PDB-4uik: crystal structure of quinine-dependent Fab 314.1

ID or keywords:

Entry

Database: PDB / ID: 4uik

Title

crystal structure of quinine-dependent Fab 314.1

Components

(FAB 314.1) x 2

Keywords

IMMUNE SYSTEM / QUININE-DEPENDENT / MOUSE MAB

Function / homology

Immunoglobulins /

Immunoglobulin-like /

Sandwich / Mainly Beta

Function and homology information

Biological species

MUS MUSCULUS (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Zhu, J. / Zhu, J. / Bougie, D.W. / Aster, R.H. / Springer, T.A.

Citation

Journal: Blood / Year: 2015
Title: Structural Basis for Quinine-Dependent Antibody Binding to Platelet Integrin Alphaiib Beta3
Authors: Zhu, J. / Zhu, J. / Bougie, D.W. / Aster, R.H. / Springer, T.A.

History

Deposition	Mar 30, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 2, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 11, 2015	Group: Database references
Revision 2.0	Oct 23, 2019	Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4uik.cif.gz	254.8 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ui/4uik ftp://data.pdbj.org/pub/pdb/validation_reports/ui/4uik	HTTPS FTP

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Related structure data

Related structure data	4uilC 4uimC 4uinC 3t3pS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5dd6-1 1hh6-d 3qpq-4 1dbm-d 1jgu-d 4evn-8 4kjw-2 4wht-2 2a6j-2 5u4r-1 6ugs-1 2ok0-d 4yr6-1 6a0x-4 6ugu-2 4yr6-2 4kmt-d 4uil-d 3g5x-2 4kzd-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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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: FAB 314.1

L: FAB 314.1

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	73.750, 73.750, 190.250
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Antibody	FAB 314.1 Mass: 23971.738 Da / Num. of mol.: 1 / Fragment: FAB, HEAVY CHAIN, RESIDUES 1-223 / Source method: isolated from a natural source / Details: ASCITES FLUID / Source: (natural) MUS MUSCULUS (house mouse)
#2: Antibody	FAB 314.1 Mass: 23688.979 Da / Num. of mol.: 1 / Fragment: FAB, LIGHT CHAIN, RESIDUES 1 215 / Source method: isolated from a natural source / Details: ASCITES FLUID / Source: (natural) MUS MUSCULUS (house mouse)
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.13 Å³/Da / Density % sol: 60.75 % / Description: NONE
Crystal grow	pH: 7.5 / Details: 15% PEG 6000, 10 MM MGCL2, AND 50 MM KCL, pH 7.5

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Data collection

Diffraction	Mean temperature: 287 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97936
Detector	Type: MARRESEARCH / Detector: CCD / Date: Nov 14, 2009 / Details: DOUBLE MIRROR
Radiation	Monochromator: SI CRYTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97936 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. obs: 40094 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / B_iso Wilson estimate: 21.7 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 18.2
Reflection shell	Resolution: 2→2.05 Å / Redundancy: 4.5 % / R_merge(I) obs: 0.17 / Mean I/σ(I) obs: 8.7 / % possible all: 80.4

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: FAB FRAGMENT FROM PDB ENTRY 3T3P

3t3p

Resolution: 2→38.147 Å / SU ML: 0.19 / σ(F): 2.71 / Phase error: 21.09 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2185	994	2.5 %
R_work	0.1877	-	-
obs	0.1884	40075	96.74 %

Solvent computation

Shrinkage radii: 0.5 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 34.8 Å²

Refinement step

Cycle: LAST / Resolution: 2→38.147 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3297	0	0	350	3647

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3390
X-RAY DIFFRACTION	f_angle_d	1.149	4617
X-RAY DIFFRACTION	f_dihedral_angle_d	12.927	1207
X-RAY DIFFRACTION	f_chiral_restr	0.066	524
X-RAY DIFFRACTION	f_plane_restr	0.006	585

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 (%)
2-2.1055	0.2312	116	0.2026	4698	X-RAY DIFFRACTION	83
2.1055-2.2374	0.2297	146	0.2048	5612	X-RAY DIFFRACTION	98
2.2374-2.4101	0.2331	146	0.2075	5662	X-RAY DIFFRACTION	100
2.4101-2.6526	0.2431	150	0.2071	5720	X-RAY DIFFRACTION	100
2.6526-3.0363	0.2461	143	0.1906	5742	X-RAY DIFFRACTION	100
3.0363-3.8249	0.216	147	0.169	5761	X-RAY DIFFRACTION	99
3.8249-38.154	0.1875	146	0.1793	5886	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	0.9925	0.2991	0.2864	0.9232	-0.7649	0.849	0.2558	-0.0729	0.14	0.8154	-0.247	-0.2468	0.3522	-0.7419	-0.0008	0.3446	-0.0282	0.0196	0.3396	0.0357	0.3169	19.4412	-19.4665	13.0846
2	0.23	0.3888	0.3574	1.0171	-0.1603	0.5193	-0.0493	-0.1194	-0.0349	0.0947	0.1675	0.1714	0.1886	-0.1362	0	0.2605	0.001	-0.0096	0.2932	0.008	0.3934	19.105	-19.1098	4.6631
3	1.3814	0.887	0.7154	1.0238	-0.054	1.617	-0.0982	-0.054	0.0964	0.2855	0.0644	-0.0301	0.2153	-0.0988	-0.0004	0.2627	0.0059	-0.0309	0.2162	0.0101	0.2897	26.2488	-11.8394	6.7792
4	0.0467	-0.02	0.0387	0.4184	0.0058	0.099	-0.9319	-0.4971	-0.922	-0.5945	-0.1075	-1.4773	1.4666	1.2104	0.0044	0.6627	0.1229	-0.0923	0.5563	0.0491	1.1587	39.8842	-21.6338	8.9447
5	1.0204	0.7884	-1.1261	1.7092	0.8853	2.2687	0.0401	0.4447	0.0705	-0.3301	-0.1357	0.09	-0.1498	-0.0096	0.0003	0.2665	-0.0195	-0.025	0.2366	0.0184	0.2563	25.3332	-8.1976	0.481
6	0.2542	-0.3589	-0.2845	0.5127	0.0402	1.0716	-0.2707	0.5305	0.4047	-0.2171	0.1934	-0.395	-0.4166	-0.0183	-0.0009	0.3572	-0.0188	-0.0075	0.2699	-0.0153	0.3229	29.2166	-15.1133	-5.2096
7	0.6419	0.2729	0.6782	1.0878	-0.6234	1.6164	0.0652	-0.0011	0.0475	-0.0862	-0.0593	0.1966	-0.1455	-0.1102	-0.0001	0.2605	0.0152	-0.0128	0.2587	0.0139	0.3278	16.5603	-15.4926	1.9192
8	0.2223	0.192	-0.0095	0.1736	0.1152	0.3829	-0.1043	0.6373	-0.7581	-0.4086	0.2873	-0.8858	-0.1831	1.0302	-0.0008	0.3249	0.0229	-0.0177	0.4049	-0.0651	0.3572	32.5595	-26.451	-2.8625
9	1.2651	-0.6454	1.3343	0.5592	-0.6424	0.8637	-0.0126	-0.1003	0.1057	0.1713	0.0463	0.1155	-0.0346	-0.0199	0.0004	0.2692	-0.0052	0.0228	0.2389	-0.0114	0.2637	26.2543	-12.0738	10.2611
10	0.2847	-0.034	-0.4482	0.396	-0.2741	0.4272	-0.0333	-0.1281	0.2935	0.0926	0.0447	-0.137	0.0379	0.0953	0.0003	0.2494	-0.0088	-0.0052	0.308	-0.0221	0.3417	25.7415	-0.1143	9.108
11	0.6983	0.1759	0.7408	0.3865	-0.1472	0.8616	0.0625	0.0237	0.0131	0.4301	0.0683	-0.1527	0.3314	-0.0098	0.0001	0.2496	0.0174	0.0068	0.2236	0.0075	0.2747	26.6711	-22.3223	8.9498
12	1.7803	-0.343	-1.0851	3.6125	0.883	1.2875	0.1687	-0.2897	-0.557	0.3487	0.0148	0.0797	0.3926	0.1931	0.0025	0.2917	0.0113	0.038	0.2919	0.076	0.3892	39.2046	-48.5168	18.9224
13	0.41	-0.0156	0.2085	0.1874	0.1521	0.1716	0.8549	0.3118	-0.4767	-0.143	-0.3462	0.4088	0.9271	0.0967	-0.0002	0.344	0.0203	-0.0297	0.2984	0.0032	0.3558	37.7182	-46.4775	14.4811
14	1.2615	-0.2931	-0.4602	0.9583	0.7198	0.5322	0.0089	-0.343	-0.2046	0.1036	-0.2024	0.3624	0.081	0.0247	0.0001	0.3108	0.0123	0.0274	0.354	0.0236	0.4072	30.9793	-42.0467	18.7781
15	2.9598	1.4265	0.888	2.5116	-0.1641	0.3399	-0.137	-0.3094	-0.0086	0.0715	0.1346	0.2441	0.1845	-0.5128	0.0018	0.3604	0.0501	0.0208	0.3192	-0.0046	0.3561	38.8515	-38.8411	20.2752
16	1.3672	-0.1342	0.4036	0.4895	0.0925	0.2062	0.0065	0.994	-0.4207	-0.343	0.0729	-0.0467	-0.3035	1.1739	-0.0176	0.3474	0.0316	-0.0248	0.3285	-0.0377	0.3606	36.1119	-40.4167	6.7191
17	0.5954	0.0198	-0.2881	0.887	0.5548	0.3766	-0.1174	-0.7625	-0.5875	0.695	0.0968	0.5425	0.5826	0.1793	-0.0094	0.5395	0.0527	0.0806	0.5335	0.1754	0.3703	42.2143	-48.2048	30.297
18	0.4885	0.0254	-0.1151	0.3192	0.2392	0.1615	-0.0683	-0.1894	-0.3645	1.1391	-0.0986	0.2352	0.1385	0.0881	-0.002	0.6384	-0.0064	0.0432	0.5298	0.1296	0.4793	35.1244	-52.1897	28.2417
19	0.0693	-0.0293	-0.0903	0.0343	-0.0093	0.1223	-0.1103	-0.3807	-0.696	0.3373	0.4891	0.6341	0.4977	-0.7376	0.0013	0.3272	-0.0428	-0.0017	0.3621	-0.0154	0.4691	23.9673	-43.236	13.0053
20	0.2836	0.0914	0.6657	0.3093	0.2415	0.9919	-0.0622	-0.3989	-0.9815	0.1548	0.2611	0.3959	0.3075	-0.2523	0.0065	0.5277	-0.0994	0.0499	0.4009	0.1722	0.656	34.6233	-53.8487	21.5019
21	0.7538	0.7259	-0.3679	1.0541	-0.2395	0.4365	-0.1232	0.0685	-0.0872	-0.0799	-0.0939	-0.7156	0.5653	0.433	0.0007	0.398	0.054	-0.0288	0.3675	-0.0087	0.3039	45.6677	-10.1153	10.9998
22	0.1052	-0.0794	-0.1197	0.0818	0.066	0.0601	0.0354	-0.2451	0.1559	0.111	-0.2173	-1.0853	-0.3572	0.4829	0.0066	0.4722	0.0705	-0.0333	0.3519	-0.0422	0.4002	46.3173	-15.7423	31.042
23	0.6959	0.2673	-0.1626	0.4004	-0.0313	0.1983	-0.2425	0.1284	0.3069	0.3997	-0.0314	0.0065	-1.2119	-0.8983	0.0002	0.441	0.001	-0.0655	0.3407	-0.0153	0.4248	45.5458	-7.6031	23.9517
24	0.528	0.6243	-0.3214	1.0456	0.222	1.1584	0.0178	-0.1057	0.2219	0.1167	0.1599	-0.2632	-0.3569	0.4759	0	0.3251	-0.022	-0.0412	0.2983	0.0063	0.2606	42.1595	0.9124	10.156
25	0.6354	-0.1276	0.4086	0.4111	0.2047	0.4244	0.1887	-0.2811	0.1708	0.2	-0.2112	0.3079	0.4649	0.1026	0.0017	0.3493	0.0447	0.0303	0.2442	0.0213	0.2463	34.9473	-11.9311	18.7167
26	0.4253	-0.1189	-0.4739	0.4374	0.9132	2.082	0.0704	-0.0629	-0.0674	0.3137	-0.1095	0.5988	0.2619	-0.152	-0.0003	0.34	0.0174	0.0012	0.269	0.0062	0.2814	31.543	-10.319	19.4377
27	0.9536	-0.2943	-0.4347	0.7805	0.8085	1.1211	-0.0552	-0.0381	-0.1362	0.2869	0.1723	0.277	-0.0728	-0.4068	-0.0008	0.4167	-0.0037	0.0059	0.3053	0.0078	0.2775	32.3521	-4.172	25.9511
28	0.7891	0.1399	0.5393	0.3226	0.5351	0.7351	-0.0188	-0.161	0.0247	0.3971	-0.0398	-0.0188	-0.4549	0.3971	0.0001	0.3134	0.0166	-0.0211	0.2597	-0.0031	0.2573	43.2924	-2.0988	20.8262
29	0.1094	-0.037	-0.0897	0.3723	0.0399	0.2893	0.2794	-0.4774	0.0186	1.7654	-0.0588	0.9754	0.6157	-0.4179	0.0017	0.6334	-0.0108	0.0499	0.3882	-0.0397	0.501	37.9338	-15.3081	32.8411
30	1.1126	0.0733	0.211	1.0139	0.6692	1.1254	0.0024	0.0398	0.0033	0.1517	0.0357	0.0725	-0.0076	0.2656	-0	0.2698	-0.0107	-0.0152	0.2116	-0.0059	0.2378	37.7542	-9.2375	12.5424
31	-0.0064	-0.4068	-0.0606	0.3324	-0.2692	0.4099	-0.0153	-0.2622	0.1262	0.3127	0.3181	0.0735	0.0531	-0.2656	0.0002	0.4099	0.0308	-0.067	0.3524	-0.0208	0.2832	46.2865	-20.5881	26.6037
32	1.0664	-1.7345	0.3836	1.7908	-0.086	1.4786	-0.003	-0.1168	-0.3213	0.5815	0.1707	-0.1056	0.3195	-0.0264	0.0036	0.3448	0.051	0.01	0.2905	0.0113	0.2328	48.4898	-45.5446	20.9384
33	1.7255	-1.2588	-0.0245	1.4713	-0.2673	0.0349	0.0801	-0.0592	-0.3235	0.1774	-0.0328	0.025	0.0541	-0.1791	-0.0002	0.3135	0.0367	-0.0111	0.3058	0.0057	0.2745	47.2166	-42.944	17.9048
34	0.13	0.1582	0.1795	0.5017	0.7349	1.0666	0.1425	-0.0291	0.3325	-0.5127	0.391	-0.8967	-0.5692	0.251	0.0041	0.4164	0.0072	0.0201	0.3151	0.0003	0.3768	55.3267	-36.1674	15.578
35	0.5821	0.1405	-0.367	0.2156	0.1283	0.4688	-0.3711	0.2011	0.3916	-0.3211	0.3632	-0.3246	-0.3971	0.1954	0.0006	0.4637	0.0489	-0.0022	0.3794	0.0094	0.3954	58.8754	-45.4345	7.5541
36	1.5908	-0.8717	1.9871	3.2231	0.2689	1.5858	-0.1671	-0.0762	-0.0329	0.052	-0.057	0.3206	-0.1755	-0.019	-0.0003	0.2979	0.0172	-0.0182	0.2433	0.0165	0.2428	45.6139	-34.5949	19.1865
37	0.5801	-0.667	-0.0335	0.5154	0.0607	0.429	-0.257	0.2119	-0.2482	-0.7983	-0.2698	0.4284	0.042	-0.2538	0.0005	0.4648	0.0703	-0.0428	0.341	-0.01	0.4073	50.6853	-55.2822	4.8799
38	-0.0485	0.1535	0.2602	0.3942	-0.0523	0.474	-0.1818	-0.0495	0.0664	-0.4295	0.4049	-0.2535	-0.2079	0.6614	-0.0001	0.3394	0.0523	-0.0211	0.3013	-0.0135	0.3558	57.5219	-47.2056	14.2352
39	0.463	0.1461	0.109	0.2406	-0.1992	0.4058	-0.4664	-0.8143	1.0426	0.0162	0.8945	-1.5195	-0.4698	0.3151	0.0018	0.4434	0.003	-0.1052	0.4122	-0.1309	0.5076	61.7558	-33.3615	24.0603
40	0.455	-0.1113	0.6296	0.1288	-0.2155	0.5661	-0.1534	0.0183	-0.2342	0.8067	0.3922	-0.4649	0.5347	0.2643	0.0013	0.407	0.0407	-0.0155	0.3853	0.0077	0.4641	56.6038	-51.6063	18.4351

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN H AND RESID 1:10)
2	X-RAY DIFFRACTION	2	(CHAIN H AND RESID 11:30)
3	X-RAY DIFFRACTION	3	(CHAIN H AND RESID 31:40)
4	X-RAY DIFFRACTION	4	(CHAIN H AND RESID 41:44)
5	X-RAY DIFFRACTION	5	(CHAIN H AND RESID 45:62)
6	X-RAY DIFFRACTION	6	(CHAIN H AND RESID 63:69)
7	X-RAY DIFFRACTION	7	(CHAIN H AND RESID 70:84)
8	X-RAY DIFFRACTION	8	(CHAIN H AND RESID 85:91)
9	X-RAY DIFFRACTION	9	(CHAIN H AND RESID 92:101)
10	X-RAY DIFFRACTION	10	(CHAIN H AND RESID 102:109)
11	X-RAY DIFFRACTION	11	(CHAIN H AND RESID 110:123)
12	X-RAY DIFFRACTION	12	(CHAIN H AND RESID 124:148)
13	X-RAY DIFFRACTION	13	(CHAIN H AND RESID 149:152)
14	X-RAY DIFFRACTION	14	(CHAIN H AND RESID 153:167)
15	X-RAY DIFFRACTION	15	(CHAIN H AND RESID 168:180)
16	X-RAY DIFFRACTION	16	(CHAIN H AND RESID 181:186)
17	X-RAY DIFFRACTION	17	(CHAIN H AND RESID 187:197)
18	X-RAY DIFFRACTION	18	(CHAIN H AND RESID 198:206)
19	X-RAY DIFFRACTION	19	(CHAIN H AND RESID 207:212)
20	X-RAY DIFFRACTION	20	(CHAIN H AND RESID 213:222)
21	X-RAY DIFFRACTION	21	(CHAIN L AND RESID 1:10)
22	X-RAY DIFFRACTION	22	(CHAIN L AND RESID 11:17)
23	X-RAY DIFFRACTION	23	(CHAIN L AND RESID 18:23)
24	X-RAY DIFFRACTION	24	(CHAIN L AND RESID 24:33)
25	X-RAY DIFFRACTION	25	(CHAIN L AND RESID 34:39)
26	X-RAY DIFFRACTION	26	(CHAIN L AND RESID 40:50)
27	X-RAY DIFFRACTION	27	(CHAIN L AND RESID 51:62)
28	X-RAY DIFFRACTION	28	(CHAIN L AND RESID 63:76)
29	X-RAY DIFFRACTION	29	(CHAIN L AND RESID 77:81)
30	X-RAY DIFFRACTION	30	(CHAIN L AND RESID 82:101)
31	X-RAY DIFFRACTION	31	(CHAIN L AND RESID 102:108)
32	X-RAY DIFFRACTION	32	(CHAIN L AND RESID 109:124)
33	X-RAY DIFFRACTION	33	(CHAIN L AND RESID 125:141)
34	X-RAY DIFFRACTION	34	(CHAIN L AND RESID 142:149)
35	X-RAY DIFFRACTION	35	(CHAIN L AND RESID 150:156)
36	X-RAY DIFFRACTION	36	(CHAIN L AND RESID 157:180)
37	X-RAY DIFFRACTION	37	(CHAIN L AND RESID 181:188)
38	X-RAY DIFFRACTION	38	(CHAIN L AND RESID 189:197)
39	X-RAY DIFFRACTION	39	(CHAIN L AND RESID 198:204)
40	X-RAY DIFFRACTION	40	(CHAIN L AND RESID 205:212)

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