PDB-8gja: RAD51C-XRCC3 structure

ID or keywords:

Entry

Database: PDB / ID: 8gja

Title

RAD51C-XRCC3 structure

Components

RAD51C
XRCC3

Keywords

DNA BINDING PROTEIN / DNA-binding DNA damage DNA repair ATP binding

Function / homology

P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION

Function and homology information

Biological species

Alvinella pompejana (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Arvai, A.S. / Tainer, J.A. / Williams, G. / Longo, M.A.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Cancer Institute (NIH/NCI)	R35CA220430	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	P01 CA092584	United States

Citation

Journal: Nat Commun / Year: 2023
Title: RAD51C-XRCC3 structure and cancer patient mutations define DNA replication roles.
Authors: Longo, M.A. / Roy, S. / Chen, Y. / Tomaszowski, K.H. / Arvai, A.S. / Pepper, J.T. / Boisvert, R.A. / Kunnimalaiyaan, S. / Keshvani, C. / Schild, D. / Bacolla, A. / Williams, G.J. / Tainer, J.A. / Schlacher, K.

History

Deposition	Mar 15, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 16, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Structure summary / Category: audit_author

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8gja.cif.gz	733.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8gja.ent.gz	610.6 KB	Display	PDB format
PDBx/mmJSON format	8gja.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8gja_validation.pdf.gz	3.3 MB	Display	wwPDB validaton report
Full document	8gja_full_validation.pdf.gz	3.3 MB	Display
Data in XML	8gja_validation.xml.gz	67.7 KB	Display
Data in CIF	8gja_validation.cif.gz	89.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gj/8gja ftp://data.pdbj.org/pub/pdb/validation_reports/gj/8gja	HTTPS FTP

-
Related structure data

Related structure data	8gj8C 8gj9C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#150 - Jun 2012 Sliding Clamps similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #190 - Oct 2015 Two-component Systems similarity (1)

Deposited unit

A: RAD51C

B: XRCC3

C: RAD51C

D: XRCC3

E: RAD51C

F: XRCC3

hetero molecules

216 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: RAD51C

B: XRCC3

hetero molecules

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

2

C: RAD51C

D: XRCC3

hetero molecules

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

3

E: RAD51C

F: XRCC3

hetero molecules

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

Unit cell

Length a, b, c (Å)	65.940, 112.300, 259.500
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	RAD51C Mass: 32077.500 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alvinella pompejana (invertebrata) / Production host: Escherichia coli (E. coli)
#2: Protein	XRCC3 Mass: 39028.309 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alvinella pompejana (invertebrata) / Production host: Escherichia coli (E. coli)
#3: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical	ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION Mass: 66.007 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: BeF₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.49 %
Crystal grow	Temperature: 288 K / Method: vapor diffusion, sitting drop Details: (25 mg/mL protein)+ 2.5 mM ADP601 BeF + 5mM MgCl2, grew with a 1:2 protein:crystallization reagent (1 M HEPES pH 7.5, 20% PEG 3,350, 2% Tacsimate pH 7.0,) ratio and reached maximum growth after 15 days.

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.11583 Å / Relative weight: 1
Reflection	Resolution: 2.6→38.33 Å / Num. obs: 60211 / % possible obs: 99.9 % / Redundancy: 26.4 % / B_iso Wilson estimate: 55.55 Å² / CC_1/2: 0.999 / Net I/σ(I): 15.5
Reflection shell	Resolution: 2.6→2.67 Å / Num. unique obs: 4378 / CC_1/2: 0.444

-
Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.6→38.33 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.38 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2318	1865	3.33 %
R_work	0.1856	-	-
obs	0.1871	56007	92.97 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.6→38.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14177	0	182	175	14534

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003
X-RAY DIFFRACTION	f_angle_d	0.854
X-RAY DIFFRACTION	f_dihedral_angle_d	15.811	5425
X-RAY DIFFRACTION	f_chiral_restr	0.048	2344
X-RAY DIFFRACTION	f_plane_restr	0.005	2507

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 (%)
2.6-2.67	0.3629	121	0.3164	3414	X-RAY DIFFRACTION	77
2.67-2.75	0.3372	120	0.2886	3591	X-RAY DIFFRACTION	81
2.75-2.84	0.3223	137	0.2672	3741	X-RAY DIFFRACTION	85
2.84-2.94	0.3004	130	0.2428	3882	X-RAY DIFFRACTION	88
2.94-3.06	0.3073	139	0.2315	4066	X-RAY DIFFRACTION	92
3.06-3.2	0.2822	145	0.2298	4181	X-RAY DIFFRACTION	94
3.2-3.37	0.2591	143	0.2091	4278	X-RAY DIFFRACTION	96
3.37-3.58	0.2245	150	0.1776	4336	X-RAY DIFFRACTION	97
3.58-3.85	0.204	154	0.174	4405	X-RAY DIFFRACTION	98
3.85-4.24	0.2184	151	0.161	4436	X-RAY DIFFRACTION	99
4.24-4.85	0.1899	155	0.1386	4510	X-RAY DIFFRACTION	100
4.85-6.11	0.2239	156	0.1805	4546	X-RAY DIFFRACTION	100
6.11-38.33	0.2016	164	0.1718	4756	X-RAY DIFFRACTION	100

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	0.23	-0.1692	-0.0515	0.1943	-0.0779	0.0624	0.4622	-0.0631	0.3266	0.2271	-0.1584	0.3062	-0.3136	0.1171	0.0131	0.3988	-0.052	0.0872	0.3904	-0.1278	0.5056	-7.5376	109.3498	114.849
2	0.6394	-0.2152	0.0488	0.1368	0.1572	0.6769	0.1177	0.3497	0.5099	-0.0586	0.2202	0.4025	0.0642	-0.2499	0.1569	0.3021	0.0337	0.0372	0.3691	0.1009	0.5966	-7.7149	108.8651	102.0824
3	0.0537	0.001	-0.0635	0.3683	-0.4426	0.5562	0.2702	0.0896	0.493	0.0116	0.1439	0.0675	-0.6627	0.0814	0.8748	0.5358	-0.0461	0.2698	0.3579	-0.1581	0.8319	1.6455	123.6724	109.6575
4	0.0576	0.1373	-0.0619	0.3852	-0.1265	0.2282	0.508	-0.8213	0.8576	0.9493	-0.522	0.9924	-0.5572	0.222	-0.0141	0.7652	-0.1563	0.4391	-0.4769	-0.7843	0.9279	0.1921	124.5899	118.5676
5	0.8528	-0.3995	0.9268	0.5622	-0.5141	1.2605	0.8175	-0.8834	-0.2801	0.464	-0.236	0.1183	0.4397	-0.0313	0.7151	0.4665	-0.2484	0.1729	0.6179	-0.1137	0.1984	1.3589	105.8492	122.4486
6	0.0859	0.0868	-0.0971	0.0893	-0.1023	0.1086	-0.2832	-0.1758	0.4808	-0.066	-0.2768	0.155	0.243	-0.0931	-0.0566	1.0047	-0.2859	-0.3741	0.9403	0.1618	0.8743	-2.4267	101.7779	130.3951
7	0.321	0.0656	0.125	0.032	0.1129	0.1455	-0.1485	0.5044	-0.3331	0.1923	0.1031	0.2829	-0.0492	-0.1182	-0.0789	1.1012	0.2699	0.4207	0.1289	-0.0495	1.9886	-6.1351	144.3	103.9429
8	0.8552	0.4611	-0.7454	1.1214	-0.6089	0.6633	0.1348	0.1379	-0.0324	-0.0455	-0.1107	-0.0353	0.0608	0.0715	0.0057	0.3347	0.0424	-0.0113	0.3407	0.0529	0.3267	23.4717	109.8245	93.8367
9	2.0089	-0.6929	0.1909	1.2019	-0.7773	0.5624	0.0133	-0.4304	0.4956	0.6911	-0.1422	-0.16	-0.5923	0.1682	-0.0118	0.5131	-0.0737	0.0354	0.3966	0.0391	0.4298	28.2957	123.6079	102.6049
10	1.9614	0.0672	-0.5118	0.7492	-0.2407	1.314	0.2965	-0.862	0.2267	0.3094	-0.1193	-0.0062	-0.4577	0.1133	0.2764	0.5106	-0.0771	0.001	0.5802	0.0161	0.3497	22.53	116.0746	111.2564
11	0.5926	-0.6082	-0.4707	0.6608	0.5078	0.5712	0.0019	0.297	-0.5706	0.0279	-0.2388	0.1063	-0.0069	-0.0868	-0.1654	0.2583	0.0298	-0.0345	0.1866	0.1036	0.4757	29.5975	93.2968	101.5521
12	0.0854	-0.0004	0.0588	0.0103	0.0031	0.0537	0.0124	0.1628	-0.1929	-0.7878	-0.0021	0.2293	0.4852	-0.4177	0.0006	0.4782	-0.0925	0.0172	0.4728	-0.076	0.4906	19.7377	80.7721	50.2556
13	0.9669	0.4094	-0.1512	0.5774	-0.0274	0.5548	0.0143	-0.4475	0.0882	-0.0824	0.0478	0.1037	-0.0335	-0.1659	0.0003	0.2913	0.0041	0.014	0.4538	-0.0252	0.2598	26.6582	88.9029	60.3348
14	0.4003	0.1758	0.5296	0.3527	0.0931	0.4919	0.297	-0.4269	-0.5227	0.2201	-0.0329	0.0066	0.1762	-0.2484	0.0216	0.4919	-0.1029	-0.0244	0.5356	0.1393	0.5486	31.7313	71.2849	64.0255
15	0.0105	0.0077	-0.0128	0.0005	-0.0062	-0.0036	-0.2078	-0.0025	-0.0931	-0.2713	-0.3737	-0.0958	0.1149	0.0947	-0.0014	0.8755	0.0482	-0.0007	0.7004	0.055	0.7893	49.7958	63.1307	48.8678
16	1.3279	-0.4352	0.4263	0.482	-0.1746	1.3208	0.2122	0.2353	-0.6512	-0.5056	0.0644	-0.5371	0.4272	0.0987	0.5707	0.5123	-0.0253	-0.0254	0.2518	-0.1167	0.4892	33.7051	72.2772	47.4975
17	0.1665	-0.0874	0.0436	0.0266	-0.0181	0.0602	0.0144	0.1755	-0.0761	-0.5158	0.0173	-0.0183	-0.3493	0.0625	-0.003	0.5205	-0.026	0.0476	0.3066	-0.0805	0.3375	31.8381	83.0577	40.5536
18	0.0226	-0.0042	-0.0227	0.0135	-0.0095	0.0502	-0.1046	0.0076	-0.099	0.0429	0.1635	0.0316	-0.039	-0.1951	-0.0005	1.1474	0.0264	0.2978	1.5312	0.6103	1.0974	27.4044	62.9465	91.2607
19	0.106	0.0605	-0.0458	0.0567	-0.0035	0.0107	0.0733	-0.1606	-0.1842	-0.1356	0.1674	0.2143	0.0548	-0.1425	0.0752	0.9953	-0.4177	-0.0797	0.9699	0.3645	0.7918	26.9979	59.6059	80.1548
20	0.164	-0.2075	-0.279	0.6836	0.7281	1.1447	0.0673	-0.9856	-0.2044	-0.1709	0.4464	0.5947	-0.171	-0.4903	0.3499	0.1929	-0.1429	-0.0763	0.9647	0.252	0.4142	27.3231	78.2924	79.0434
21	0.307	0.3667	0.2259	0.3545	0.2345	0.1779	0.0641	-0.6031	0.0179	0.1071	-0.0374	-0.0285	-0.1139	0.1856	0	0.3437	-0.0514	-0.0006	0.6209	-0.0814	0.398	55.0119	94.335	65.9802
22	0.8417	0.1701	-0.6337	0.5133	-0.0198	0.5838	0.1696	-0.9252	-0.2647	0.0548	-0.3495	-0.1964	0.0552	0.4512	-0.1238	0.4246	0.046	-0.1412	0.7792	0.0442	0.5433	61.8985	85.1589	70.1475
23	0.4459	-0.1474	0.1409	0.1628	0.0074	0.4013	0.0202	-0.0152	-0.2754	0.053	-0.1495	-0.2698	-0.1138	-0.0264	-0.0024	0.2661	0.0182	0.0043	0.3267	-0.0774	0.3168	62.0904	93.3536	52.5655
24	0.1266	0.0683	0.0395	0.0008	-0.0336	0.1075	0.0073	-0.191	0.2271	0.1013	-0.0623	0.1102	0.1761	0.0107	-0.0002	0.2611	-0.032	-0.0103	0.4617	-0.0394	0.3294	56.5216	97.5435	52.534
25	0.0558	-0.0727	-0.0119	0.1981	-0.0098	-0.0106	-0.1251	0.4344	0.0429	0.341	0.1222	-0.6122	-0.1913	0.1624	0.0023	0.3586	-0.1002	-0.026	0.6669	-0.0869	0.5633	80.3601	66.8322	96.2126
26	0.1618	-0.0312	0.1702	0.4743	-0.2359	0.2358	-0.182	0.2676	-0.2339	0.0463	0.2059	0.1118	-0.0824	0.2029	0.0751	0.3714	-0.0094	-0.002	0.4014	-0.1489	0.4115	72.6787	57.6115	101.1466
27	0.0173	0.0323	0.0275	0.0396	0.0581	0.061	-0.0599	-0.2144	0.2841	0.1293	0.2452	-0.0431	-0.0204	-0.3803	0.01	0.4775	0.213	-0.121	0.8892	-0.2402	0.9569	86.9254	45.7958	98.7756
28	0.0144	-0.025	0.1017	0.0581	0.08	0.2275	0.0108	-0.3646	-0.2793	0.359	-0.0837	-0.0846	-0.0789	-0.04	-0	0.5154	0.0396	-0.092	0.5224	-0.0813	0.4762	73.4641	64.0542	115.2237
29	-0.0057	0.0011	-0.0026	0.0121	0.0212	0.0327	-0.1671	0.3768	0.0796	0.1626	0.0992	0.1625	0.0387	-0.1205	0.0001	0.6162	0.0023	-0.0501	0.4054	-0.1455	0.6574	57.7847	77.3935	112.4036
30	0.0518	0.0077	-0.0686	-0.0012	0.0003	0.0271	0.2352	0.185	0.2171	0.6463	-0.199	-0.2517	-0.4374	0.2991	-0.0003	0.6657	-0.029	-0.1296	0.5269	-0.0758	0.6686	71.4609	80.4773	112.276
31	0.1054	0.0359	-0.1304	0.132	0.0047	0.1141	0.0654	0.3809	0.3622	0.1813	-0.021	0.0615	-0.4322	0.2558	0.0142	0.4075	-0.0439	-0.0791	0.4498	-0.001	0.5692	63.1103	76.9353	100.0307
32	0.0862	0.0959	-0.0982	0.0808	-0.0925	0.1053	-0.1581	-0.0587	0.5391	-0.2537	-0.4074	0.0077	-0.5768	-0.2572	-0.001	0.6154	-0.0838	-0.0856	0.516	-0.0191	0.4863	64.9794	74.6234	94.9805
33	1.1991	-0.272	0.1028	0.1326	-0.0023	0.0422	0.1173	0.678	-0.3728	0.1469	0.0008	-0.062	-0.1138	0.4205	0.0536	0.472	-0.1102	0.0585	0.6122	-0.0465	0.2721	69.342	65.5268	88.3406
34	0.5992	0.1752	-0.2549	0.3137	-0.0437	0.5011	-0.0454	-0.2837	0.1472	0.3204	-0.2316	-0.1727	-0.2167	-0.0297	-1.0368	0.8609	0.0722	-0.3222	0.5081	-0.2438	0.4562	70.3069	77.3573	129.6208
35	0.3066	0.1792	0.0547	0.0941	-0.0448	0.2782	-0.174	0.0149	-0.2168	0.1308	0.1262	-0.1655	0.0747	-0.105	0.0001	0.4631	0.0316	0.0143	0.3378	-0.0626	0.3532	46.0105	51.5121	110.5976
36	1.5927	-0.0756	-0.4293	1.5158	0.3899	0.8707	-0.0691	-0.0333	0.2202	0.3182	0.0713	0.1003	-0.1042	-0.2238	0.2758	0.478	0.0338	0.0348	0.3574	-0.0424	0.3351	39.664	62.712	111.3833
37	0.101	-0.0059	-0.1525	0.0883	0.2706	0.5329	-0.0451	0.112	-0.171	-0.1699	-0.1045	0.1366	-0.0879	0.0391	-0.0901	0.3752	-0.0293	-0.0145	0.3497	-0.174	0.421	38.6863	46.7697	95.8926

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 52 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 53 through 141 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 142 through 163 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 164 through 222 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 223 through 260 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 261 through 274 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 5 through 54 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 55 through 181 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 182 through 219 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 220 through 290 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 291 through 345 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1 through 28 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 29 through 141 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 142 through 198 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 199 through 211 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 212 through 247 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 248 through 274 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 1 through 16 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 17 through 40 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 41 through 66 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 67 through 145 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 146 through 244 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 245 through 313 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 314 through 345 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 2 through 28 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 29 through 96 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 97 through 109 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 110 through 151 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 152 through 163 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 164 through 184 )
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 185 through 211 )
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 212 through 240 )
33	X-RAY DIFFRACTION	33	chain 'E' and (resid 241 through 264 )
34	X-RAY DIFFRACTION	34	chain 'F' and (resid 3 through 66 )
35	X-RAY DIFFRACTION	35	chain 'F' and (resid 67 through 145 )
36	X-RAY DIFFRACTION	36	chain 'F' and (resid 146 through 283 )
37	X-RAY DIFFRACTION	37	chain 'F' and (resid 284 through 344 )

-
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