PDB-6bi2: Trastuzumab Fab D185A (Light Chain) Mutant Biotin Conjugation.

ID or keywords:

Entry

Database: PDB / ID: 6bi2

Title

Trastuzumab Fab D185A (Light Chain) Mutant Biotin Conjugation.

Components

Trastuzumab Anti-HER2 Fab Heavy Chain
Trastuzumab Anti-HER2 Fab Light Chain

Keywords

IMMUNE SYSTEM / Fab / immunoglobulin

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / BIOTIN

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.801 Å

Authors

DiDonato, M. / Spraggon, G.

Citation

Journal: Chembiochem / Year: 2018
Title: Tuning a Protein-Labeling Reaction to Achieve Highly Site Selective Lysine Conjugation.
Authors: Pham, G.H. / Ou, W. / Bursulaya, B. / DiDonato, M. / Herath, A. / Jin, Y. / Hao, X. / Loren, J. / Spraggon, G. / Brock, A. / Uno, T. / Geierstanger, B.H. / Cellitti, S.E.

History

Deposition	Oct 31, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 14, 2018	Provider: repository / Type: Initial release
Revision 1.1	Mar 28, 2018	Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2	Apr 25, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Oct 4, 2023	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
Revision 1.4	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6bi2.cif.gz	369.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6bi2.ent.gz	302.3 KB	Display	PDB format
PDBx/mmJSON format	6bi2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6bi2_validation.pdf.gz	896 KB	Display	wwPDB validaton report
Full document	6bi2_full_validation.pdf.gz	901.3 KB	Display
Data in XML	6bi2_validation.xml.gz	40.4 KB	Display
Data in CIF	6bi2_validation.cif.gz	59.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bi/6bi2 ftp://data.pdbj.org/pub/pdb/validation_reports/bi/6bi2	HTTPS FTP

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Related structure data

Related structure data	6bhzC 6bi0C 1n8zS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6vl8-4 6xuk-d 1xf2-2 6bb4-3 6rco-2 1kno-2 4oz4-1 4xh2-4 1kel-d 5xli-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 - 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: Trastuzumab Anti-HER2 Fab Heavy Chain

L: Trastuzumab Anti-HER2 Fab Light Chain

I: Trastuzumab Anti-HER2 Fab Heavy Chain

M: Trastuzumab Anti-HER2 Fab Light Chain

hetero molecules

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

1

H: Trastuzumab Anti-HER2 Fab Heavy Chain

L: Trastuzumab Anti-HER2 Fab Light Chain

hetero molecules

defined by author&software
Evidence: homology
47.9 kDa, 2 polymers

2

I: Trastuzumab Anti-HER2 Fab Heavy Chain

M: Trastuzumab Anti-HER2 Fab Light Chain

hetero molecules

defined by author&software
Evidence: homology
47.8 kDa, 2 polymers

Unit cell

Length a, b, c (Å)	38.646, 69.139, 91.471
Angle α, β, γ (deg.)	109.80, 100.29, 90.08
Int Tables number	1
Space group name H-M	P1

#1: Antibody	Trastuzumab Anti-HER2 Fab Heavy Chain Mass: 23988.850 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody	Trastuzumab Anti-HER2 Fab Light Chain Mass: 23422.021 Da / Num. of mol.: 2 / Mutation: D185A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-BTN / BIOTIN Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₂O₃S / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 742 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.34 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.0% trptone, 20% PEG 3350, 100 mM HEPES pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2017
Radiation	Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97648 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. obs: 78712 / % possible obs: 97.5 % / Redundancy: 3.9 % / B_iso Wilson estimate: 29.76 Å² / R_merge(I) obs: 0.047 / R_pim(I) all: 0.028 / R_rim(I) all: 0.055 / Χ²: 0.874 / Net I/σ(I): 25
Reflection shell	Resolution: 1.8→1.86 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.461 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 7683 / CC_1/2: 0.882 / R_pim(I) all: 0.276 / R_rim(I) all: 0.538 / Χ²: 0.599 / % possible all: 95.1

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1N8Z

1n8z

Resolution: 1.801→37.37 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 21.99

	R_factor	Num. reflection	% reflection
R_free	0.2021	3780	4.8 %
R_work	0.1658	-	-
obs	0.1675	78687	97.28 %

Solvent computation

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

Displacement parameters

B_iso mean: 42.1 Å²

Refinement step

Cycle: LAST / Resolution: 1.801→37.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6551	0	58	742	7351

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6981
X-RAY DIFFRACTION	f_angle_d	0.908	9530
X-RAY DIFFRACTION	f_dihedral_angle_d	12.446	4183
X-RAY DIFFRACTION	f_chiral_restr	0.059	1066
X-RAY DIFFRACTION	f_plane_restr	0.006	1226

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 (%)
1.8015-1.8243	0.263	147	0.2558	2557	X-RAY DIFFRACTION	90
1.8243-1.8483	0.251	129	0.246	2723	X-RAY DIFFRACTION	95
1.8483-1.8736	0.2824	165	0.2312	2681	X-RAY DIFFRACTION	96
1.8736-1.9004	0.3067	129	0.2238	2758	X-RAY DIFFRACTION	97
1.9004-1.9287	0.2695	138	0.213	2792	X-RAY DIFFRACTION	96
1.9287-1.9589	0.2403	120	0.21	2737	X-RAY DIFFRACTION	97
1.9589-1.991	0.2092	138	0.2072	2754	X-RAY DIFFRACTION	96
1.991-2.0253	0.3027	141	0.2024	2818	X-RAY DIFFRACTION	97
2.0253-2.0621	0.2362	151	0.1934	2696	X-RAY DIFFRACTION	97
2.0621-2.1018	0.2243	145	0.1913	2755	X-RAY DIFFRACTION	97
2.1018-2.1447	0.2322	150	0.19	2813	X-RAY DIFFRACTION	97
2.1447-2.1913	0.2547	158	0.1824	2723	X-RAY DIFFRACTION	98
2.1913-2.2423	0.2337	156	0.1822	2772	X-RAY DIFFRACTION	98
2.2423-2.2983	0.2672	154	0.1808	2779	X-RAY DIFFRACTION	98
2.2983-2.3605	0.2373	139	0.1878	2761	X-RAY DIFFRACTION	97
2.3605-2.4299	0.255	125	0.1869	2818	X-RAY DIFFRACTION	98
2.4299-2.5083	0.2199	134	0.1854	2791	X-RAY DIFFRACTION	98
2.5083-2.598	0.2063	149	0.1827	2798	X-RAY DIFFRACTION	98
2.598-2.702	0.2379	144	0.1817	2795	X-RAY DIFFRACTION	98
2.702-2.8249	0.2154	131	0.1754	2803	X-RAY DIFFRACTION	98
2.8249-2.9738	0.1981	141	0.1741	2836	X-RAY DIFFRACTION	99
2.9738-3.16	0.2045	131	0.1722	2800	X-RAY DIFFRACTION	98
3.16-3.4038	0.1836	147	0.166	2804	X-RAY DIFFRACTION	99
3.4038-3.7461	0.2152	136	0.1527	2824	X-RAY DIFFRACTION	99
3.7461-4.2875	0.1709	111	0.1402	2878	X-RAY DIFFRACTION	99
4.2875-5.3992	0.1197	119	0.1196	2846	X-RAY DIFFRACTION	99
5.3992-37.3784	0.1613	152	0.1436	2795	X-RAY DIFFRACTION	98

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	3.2714	3.2857	-0.873	7.5659	-2.8108	4.036	-0.0447	-0.1086	0.0929	0.2032	0.035	0.0677	-0.3655	0.1681	0.0451	0.2295	-0.0068	0.0114	0.2663	-0.0148	0.2358	16.654	31.8558	-6.7471
2	1.5041	0.2917	0.0942	3.1975	-0.0815	3.6795	-0.0717	-0.0231	0.1464	-0.0891	0.0725	0.4183	-0.2792	-0.1727	0.0043	0.1784	0.0126	0.019	0.1794	0.0028	0.2847	9.3971	32.001	-11.539
3	2.7566	-0.8897	-0.8714	4.0248	0.482	2.6732	-0.0344	0.3658	-0.269	-0.0715	0.0946	-0.174	0.4952	0.2904	0.0224	0.2977	0.0014	-0.0574	0.2929	-0.085	0.2053	26.5666	2.2451	-14.7945
4	4.4438	-1.0646	-2.195	3.2672	1.7918	4.7003	0.0453	-0.0614	-0.0497	0.1329	0.2297	-0.42	0.0043	0.5714	-0.2613	0.2599	0.0089	-0.0324	0.2266	-0.0698	0.2605	31.9013	4.1616	-16.2061
5	8.884	-4.7188	-2.0692	4.6705	1.9043	2.0719	0.0905	0.3818	-0.2244	-0.2046	-0.2078	0.2266	0.16	-0.4009	0.0722	0.3312	-0.0279	-0.0397	0.3083	0.0018	0.1952	10.0332	26.4089	-36.5598
6	3.0364	0.9734	-0.8858	3.6072	-0.0966	5.4711	0.0322	0.3057	0.4448	-0.2297	-0.1025	-0.113	-0.4106	-0.0756	0.0809	0.2367	0.0259	0.0237	0.2059	0.0159	0.2035	14.0735	34.8986	-31.693
7	3.0611	-2.803	-3.6774	4.9743	2.1524	8.6916	-0.0846	0.1384	0.05	-0.0278	-0.101	0.1641	-0.0879	-0.1711	0.1398	0.2157	-0.0276	-0.0507	0.2379	-0.001	0.1861	12.6284	29.2733	-29.2456
8	9.3296	-8.6328	-1.5152	8.766	2.1544	1.0441	0.1019	0.4532	-0.0866	-0.2275	-0.3696	-0.0329	0.3369	0.2937	0.3036	0.5869	0.0875	0.0995	0.325	0.0169	0.2681	23.3971	13.8426	-38.7984
9	4.9645	1.0914	-2.355	5.1977	-4.1235	4.0609	0.2226	-0.4221	-0.2913	0.9061	-0.1737	-0.2571	-0.3892	0.7081	-0.1472	0.562	0.0756	-0.0783	0.2466	-0.0653	0.3622	29.4805	-8.4038	-17.7125
10	2.3091	0.8148	-1.1772	8.236	-6.2677	5.7373	0.3539	0.3954	-0.0962	-0.4059	0.1025	0.586	-0.1911	-0.1596	-0.4466	0.4565	0.1067	-0.0247	0.3231	-0.0796	0.314	23.2542	-1.2937	-30.8956
11	1.3518	-1.0683	-0.1886	9.0211	-0.968	4.0036	0.3383	0.2597	-0.5756	-0.591	-0.3976	0.7154	0.1551	-0.0041	-0.1063	0.3588	0.0363	-0.1298	0.3184	-0.1278	0.4736	17.5419	-6.3159	-27.1873
12	3.0614	-1.7122	0.6822	2.098	-2.4331	9.2521	0.2391	0.2378	0.3269	-0.1612	-0.1741	-0.5934	-1.6723	0.9249	0.0946	0.6597	-0.0647	0.0808	0.4359	-0.0078	0.3494	28.1678	13.3526	-32.3872
13	1.7763	-0.5529	-0.2606	9.1754	-2.0432	4.2891	0.2028	0.1611	-0.4185	-0.2332	-0.1608	0.6454	0.4921	0.0175	0.0109	0.3529	0.0092	-0.0735	0.2562	-0.076	0.3947	22.6991	-11.7486	-24.5253
14	2.2519	1.183	-0.6542	0.7615	-1.1865	8.0289	0.2312	0.3369	-0.4566	-1.7121	-0.2276	-0.0974	0.6064	0.2036	-0.0671	0.7593	0.1514	-0.0611	0.3172	-0.1247	0.3272	27.8934	-8.9779	-34.6806
15	6.1498	-4.9165	-0.525	8.5409	1.4904	3.9235	0.057	0.2185	-0.3224	-0.1513	-0.2649	0.4421	-0.2257	-0.138	0.2254	0.1801	-0.0743	0.0262	0.2091	-0.0139	0.1843	24.8468	25.0756	6.3158
16	8.4771	-3.4779	-0.838	6.1933	1.2427	6.6216	0.0361	-0.0614	0.4487	0.1798	-0.1028	0.1597	-0.8526	0.0541	0.0061	0.2635	-0.0143	0.0049	0.2033	0.018	0.1872	24.9209	36.3499	6.1008
17	3.65	0.2171	-0.3259	6.3415	0.4955	3.8291	0.076	-0.0977	0.2853	0.3006	-0.0998	-0.6082	-0.3803	0.5416	0.0564	0.2536	-0.1059	-0.0386	0.275	-0.0227	0.2639	35.4353	31.8572	12.2152
18	0.6361	1.5211	-0.361	3.646	-1.1698	2.9137	-0.0591	-0.0169	0.0738	-0.084	-0.2031	-0.6451	-0.1656	0.346	0.283	0.2004	-0.049	0.0362	0.2138	0.0006	0.2477	32.2522	28.9467	4.2109
19	5.1361	-1.644	-1.1884	3.3133	3.8502	4.7647	-0.1027	-0.2565	0.604	0.415	-0.0882	0.0608	-0.8827	0.0773	0.1708	0.5177	-0.0582	-0.0457	0.2382	-0.0584	0.2606	26.3789	35.0845	16.9681
20	1.4768	-0.0264	0.7701	2.4658	-1.5989	3.4095	0.0444	-0.3504	-0.2336	-0.0739	0.4305	0.391	0.2831	-0.9443	-0.2405	0.2433	-0.0679	-0.0106	0.4291	0.1293	0.2796	12.5573	5.1693	15.1155
21	7.0957	6.0518	-5.4478	6.7139	-4.3233	4.2559	0.0134	-0.1274	-0.6715	-0.401	0.4904	0.3171	0.5297	-1.8408	-0.3441	0.2978	-0.3185	-0.1437	0.7756	0.2683	0.4379	5.5837	1.4803	9.8747
22	2.2699	-0.7189	-0.8349	2.895	-0.1327	6.3428	-0.0544	-0.6222	0.2934	0.9911	0.0397	0.0326	-0.1843	0.659	0.03	0.7401	-0.0259	-0.0308	0.513	-0.1051	0.2823	27.5376	31.012	33.0122
23	1.1378	0.7137	-0.0048	3.9571	-2.2896	3.2855	0.0123	-0.1782	-0.0648	0.41	0.2975	0.0224	-0.1467	-0.1847	-0.2608	0.2122	0.0903	-0.0002	0.4245	0.0138	0.2533	21.411	10.4355	26.326
24	1.9706	-0.5801	0.4691	4.1984	-0.8916	5.8052	0.111	-0.2909	-0.3363	-0.3099	0.3574	0.0848	0.3332	-0.6323	-0.314	0.2799	-0.0995	-0.0505	0.4078	0.1406	0.2859	18.0483	-4.6844	29.0089

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 32 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 33 through 113 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 114 through 141 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 142 through 222 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 1 through 25 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 26 through 75 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 76 through 101 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 102 through 113 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 114 through 128 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 129 through 150 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 151 through 163 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 164 through 174 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 175 through 197 )
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 198 through 213 )
15	X-RAY DIFFRACTION	15	chain 'I' and (resid 1 through 17 )
16	X-RAY DIFFRACTION	16	chain 'I' and (resid 18 through 32 )
17	X-RAY DIFFRACTION	17	chain 'I' and (resid 33 through 67 )
18	X-RAY DIFFRACTION	18	chain 'I' and (resid 68 through 91 )
19	X-RAY DIFFRACTION	19	chain 'I' and (resid 92 through 113 )
20	X-RAY DIFFRACTION	20	chain 'I' and (resid 114 through 210 )
21	X-RAY DIFFRACTION	21	chain 'I' and (resid 211 through 220 )
22	X-RAY DIFFRACTION	22	chain 'M' and (resid 1 through 90 )
23	X-RAY DIFFRACTION	23	chain 'M' and (resid 91 through 128 )
24	X-RAY DIFFRACTION	24	chain 'M' and (resid 129 through 214 )

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-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

-
Basic information

-
Structure visualization

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Downloads & links

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Download

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Validation report

-
Related structure data

-
Links

-
Assembly

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Components

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Experimental details

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Experiment

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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

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Yorodumi