PDB-5drx: Crystal structure of the BCR Fab fragment from subset #4 case CLL240

ID or keywords:

Entry

Database: PDB / ID: 5drx

Title

Crystal structure of the BCR Fab fragment from subset #4 case CLL240

Components

CLL240 BCR light chain
CLL240 heavy chain (VH and CH1 domains)

Keywords

IMMUNE SYSTEM / Immunoglobulin fold / B cell receptor / chronic lymphocytic leukemia / Receptor-ligand complex

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.104 Å

Authors

Minici, C. / Degano, M.

Funding support

Italy, 2items

Citation

Journal: Nat Commun / Year: 2017
Title: Distinct homotypic B-cell receptor interactions shape the outcome of chronic lymphocytic leukaemia.
Authors: Minici, C. / Gounari, M. / Ubelhart, R. / Scarfo, L. / Duhren-von Minden, M. / Schneider, D. / Tasdogan, A. / Alkhatib, A. / Agathangelidis, A. / Ntoufa, S. / Chiorazzi, N. / Jumaa, H. / ...

History

Deposition	Sep 16, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Sep 28, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 26, 2022	Group: Database references / Category: citation / citation_author / database_2 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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	May 1, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5drx.cif.gz	369.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5drx.ent.gz	303.5 KB	Display	PDB format
PDBx/mmJSON format	5drx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5drx_validation.pdf.gz	463.2 KB	Display	wwPDB validaton report
Full document	5drx_full_validation.pdf.gz	468.1 KB	Display
Data in XML	5drx_validation.xml.gz	39.4 KB	Display
Data in CIF	5drx_validation.cif.gz	57.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dr/5drx ftp://data.pdbj.org/pub/pdb/validation_reports/dr/5drx	HTTPS FTP

-
Related structure data

Related structure data	5drwC 5ifhC C: citing same article (ref.)
Similar structure data	6umj-d 5my4-d 5wl2-2 3ifp-4 3ifn-d 6b5t-d 5w3p-d 4osu-d 6vbo-d 5xaj-2 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 - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

H: CLL240 heavy chain (VH and CH1 domains)

L: CLL240 BCR light chain

A: CLL240 heavy chain (VH and CH1 domains)

B: CLL240 BCR light chain

hetero molecules

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

1

H: CLL240 heavy chain (VH and CH1 domains)

L: CLL240 BCR light chain

hetero molecules

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

2

A: CLL240 heavy chain (VH and CH1 domains)

B: CLL240 BCR light chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	86.187, 92.327, 135.130
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	CLL240 heavy chain (VH and CH1 domains) Mass: 24563.494 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Chronic lymphocytic leukemia clone / Source: (gene. exp.) Homo sapiens (human) / Cell: B lymphocyte / Gene: IGHV4-34, IGHJ6, IGHG103 / Production host: Escherichia coli* (E. coli)
#2: Antibody	CLL240 BCR light chain Mass: 24346.057 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Chronic lymphocytic leukemia clone / Source: (gene. exp.) Homo sapiens (human) / Cell: B lymphocyte / Gene: IGKV2-30, IGKJ2, IGKC01 / Production host: Escherichia coli* (E. coli)
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 647 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.75 Å³/Da / Density % sol: 55.24 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: 0.2 M BisTris, 8% (w/v) PEG 20000

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID29 / Wavelength: 0.9726 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 6, 2013

Radiation

Monochromator: SI[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9726 Å / Relative weight: 1

Reflection

Resolution: 2.1→50 Å / Num. obs: 63033 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 13.28 % / B_iso Wilson estimate: 44.67 Å² / R_merge F obs: 0.999 / R_merge(I) obs: 0.138 / R_rim(I) all: 0.144 / Χ²: 1.088 / Net I/σ(I): 12.34 / Num. measured all: 837112

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2.1-2.23		12.32	0.668	1.23	1.26	121258	10029	9838	1.283	98.1
2.23-2.38			0.835	0.864	2.34	131207	9525	9522	0.898	100
2.38-2.58			0.923	0.551	3.78	116670	8863	8859	0.573	100
2.58-2.82			0.97	0.352	6.59	113326	8156	8154	0.365	100
2.82-3.15			0.989	0.205	11.59	97434	7437	7435	0.213	100
3.15-3.64			0.996	0.121	20.25	91398	6598	6598	0.126	100
3.64-4.45			0.998	0.081	29.67	74423	5607	5607	0.084	100
4.45-6.26			0.999	0.066	35.8	58112	4421	4420	0.068	100
	6.26		0.999	0.051	42.9	33284	2607	2600	0.053	99.7

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: CLL183 Fab fragment

Resolution: 2.104→46.163 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.53 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2219	3194	5.07 %	Random selection
R_work	0.1938	59826	-	-
obs	0.1953	63020	99.66 %	-

Solvent computation

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

Displacement parameters

B_iso max: 118.65 Å² / B_iso mean: 47.3515 Å² / B_iso min: 17.85 Å²

Refinement step

Cycle: final / Resolution: 2.104→46.163 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6752	0	36	647	7435
B_iso mean	-	-	57.36	42.54	-
Num. residues	-	-	-	-	877

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	7039
X-RAY DIFFRACTION	f_angle_d	1.06	9583
X-RAY DIFFRACTION	f_chiral_restr	0.041	1061
X-RAY DIFFRACTION	f_plane_restr	0.005	1225
X-RAY DIFFRACTION	f_dihedral_angle_d	13.077	2551

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.1037-2.1351	0.3012	116	0.2996	2348	2464	93
2.1351-2.1685	0.3729	139	0.2854	2581	2720	100
2.1685-2.204	0.3381	147	0.2743	2579	2726	100
2.204-2.242	0.3274	115	0.2535	2579	2694	100
2.242-2.2828	0.2829	147	0.2491	2589	2736	100
2.2828-2.3267	0.3017	125	0.2504	2590	2715	100
2.3267-2.3742	0.2922	138	0.24	2583	2721	100
2.3742-2.4258	0.2633	154	0.2442	2579	2733	100
2.4258-2.4823	0.2748	134	0.2397	2554	2688	100
2.4823-2.5443	0.3063	152	0.2362	2596	2748	100
2.5443-2.6131	0.2697	140	0.246	2586	2726	100
2.6131-2.69	0.279	126	0.2379	2601	2727	100
2.69-2.7768	0.3209	162	0.2305	2575	2737	100
2.7768-2.876	0.2614	125	0.2194	2634	2759	100
2.876-2.9912	0.2258	140	0.209	2579	2719	100
2.9912-3.1273	0.2273	147	0.2011	2592	2739	100
3.1273-3.2921	0.2782	133	0.1996	2627	2760	100
3.2921-3.4983	0.2094	134	0.1923	2622	2756	100
3.4983-3.7683	0.1899	151	0.1762	2625	2776	100
3.7683-4.1473	0.1798	135	0.1593	2636	2771	100
4.1473-4.7469	0.1933	156	0.1413	2652	2808	100
4.7469-5.9786	0.1532	159	0.1506	2669	2828	100
5.9786-46.1746	0.1817	119	0.1921	2850	2969	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	2.0615	2.5053	1.6938	3.7124	2.7029	3.5587	-0.02	0.2062	-0.2814	0.1843	0.2624	-0.5555	0.2314	0.5886	-0.2472	0.3908	0.1076	-0.0515	0.5545	-0.0704	0.4918	95.3798	56.7016	1.3617
2	4.4822	0.21	-1.039	0.9786	-0.0811	1.7873	0.0609	-0.4871	0.1247	0.2402	-0.0274	0.0215	-0.1181	-0.0559	-0.0121	0.4592	0.028	-0.066	0.4774	-0.019	0.4435	84.6266	73.9991	32.4067
3	4.623	1.303	-5.4887	2.6193	-2.1601	8.2654	0.1878	0.1415	0.0877	0.0265	-0.0426	0.1218	-0.2997	-0.1593	0.0167	0.3591	0.0024	-0.0477	0.356	-0.017	0.3228	69.5076	61.3822	1.6988
4	2.7697	-0.1931	-0.6357	2.7614	0.2532	2.0619	-0.0415	-0.1285	-0.1363	0.1518	0.0012	0.0067	0.2437	-0.0454	-0.0086	0.3473	0.0006	-0.0246	0.3862	-0.0367	0.2937	75.6902	51.8186	-1.0658
5	2.96	0.7483	-3.7678	1.1474	-0.0454	5.68	0.0424	-0.314	-0.038	0.1315	-0.0462	-0.0679	0.1041	0.4769	-0.0452	0.3745	0.0274	-0.0324	0.4267	-0.0053	0.329	77.8376	57.3546	1.4228
6	2.6253	-1.8154	-1.5372	4.786	5.7583	7.1697	0.0183	-0.3976	0.5523	-0.0329	-0.1064	0.1543	-0.2086	-0.1048	0.056	0.4082	-0.0181	0.0189	0.4509	-0.0701	0.4402	64.2393	65.7089	17.207
7	3.1336	5.1646	0.1818	9.6368	1.8566	4.3126	-0.0533	-1.4154	0.217	0.5644	-0.2578	-0.7345	-0.3759	0.132	0.2628	0.5511	0.0747	-0.1145	0.5514	-0.1043	0.6836	79.6873	86.0531	33.8682
8	2.9155	3.5612	0.6468	8.0306	2.8093	2.819	-0.0414	0.1272	0.1043	-0.3742	-0.0998	-0.1654	-0.2378	-0.1656	0.1561	0.4465	0.0768	-0.0184	0.4558	-0.0345	0.4829	70.7895	80.4022	22.6961
9	1.5706	0.8038	-0.6101	5.0318	1.2181	1.8539	-0.0455	0.1038	-0.0326	-0.1423	-0.152	-0.3581	-0.0678	-0.1303	0.1498	0.3552	0.0073	-0.0457	0.4873	0.0057	0.3872	72.6031	76.8393	21.2812
10	3.5546	0.6244	0.5697	6.1115	1.0019	2.6678	0.0022	-0.0577	0.5657	-0.1084	-0.1892	0.0083	-0.3355	-0.1077	0.228	0.5527	0.0843	-0.075	0.4513	-0.0193	0.5794	71.8769	89.4872	27.1736
11	9.0926	-0.192	4.1523	3	-0.6701	4.3395	0.4832	-0.8779	-0.611	-0.1816	-0.0292	0.3817	0.4343	-0.1363	-0.4109	0.5402	-0.008	-0.1168	0.4253	0.0678	0.5392	121.6223	55.1234	43.4377
12	4.1043	-0.1073	1.6348	1.8249	-1.3007	3.7491	0.115	-0.0182	-0.9701	-0.1814	0.226	0.4438	0.5006	-0.4013	-0.388	0.5332	-0.0384	-0.1277	0.4369	0.0245	0.6251	111.6652	55.7125	34.9337
13	6.764	-0.5218	3.2681	6.3683	0.6152	2.4644	-0.072	0.198	0.2043	0.3124	0.3513	-0.3949	-0.1647	0.374	-0.3348	0.4391	-0.0389	-0.0449	0.4874	0.0002	0.4529	123.1419	65.8906	38.1659
14	5.5617	0.5984	0.2341	6.4025	-0.9075	5.6744	0.0546	0.7728	-0.2807	-0.5908	0.1905	-0.1116	0.47	0.1217	-0.2848	0.4803	0.0689	-0.1148	0.3919	-0.0687	0.5051	119.2312	58.9334	27.4116
15	6.0805	2.249	0.6632	3.6584	-0.1774	3.5812	0.0766	0.4608	-0.8761	-0.422	0.1047	-0.3843	0.5564	0.4094	-0.215	0.5722	0.1396	-0.0711	0.5476	-0.1013	0.5352	123.4197	54.9615	30.6227
16	3.8465	-0.707	3.1639	1.4208	-1.083	3.7189	0.1957	0.2392	-0.459	-0.0989	-0.0722	0.0669	0.3196	0.2268	-0.1538	0.4493	0.0492	-0.0498	0.3893	-0.0398	0.4542	117.8761	61.419	32.6108
17	8.7039	-3.8733	5.8788	5.8201	-3.7182	4.2645	-0.0615	-0.6273	-0.3786	-0.0251	0.2516	0.2025	-0.0917	-0.9713	-0.2836	0.3981	-0.0197	-0.0509	0.3894	-0.003	0.4551	109.6832	66.1435	35.3636
18	2.4214	-0.3815	-0.0152	3.3379	-1.1022	0.9961	-0.1655	-0.1531	0.1863	0.6822	-0.0942	-0.4162	-0.3514	0.5858	0.2274	0.5471	-0.0203	-0.0708	0.5056	0.0696	0.4268	136.2371	65.2404	61.9133
19	1.4654	-0.2487	0.6557	5.2291	-0.368	7.2654	-0.3787	-0.3741	-0.05	1.1642	-0.316	0.1301	-0.3553	-0.0577	0.5427	0.7254	-0.0255	-0.0765	0.547	-0.0064	0.4418	130.2847	72.2428	66.9321
20	3.6102	-0.8738	0.5218	4.3877	3.2006	7.1681	-0.2514	-0.5525	0.5207	1.0383	0.1661	-0.6069	-0.6535	0.71	0.1203	1.0124	-0.0891	-0.1405	0.565	0.0457	0.5567	135.607	73.8279	68.8657
21	2.6227	-0.519	-0.8592	6.5025	2.6269	4.5113	0.0773	-0.2641	0.2332	1.9197	-0.2057	-0.4627	-0.6464	0.3373	0.2548	1.0422	-0.0376	-0.1255	0.5698	0.0771	0.5081	134.4294	63.4392	72.1705
22	0.8527	0.1176	-0.3568	2.4097	1.9143	6.0198	0.0046	-0.0778	0.0391	-0.1263	0.1892	-0.0732	-0.2126	0.4858	-0.1848	0.329	-0.0145	-0.0059	0.3635	0.0067	0.3298	118.6048	82.5783	32.3638
23	4.5742	-1.0372	3.7111	6.7125	-2.0978	4.878	0.0884	-0.5615	-0.0821	0.6159	0.1896	0.0059	0.0509	-0.505	-0.2524	0.4101	0.0249	-0.0217	0.3822	-0.0036	0.3451	113.404	74.4438	41.2287
24	1.9676	0.7902	-0.2352	2.8658	-0.2564	6.534	0.028	-0.014	0.1241	0.0982	0.0174	0.3369	-0.3363	-0.286	-0.0458	0.3142	0.0167	-0.027	0.348	-0.0014	0.3612	108.4602	82.1379	35.0264
25	2.0454	-1.3356	-0.4509	4.261	3.1629	5.5504	-0.0247	-0.0113	-0.0165	0.1893	0.1911	-0.0076	0.2142	0.1956	-0.1026	0.3382	-0.0299	-0.0266	0.3861	0.0094	0.3414	117.0349	76.9827	37.0334
26	3.2052	-1.5939	1.7439	1.3374	-1.422	2.595	-0.0051	-0.0673	0.4114	0.7591	-0.5299	-1.2024	-0.3704	0.2149	0.512	0.6973	-0.1331	-0.3058	0.516	0.0653	0.8597	131.7561	85.4616	59.1752
27	6.3135	-3.6733	2.6327	5.844	-0.7238	2.0079	-0.4397	0.5353	0.5861	1.534	-0.4021	-1.6083	-0.1949	0.5227	0.8794	0.695	-0.1116	-0.2308	0.6932	0.2122	1.0202	141.9024	76.3726	63.2208
28	4.5607	0.1019	0.2606	3.4543	0.6946	4.714	-0.0211	0.8487	-0.5945	-0.3283	0.0873	-1.1124	-0.7705	0.5985	0.1123	0.878	-0.2573	-0.1214	1.0493	0.2369	1.1117	145.3187	81.9074	52.6711
29	2.1896	-2.5181	0.3828	6.3027	-0.7378	4.4752	-0.1691	-0.0598	-0.1671	0.3153	-0.0856	-0.3364	-0.479	0.1903	0.1432	0.5458	-0.0318	-0.0797	0.4984	-0.0099	0.4699	131.043	79.8481	58.6089
30	0.5433	-1.0162	0.1297	2.0225	0.5273	1.4763	-0.2569	0.7185	0.8705	0.5106	-0.1995	-1.6341	0.0697	0.8189	0.3639	0.7705	-0.1682	-0.27	0.9997	0.3918	1.555	149.9432	81.2496	58.5116
31	1.2783	-1.6547	0.8045	3.9941	0.5627	5.4816	0.2977	0.1779	0.5413	0.5424	0.2364	-0.5627	0.2957	0.8776	-0.5011	0.8062	-0.2549	-0.4773	0.8676	0.1799	1.6244	149.6289	86.4693	63.6314

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 208 through 219 )	H	1 - 119
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 120 through 228 )	H	120 - 228
3	X-RAY DIFFRACTION	3	chain 'L' and (resid 0 through 25 )	L	0 - 25
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 26 through 80 )	L	26 - 80
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 81 through 107 )	L	81 - 107
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 108 through 119 )	L	108 - 119
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 120 through 134 )	L	120 - 134
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 135 through 156 )	L	135 - 156
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 157 through 180 )	L	157 - 180
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 181 through 220 )	L	181 - 220
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 1 through 17 )	A	1 - 17
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 18 through 33 )	A	18 - 33
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 34 through 45 )	A	34 - 45
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 46 through 59 )	A	46 - 59
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 60 through 75 )	A	0
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 76 through 108 )	A	76 - 108
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 109 through 119 )	A	109 - 119
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 120 through 164 )	A	120 - 164
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 165 through 184 )	A	165 - 184
20	X-RAY DIFFRACTION	20	chain 'A' and (resid 185 through 207 )	A	185 - 207
21	X-RAY DIFFRACTION	21	chain 'A' and (resid 208 through 226 )	A	208 - 226
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 0 through 37 )	B	0 - 37
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 38 through 53 )	B	38 - 53
24	X-RAY DIFFRACTION	24	chain 'B' and (resid 54 through 80 )	B	54 - 80
25	X-RAY DIFFRACTION	25	chain 'B' and (resid 81 through 107 )	B	81 - 107
26	X-RAY DIFFRACTION	26	chain 'B' and (resid 108 through 127 )	B	108 - 127
27	X-RAY DIFFRACTION	27	chain 'B' and (resid 128 through 147 )	B	128 - 147
28	X-RAY DIFFRACTION	28	chain 'B' and (resid 148 through 167 )	B	148 - 167
29	X-RAY DIFFRACTION	29	chain 'B' and (resid 168 through 187 )	B	168 - 187
30	X-RAY DIFFRACTION	30	chain 'B' and (resid 188 through 207 )	B	188 - 207
31	X-RAY DIFFRACTION	31	chain 'B' and (resid 208 through 219 )	B	208 - 219

-
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