citing same article (ref.)
Similar structure data	7k08-d 11928 4nhg-1 22589 4llf-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

Deposited unit

A: Low calcium response locus protein D

B: Low calcium response locus protein D

C: Low calcium response locus protein D

D: Low calcium response locus protein D

E: Low calcium response locus protein D

F: Low calcium response locus protein D

G: Low calcium response locus protein D

H: Low calcium response locus protein D

I: Low calcium response locus protein D

hetero molecules

395 kDa, 9 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)	66.650, 280.440, 290.410
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Low calcium response locus protein D / CdsV / Low calcium response D / Type III secretion inner membrane protein SctV Mass: 43706.141 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydia pneumoniae (bacteria) Gene: lcrD, CP_0434, CPn_0323, BN1224_CV15_B_02600, BN1224_GiD_A_03360, BN1224_H12_DC_00060, BN1224_MUL2216_E_00600, BN1224_Panola_E_01450, BN1224_PB1_B_03220, BN1224_U1271_C_01630, BN1224_UZG1_A_ ...Gene: lcrD, CP_0434, CPn_0323, BN1224_CV15_B_02600, BN1224_GiD_A_03360, BN1224_H12_DC_00060, BN1224_MUL2216_E_00600, BN1224_Panola_E_01450, BN1224_PB1_B_03220, BN1224_U1271_C_01630, BN1224_UZG1_A_03350, BN1224_Wien2_E_01080, BN1224_YK41_BG_00210, CWL029c_C_01630 Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q9Z8L5
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.45 Å³/Da / Density % sol: 64.35 %
Crystal grow	Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.75 / Details: 100 mM HEPES pH 6.75, 5% w/v PEG 6000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 9, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 2.8→126.27 Å / Num. obs: 134510 / % possible obs: 99.4 % / Redundancy: 6 % / CC_1/2: 0.999 / Net I/σ(I): 15.6
Reflection shell	Resolution: 2.8→2.85 Å / Num. unique obs: 13227 / CC_1/2: 0.718

-
Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
XDS		data reduction
XDS		data scaling
SHARP		phasing

Refinement

Method to determine structure:

MIRAS / Resolution: 2.8→126.27 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.24

	R_factor	Num. reflection	% reflection
R_free	0.2442	6708	4.99 %
R_work	0.1959	-	-
obs	0.1983	134496	99.37 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.8→126.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24779	0	78	58	24915

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	25455
X-RAY DIFFRACTION	f_angle_d	1.092	34525
X-RAY DIFFRACTION	f_dihedral_angle_d	20.736	9784
X-RAY DIFFRACTION	f_chiral_restr	0.062	3994
X-RAY DIFFRACTION	f_plane_restr	0.008	4337

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 (%)
2.8-2.83	0.3416	205	0.3111	4094	X-RAY DIFFRACTION	98
2.83-2.87	0.3437	248	0.2937	4209	X-RAY DIFFRACTION	100
2.87-2.9	0.3523	242	0.2912	4229	X-RAY DIFFRACTION	100
2.9-2.94	0.3146	229	0.2797	4134	X-RAY DIFFRACTION	99
2.94-2.98	0.3461	221	0.2726	4233	X-RAY DIFFRACTION	100
2.98-3.02	0.3035	201	0.2667	4300	X-RAY DIFFRACTION	100
3.02-3.06	0.3486	215	0.2689	4188	X-RAY DIFFRACTION	99
3.06-3.1	0.3539	246	0.2907	4200	X-RAY DIFFRACTION	100
3.11-3.15	0.3146	214	0.2712	4269	X-RAY DIFFRACTION	100
3.15-3.21	0.3192	236	0.2506	4197	X-RAY DIFFRACTION	100
3.21-3.26	0.2751	205	0.2342	4232	X-RAY DIFFRACTION	100
3.26-3.32	0.2632	239	0.2244	4248	X-RAY DIFFRACTION	100
3.32-3.38	0.2698	227	0.2267	4205	X-RAY DIFFRACTION	100
3.38-3.45	0.2859	232	0.2194	4245	X-RAY DIFFRACTION	100
3.45-3.53	0.2868	222	0.2154	4267	X-RAY DIFFRACTION	100
3.53-3.61	0.2651	229	0.2098	4202	X-RAY DIFFRACTION	100
3.61-3.7	0.2771	251	0.2215	4302	X-RAY DIFFRACTION	100
3.7-3.8	0.2707	218	0.2095	4175	X-RAY DIFFRACTION	100
3.8-3.91	0.2348	226	0.1854	4325	X-RAY DIFFRACTION	100
3.91-4.04	0.2195	195	0.1903	4249	X-RAY DIFFRACTION	100
4.04-4.18	0.2383	228	0.1771	4280	X-RAY DIFFRACTION	99
4.18-4.35	0.2082	212	0.1607	4255	X-RAY DIFFRACTION	100
4.35-4.55	0.1953	238	0.1491	4269	X-RAY DIFFRACTION	99
4.55-4.79	0.2151	241	0.1562	4298	X-RAY DIFFRACTION	99
4.79-5.09	0.1888	208	0.1556	4304	X-RAY DIFFRACTION	99
5.09-5.48	0.2056	201	0.1584	4305	X-RAY DIFFRACTION	99
5.48-6.03	0.2214	214	0.1721	4348	X-RAY DIFFRACTION	99
6.03-6.9	0.2626	228	0.1994	4311	X-RAY DIFFRACTION	99
6.91-8.7	0.2107	205	0.177	4354	X-RAY DIFFRACTION	98
8.7-126.27	0.203	232	0.1781	4562	X-RAY DIFFRACTION	97

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	1.5398	-0.4596	0.4382	2.6104	-0.1172	1.4668	-0.1067	-0.1019	-0.1974	-0.0206	0.1472	-0.1836	0.1824	0.0935	-0.0208	0.3415	0.0271	0.0883	0.3325	0.009	0.3943	25.8629	-44.7806	-2.5778
2	6.9281	1.9782	-1.6553	6.5851	-0.6789	7.6795	0.0323	-0.5497	0.0033	0.3611	0.1497	0.7719	-0.0065	-0.1767	-0.0545	0.3948	-0.0979	0.0983	0.38	0.0312	0.5276	-1.1579	-47.4585	-5.9953
3	3.8097	-1.1569	1.612	5.0658	-1.6165	5.9577	-0.4114	-0.6198	-0.2318	1.1334	0.2977	-0.2505	-0.0466	0.3827	0.0426	0.5327	0.0659	-0.07	0.5866	0.0234	0.4674	39.1583	-17.0656	30.6759
4	2.4669	0.8816	-0.3076	4.0268	1.2597	5.6755	-0.3255	-0.2046	0.0165	-0.1449	0.0129	0.1275	-0.0971	-0.2173	0.2493	0.2378	0.0467	-0.0786	0.3383	-0.043	0.4185	19.9981	-20.4162	6.8517
5	7.5624	-1.0391	-2.9446	6.1074	2.4524	6.2957	-0.3763	-1.3494	-0.2552	0.507	0.0205	0.5762	0.057	-0.3004	0.3333	0.4234	0.0383	0.1817	0.8343	-0.1876	0.5846	6.1882	-22.361	22.7305
6	2.3155	-0.7748	-0.3299	2.2136	-0.3272	5.4166	-0.3866	-0.2189	0.3401	0.3109	-0.1083	-0.9479	0.0799	0.928	0.3638	0.844	-0.1926	-0.2281	0.7481	0.0756	0.8151	47.7514	24.253	16.6671
7	3.1461	-0.9463	0.6389	3.2995	-0.6896	2.4627	-0.5326	-0.8387	0.3282	0.7545	0.1833	0.2194	-0.5579	0.1549	0.1786	0.7818	0.0012	-0.0704	0.6512	-0.0215	0.3658	34.2785	17.9873	21.1154
8	6.4251	0.7567	3.4325	2.9791	0.2809	6.1886	-0.7582	-1.3349	0.8926	0.7976	0.5564	0.885	-2.014	-0.5242	0.2193	1.4486	0.5126	0.2984	1.1679	0.1418	1.0566	9.8247	18.0457	26.901
9	5.4469	-0.6459	1.6933	4.768	0.6717	0.7016	0.2071	-1.4988	-0.61	1.0732	0.2482	0.3121	-1.3899	-1.139	0.0724	1.4631	0.3136	0.5859	0.963	0.111	1.03	16.9794	13.7209	29.4847
10	3.8716	2.2951	0.6463	4.4468	0.2646	4.6311	0.0376	0.1259	-0.1287	-0.1687	-0.0064	-0.6527	-0.2903	0.6395	-0.0684	0.6704	-0.145	0.0809	0.511	-0.0345	0.571	50.2769	49.7926	-10.7287
11	1.3478	1.0564	0.449	3.3899	0.5795	2.0617	0.0096	-0.1263	0.0978	-0.0079	0.0201	-0.0908	-0.2139	-0.0114	-0.017	0.5211	-0.0728	0.0108	0.4059	-0.0226	0.4076	37.2897	45.8309	-0.9309
12	4.1847	-2.9082	1.6045	9.0999	-0.624	6.9779	-0.0003	-0.6654	0.6815	0.9053	-0.0679	0.8871	-0.3944	-0.5876	0.0661	0.6648	0.111	0.253	0.7278	-0.1045	0.7552	15.6042	47.8623	6.9678
13	2.1092	1.7668	-0.1816	3.4616	-0.5919	1.1907	-0.4141	0.3502	0.5143	-0.5213	0.4177	0.0506	-1.2314	0.6422	-0.0434	1.7622	-0.4498	0.0594	0.8579	0.0265	0.7	44.624	61.2806	-46.8583
14	1.9809	0.596	1.0351	2.7489	-0.18	3.5367	0.0725	-0.0078	0.1297	-0.5279	0.0324	0.0677	-0.2534	-0.1418	-0.1129	0.7011	-0.0263	0.0423	0.4396	-0.079	0.3505	27.9876	44.5013	-27.1411
15	6.2335	-2.033	2.0854	3.7322	-2.4201	6.2149	0.197	0.2456	0.3807	-1.2208	-0.291	0.681	-0.5837	-0.6175	0.0901	1.1551	0.3416	-0.2149	0.6031	-0.0998	0.6673	15.038	60.7807	-29.9474
16	5.9965	3.0571	-4.4617	1.6801	-2.6098	8.0042	0.2078	0.2281	-0.5175	-0.6094	-0.1529	-0.6271	0.3916	0.8765	0.5245	1.733	-0.175	0.4111	0.8804	-0.1833	0.4854	42.1749	20.1602	-79.8134
17	2.7383	-0.171	-1.3385	0.7757	-1.7031	5.0467	0.0625	0.3287	-0.0107	-0.9178	0.26	-0.4478	-0.3465	0.5055	-0.2366	1.7529	-0.302	0.2957	0.7801	-0.0748	0.6123	40.7895	31.253	-79.3541
18	5.2755	-6.1619	4.2904	7.2065	-5.0728	3.7037	-0.2334	0.459	0.0239	-1.1126	0.2963	0.8727	0.1151	0.2196	0.1312	2.0507	-0.4962	-0.027	1.1169	0.2109	0.8392	32.9642	46.3834	-93.3615
19	0.6229	0.3593	-1.2795	0.2457	-0.815	2.6495	-0.4204	0.2952	0.303	-1.0678	0.3347	-0.3032	-0.1186	0.0229	-0.0006	1.7094	-0.3145	0.1239	0.742	0.0266	0.6341	36.977	36.8983	-74.9324
20	3.719	0.925	0.6237	5.2574	-0.0844	4.1165	-0.1726	0.1681	0.6037	-0.4211	0.0804	0.7337	-0.6404	-0.6169	0.075	1.0231	-0.0182	-0.0796	0.5305	-0.0628	0.5294	23.1267	38.4905	-54.2186
21	8.4246	5.6792	-5.4584	7.0726	-0.3478	7.4859	0.3912	0.4708	0.6622	-1.4083	-0.4779	1.4557	0.2033	-1.7234	0.3171	0.8924	0.209	-0.4233	1.3853	0.1598	1.4536	1.5657	42.1539	-65.9207
22	3.3556	2.7101	-1.2629	2.609	0.7264	6.8502	-0.223	0.6133	1.7259	-0.538	-0.0595	0.7831	-0.1148	-1.0963	-0.0753	1.6743	0.1149	-0.4286	1.5593	0.6976	1.0434	15.2249	49.6188	-70.9323
23	4.8105	-0.8791	-1.335	4.7262	-0.8526	5.0976	-0.2309	0.3894	0.3358	-1.027	0.5997	0.3895	-1.9005	-1.001	-0.4074	1.469	0.1306	-0.6717	0.7699	-0.0176	1.0919	15.3505	48.1752	-64.3586
24	2.2781	0.0987	-3.0751	1.8942	-0.7825	7.0409	-0.0636	0.3559	-0.0254	-0.0049	0.0937	-0.1553	0.8618	-0.0133	-0.053	1.0566	-0.0648	0.0661	0.6814	-0.0102	0.4711	32.0448	-4.8369	-89.3232
25	4.2918	-0.1969	2.3114	2.4219	0.5027	5.7261	-0.1944	-0.0061	0.248	-0.2139	0.0152	0.1072	-0.1869	-0.35	0.1708	1.1302	-0.1362	0.0178	0.5051	-0.0252	0.4236	19.8029	13.2445	-67.9767
26	7.6135	0.2711	2.6412	4.2515	-0.6069	7.7913	0.4652	0.922	-0.3807	-0.7172	-0.2997	0.2467	-0.2639	-0.379	-0.1647	1.1777	-0.0693	-0.2343	0.8815	-0.0336	0.4902	7.5359	13.5027	-86.8703
27	2.527	-0.2929	2.0112	2.1493	0.779	1.9779	-0.1804	0.1754	-0.4751	-0.3997	0.3675	-0.5959	0.3748	1.2263	0.0505	2.0676	0.1534	0.3494	0.7944	0.0461	0.6611	28.7562	-40.1653	-66.598
28	0.7091	0.0074	-0.8767	0.0092	-0.0055	1.076	0.0975	-0.0523	-0.8608	-0.2946	-0.6763	0.4244	1.5906	0.3256	0.2011	2.8698	0.0974	0.1708	0.704	-0.0477	0.8469	20.3542	-50.4285	-69.0469
29	1.1626	-0.1924	-0.9667	0.6843	1.602	4.0215	0.4857	0.3741	-0.509	-0.9942	-0.9049	0.6751	0.4858	-0.2526	0.3727	2.6124	0.2108	-0.0355	0.8663	-0.2043	0.8923	17.631	-44.8849	-82.8922
30	3.9215	0.6059	-1.9426	3.9199	-0.9838	7.8059	-0.0838	0.4488	0.1045	-0.1606	0.1489	0.3406	0.3834	-0.5776	-0.0533	1.2226	-0.1883	-0.0325	0.5375	0.0505	0.4707	15.8434	-14.2224	-63.8502
31	6.4871	0.6557	0.6789	2.7758	1.863	1.2483	-0.4919	1.7516	0.0417	-1.7615	0.672	0.411	-0.0306	-0.708	0.0005	1.4149	-0.5612	-0.7367	1.7385	0.0948	0.8736	-5.4038	-23.0387	-79.3213
32	5.9684	0.7876	0.0266	5.8506	1.3847	0.3285	0.1378	0.797	-0.1627	-1.2748	0.1417	1.0131	0.7714	-1.6753	-0.0415	1.1778	-0.4705	-0.3928	1.49	0.2326	0.9048	1.0475	-21.6872	-77.7293
33	2.593	-0.9819	-1.4355	2.591	3.4653	4.586	-0.1498	-0.2314	-0.5718	-0.077	0.1603	-0.4766	0.9182	0.6977	-0.2266	0.8756	0.1892	0.0677	0.6196	0.0575	0.5489	31.0497	-54.0444	-23.1438
34	3.6911	0.5736	0.3741	3.2357	2.88	2.5886	-0.2821	0.1629	-0.0442	-0.9355	0.1839	-1.0701	0.7475	0.6362	0.0399	1.2247	0.1072	0.3195	0.6123	-0.0182	0.6713	28.8071	-55.7096	-35.3869
35	1.5523	0.1901	-0.1245	4.0967	2.9118	2.0705	-0.1004	0.2888	-0.762	-0.5986	-0.0108	0.1441	0.5857	0.0173	0.0737	1.4814	-0.0047	0.256	0.5308	-0.1057	0.8598	20.3683	-68.9803	-37.4703
36	1.9751	-0.5906	0.592	4.2082	-0.7426	4.6192	-0.1428	0.1462	-0.008	-0.7753	0.1459	0.4175	0.0673	-0.1155	0.0225	1.0327	-0.1052	0.0082	0.4569	0.0435	0.4343	13.2046	-33.4568	-43.7595
37	4.3269	-0.0485	-1.5684	3.3755	-0.8623	0.8585	0.1888	0.2613	-0.7638	-1.4454	0.1589	0.55	1.2451	-1.1802	-0.0685	0.9934	-0.7831	-0.3137	1.4393	0.1649	1.1987	-6.8756	-48.0604	-44.939
38	8.0252	0.987	0.4192	5.144	1.7898	2.4383	-0.0529	-0.2108	-0.7573	-1.4043	-0.0247	0.8701	1.1746	-1.454	-0.0618	1.3235	-0.4982	-0.3594	1.1936	0.1226	0.9113	-1.6111	-48.5282	-50.2796

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 363 through 603 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 604 through 710 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 363 through 512 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 513 through 616 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 617 through 709 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 361 through 420 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 421 through 603 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 604 through 653 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 654 through 709 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 363 through 429 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 430 through 603 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 604 through 708 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 363 through 512 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 513 through 616 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 617 through 708 )
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 363 through 385 )
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 386 through 452 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 453 through 477 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 478 through 532 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 533 through 616 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 617 through 649 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 650 through 672 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 673 through 707 )
24	X-RAY DIFFRACTION	24	chain 'G' and (resid 364 through 532 )
25	X-RAY DIFFRACTION	25	chain 'G' and (resid 533 through 603 )
26	X-RAY DIFFRACTION	26	chain 'G' and (resid 604 through 709 )
27	X-RAY DIFFRACTION	27	chain 'H' and (resid 362 through 420 )
28	X-RAY DIFFRACTION	28	chain 'H' and (resid 421 through 452 )
29	X-RAY DIFFRACTION	29	chain 'H' and (resid 453 through 517 )
30	X-RAY DIFFRACTION	30	chain 'H' and (resid 518 through 603 )
31	X-RAY DIFFRACTION	31	chain 'H' and (resid 604 through 650 )
32	X-RAY DIFFRACTION	32	chain 'H' and (resid 651 through 703 )
33	X-RAY DIFFRACTION	33	chain 'I' and (resid 362 through 385 )
34	X-RAY DIFFRACTION	34	chain 'I' and (resid 386 through 429 )
35	X-RAY DIFFRACTION	35	chain 'I' and (resid 430 through 512 )
36	X-RAY DIFFRACTION	36	chain 'I' and (resid 513 through 603 )
37	X-RAY DIFFRACTION	37	chain 'I' and (resid 604 through 679 )
38	X-RAY DIFFRACTION	38	chain 'I' and (resid 680 through 707 )

-
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