PDB-8fxj: Crystal structure of Fab460

ID or keywords:

Entry

Database: PDB / ID: 8fxj

Title

Crystal structure of Fab460

Components

Fab460, heavy chain
Fab460, light chain

Keywords

IMMUNE SYSTEM / Fab460 / MPER / Membrane-Proximal External Region / HIV / vaccine

Function / homology

ACETATE ION

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Tan, K. / Kim, M. / Reinherz, E.L.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2023
Title: Inadequate structural constraint on Fab approach rather than paratope elicitation limits HIV-1 MPER vaccine utility.
Authors: Tan, K. / Chen, J. / Kaku, Y. / Wang, Y. / Donius, L. / Khan, R.A. / Li, X. / Richter, H. / Seaman, M.S. / Walz, T. / Hwang, W. / Reinherz, E.L. / Kim, M.

History

Deposition	Jan 24, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 11, 2023	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	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	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8fxj.cif.gz	229.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8fxj.ent.gz	153 KB	Display	PDB format
PDBx/mmJSON format	8fxj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8fxj_validation.pdf.gz	469 KB	Display	wwPDB validaton report
Full document	8fxj_full_validation.pdf.gz	471.5 KB	Display
Data in XML	8fxj_validation.xml.gz	20.9 KB	Display
Data in CIF	8fxj_validation.cif.gz	30.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fx/8fxj ftp://data.pdbj.org/pub/pdb/validation_reports/fx/8fxj	HTTPS FTP

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Related structure data

Related structure data	8fwfC 8fymC 8fz2C C: citing same article (ref.)
Similar structure data	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	#163 - Jul 2013 HIV Capsid similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

L: Fab460, light chain

H: Fab460, heavy chain

hetero molecules

49.2 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)	129.546, 129.546, 96.808
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21
Space group name Hall	P3₁2"
Symmetry operation	#1: x,y,z #2: -y,x-y,z+1/3 #3: -x+y,-x,z+2/3 #4: x-y,-y,-z+2/3 #5: -x,-x+y,-z+1/3 #6: y,x,-z

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Antibody , 2 types, 2 molecules LH

#1: Antibody	Fab460, light chain Mass: 23333.951 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) / Strain (production host): 293 F cells
#2: Antibody	Fab460, heavy chain Mass: 24165.865 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) / Strain (production host): 293 F cells

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Non-polymers , 5 types, 270 molecules

#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
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: 4.94 Å³/Da / Density % sol: 75.09 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 1.5M Lithium sulfate monohydrate, 0.1M Sodium actate,

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2022
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 2→45 Å / Num. obs: 63553 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / B_iso Wilson estimate: 37.05 Å² / CC_1/2: 0.992 / CC star: 0.998 / R_merge(I) obs: 0.102 / R_pim(I) all: 0.041 / R_rim(I) all: 0.11 / Χ²: 1.165 / Net I/σ(I): 23.23
Reflection shell	Resolution: 2→2.03 Å / Redundancy: 6.4 % / R_merge(I) obs: 1.193 / Mean I/σ(I) obs: 1.36 / Num. unique obs: 3133 / CC_1/2: 0.571 / CC star: 0.853 / R_pim(I) all: 0.489 / R_rim(I) all: 1.294 / Χ²: 0.613 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
SBC-Collect	1.20.1_4487	data collection
PHENIX	1.20.1_4487	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→44.44 Å / SU ML: 0.2129 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.1962
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1939	3096	4.89 %
R_work	0.1665	60261	-
obs	0.1678	63357	99.58 %

Solvent computation

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

Displacement parameters

B_iso mean: 44.24 Å²

Refinement step

Cycle: LAST / Resolution: 2→44.44 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3313	0	90	248	3651

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0136	3487
X-RAY DIFFRACTION	f_angle_d	1.2859	4751
X-RAY DIFFRACTION	f_chiral_restr	0.0811	523
X-RAY DIFFRACTION	f_plane_restr	0.0093	596
X-RAY DIFFRACTION	f_dihedral_angle_d	7.8971	479

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 (%)
2-2.03	0.277	144	0.2535	2656	X-RAY DIFFRACTION	97.83
2.03-2.06	0.2886	130	0.24	2719	X-RAY DIFFRACTION	99.48
2.06-2.1	0.2547	141	0.2168	2717	X-RAY DIFFRACTION	99.37
2.1-2.14	0.2557	156	0.1999	2681	X-RAY DIFFRACTION	99.58
2.14-2.18	0.2294	121	0.2092	2730	X-RAY DIFFRACTION	99.34
2.18-2.22	0.2033	142	0.2031	2711	X-RAY DIFFRACTION	99.41
2.22-2.27	0.2454	144	0.1978	2702	X-RAY DIFFRACTION	99.61
2.27-2.32	0.2215	140	0.1962	2706	X-RAY DIFFRACTION	99.37
2.32-2.38	0.2066	108	0.1924	2751	X-RAY DIFFRACTION	99.72
2.38-2.45	0.1946	143	0.182	2756	X-RAY DIFFRACTION	99.59
2.45-2.52	0.2271	147	0.1869	2691	X-RAY DIFFRACTION	99.75
2.52-2.6	0.2186	126	0.1867	2761	X-RAY DIFFRACTION	99.86
2.6-2.69	0.2302	141	0.1843	2740	X-RAY DIFFRACTION	99.79
2.69-2.8	0.2057	181	0.1802	2676	X-RAY DIFFRACTION	99.72
2.8-2.93	0.2405	145	0.1998	2715	X-RAY DIFFRACTION	99.9
2.93-3.08	0.217	138	0.1772	2780	X-RAY DIFFRACTION	99.86
3.08-3.28	0.197	151	0.1786	2733	X-RAY DIFFRACTION	99.93
3.28-3.53	0.2301	122	0.1608	2788	X-RAY DIFFRACTION	99.86
3.53-3.88	0.185	141	0.1478	2768	X-RAY DIFFRACTION	99.83
3.88-4.44	0.1568	146	0.1279	2772	X-RAY DIFFRACTION	99.86
4.44-5.6	0.1395	142	0.1253	2816	X-RAY DIFFRACTION	99.86
5.6-44.44	0.1654	147	0.1672	2892	X-RAY DIFFRACTION	99.25

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	1.64570479396	0.351577765193	-0.0421523516776	6.78330862922	-0.835683920017	1.41491349695	0.0978783025883	-0.139482544655	-0.190543914531	0.489359835395	-0.515634170456	-0.925783064013	-0.0686192935214	0.561164790898	0.26409880886	0.375580838783	-0.0409855563611	-0.111226922897	0.353084763387	0.0849078228527	0.40071478511	69.270978907	-28.3010200475	5.59047955774
2	1.17441942532	0.382375567292	0.113282492337	5.05508436276	-0.731853233591	1.00302118163	0.0536979035291	-0.153053380304	0.141021736449	0.762582466268	-0.286327855825	-0.843438920484	-0.45100655741	0.471431922726	0.229776172098	0.554538355581	-0.142384768046	-0.138917646136	0.360010023583	0.0832825609477	0.431242435765	69.3931860447	-18.5137093988	6.84466296953
3	1.59272862261	0.294111983253	-0.307294130499	6.16378301006	-1.3307515717	2.20392381168	0.0850267182599	-0.290506338364	0.14835976216	1.03160658122	-0.129938667531	-0.275988450155	-0.412763748124	0.123616125291	0.123721019061	0.57413082406	-0.0483183985707	-0.0651426200652	0.224956243993	0.00468202659554	0.268515659487	62.1218902357	-20.2776560159	10.1655049561
4	1.35028775482	0.32423873476	0.718032020603	6.94934645172	-1.40628490351	2.18366279751	-0.0079036804382	-0.330721780644	0.0422005334828	0.578564069766	-0.129609524131	0.161002467096	-0.220012103266	0.0645924320815	0.0531213968958	0.369593970482	-0.0609198464939	-0.0206906726232	0.307014892496	0.0179267684054	0.324208102077	60.5336929638	-27.2571552183	7.6973711159
5	1.7334521528	0.0906757760905	-0.133124555568	5.89829389385	-0.935909273144	2.39553033227	0.239658449513	-0.380876840003	0.28946090286	0.616360095392	-0.713483925046	-0.761425020114	-0.617365632953	0.516164524369	0.248011182258	0.485585185571	-0.11710066101	-0.11866670287	0.394281757897	0.0861470168735	0.494852501358	69.6747662884	-11.9812750096	-0.263433096677
6	0.510305647253	1.01999430071	0.00578441859953	6.91479823677	-0.450455944169	0.0703378753595	0.00996947016349	-0.0114405201556	-0.00545548568757	0.00585347117826	-0.0494599952939	-0.201355108926	-0.301711719397	0.0257897081778	0.101292027568	0.31375949655	-0.0411124953952	-0.00798293269539	0.301894004079	0.0185749187467	0.290423073049	60.8127570725	-41.3375291453	3.55523017089
7	4.80916405627	-1.0812354662	3.63095146452	5.15065154946	-1.99567768344	3.31807170806	0.184395225323	-0.12074405109	-0.204515088572	-0.70858434934	0.220971287871	0.663669515209	0.151734366539	-0.973551638832	-0.192389832544	0.495540689922	-0.0714653732525	-0.051637757452	0.386918001932	-0.0188952204992	0.352033075216	44.5838548497	-49.1766114201	-21.6533765599
8	3.1687576775	-0.17691838353	3.0409290128	2.331825123	0.0148642496582	2.94696367884	-0.0921614910133	0.298759611898	0.0188685094695	-0.483632628979	-0.0189145354473	-0.202081219232	0.0242425486441	0.446401617173	0.0440870726136	0.35584465213	-0.0402181587682	0.0533262757122	0.374216165101	0.0299110158485	0.329840539262	56.7531493665	-48.5137830829	-12.3627422156
9	2.46265470867	-0.458658760887	2.08213419278	3.32266026356	0.991358546808	7.09994507153	0.0615482475371	0.756798388846	-0.171177040482	-1.03715581381	0.11477780713	-0.637211992869	0.206242504993	1.26754955916	-0.0472926835569	0.528739513671	0.0217523755807	0.190027231574	0.699546416354	0.047551947465	0.426678337123	59.4716781137	-48.8999174821	-21.2502095463
10	5.12273084721	0.438416034404	3.20623665643	6.79822011772	-1.41864212118	2.46100453434	-0.0593422121939	-0.28299263684	0.312940290645	0.495424878513	0.416488596169	0.610992877901	-1.18184232002	-1.16787983505	0.341413692117	0.412023828335	0.0494204485134	0.0392726139588	0.402439619601	0.056438703577	0.366245821214	53.6670719893	-40.1404778637	0.209736500576
11	3.26665282332	-0.74614189967	2.53945849824	3.57278885231	-0.437835839206	6.5706764631	0.176973869162	0.737423303941	-0.283103452488	-1.10499864204	-0.15924728374	0.279403585911	0.887522141089	0.78925056583	-0.202051332085	0.616262370414	-0.0185869473084	0.0231141308771	0.445364050138	-0.0547487376833	0.285815329146	53.3193059362	-52.582261455	-23.8869001764
12	4.13237171948	-0.499660728382	3.4842061035	4.09459637587	-0.0732388857382	4.06551595823	0.348927675227	0.393565626752	-0.503858842641	-0.676128732284	0.0740956291314	0.140018005193	1.14721340008	0.55357922808	-0.44147187072	0.532400167042	-0.0319905244131	0.0414404018635	0.332716220316	-0.00835115546923	0.399818878477	54.8814885984	-57.9507142858	-13.0604322426
13	1.82787822677	0.570788008307	-0.277088364554	4.64620447014	2.04038532155	6.55202905362	-0.0162110473217	-0.156874889335	-0.0110285925718	0.191846496655	-0.0663179037769	0.0704241545126	-0.317887174428	-0.331533264949	0.103812709296	0.283353717668	0.0385821054303	-4.51251893641E-5	0.173752476297	0.00907670253482	0.247640482884	53.7432968515	-10.7193225917	-9.1819459769
14	1.76138153993	1.48794308724	0.623406740038	3.10696821357	1.52596047521	4.90912404651	-0.0202605683999	-0.0171676747556	0.151887218345	-0.195599099095	0.0751507365798	-0.233439105034	-0.473119291724	0.0765703100418	-0.0670281713972	0.375364001774	0.0144894894236	0.00873194817766	0.165112221532	0.00620957859476	0.288497270353	60.6140290346	-5.95727506587	-11.7893652046
15	0.717555616553	0.0844228114825	-0.128898007054	1.55263302107	-0.240784741037	2.19341597902	0.000753473944464	-0.0971440267777	0.019253967218	0.144008503745	0.0414642776117	-0.0653527912778	-0.301119042639	-0.116775933204	0.0172327423079	0.219547003076	0.0448289470433	0.0135653037605	0.206294668468	0.038439747776	0.246282023427	52.0566904488	-22.8738727367	-8.06929871465
16	3.05911528957	3.28813148824	-1.787242263	6.33549052072	-3.80821173483	3.23813750959	0.187133320975	-0.28993254252	-0.0135036912886	0.297347194137	-0.0699482151491	0.414817862684	-0.0169441803785	-0.31955332888	-0.103055574549	0.264312913219	-0.0705532626596	0.0247307377985	0.343488692845	-0.00255744277225	0.260752521551	43.0726979715	-38.2878590054	-13.5703260065
17	4.11490326853	2.62553819249	-1.09196130718	2.77635786456	-2.77194423377	4.19248449102	0.308957478138	0.365252918227	-0.124152801532	-0.243881528569	0.167132768107	2.22685022491	0.491970178161	-0.516977289814	-0.366410615314	0.378339374098	-0.0898930995605	-0.144586130519	0.576036640756	0.0853752245612	0.537608065892	35.4554008552	-42.6371691214	-18.2107134971

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'L' and (resid 1 through 18 )	L	A	1 - 18	1 - 18
2	2	chain 'L' and (resid 19 through 37 )	L	A	19 - 37	19 - 37
3	3	chain 'L' and (resid 38 through 74 )	L	A	38 - 74	38 - 74
4	4	chain 'L' and (resid 75 through 88 )	L	A	75 - 88	75 - 88
5	5	chain 'L' and (resid 89 through 100 )	L	A	89 - 100	89 - 100
6	6	chain 'L' and (resid 101 through 112 )	L	A	101 - 112	101 - 112
7	7	chain 'L' and (resid 113 through 127 )	L	A	113 - 127	113 - 127
8	8	chain 'L' and (resid 128 through 149 )	L	A	128 - 149	128 - 149
9	9	chain 'L' and (resid 150 through 162 )	L	A	150 - 162	150 - 162
10	10	chain 'L' and (resid 163 through 173 )	L	A	163 - 173	163 - 173
11	11	chain 'L' and (resid 174 through 196 )	L	A	174 - 196	174 - 196
12	12	chain 'L' and (resid 197 through 212 )	L	A	197 - 212	197 - 212
13	13	chain 'H' and (resid 1 through 44 )	H	B	1 - 44	1 - 44
14	14	chain 'H' and (resid 45 through 91 )	H	B	45 - 91	45 - 91
15	15	chain 'H' and (resid 92 through 142 )	H	B	92 - 142	92 - 142
16	16	chain 'H' and (resid 143 through 211 )	H	B	143 - 211	143 - 211
17	17	chain 'H' and (resid 212 through 224 )	H	B	212 - 224	212 - 224

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Antibody , 2 types, 2 molecules LH

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Non-polymers , 5 types, 270 molecules

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-Antibody , 2 types, 2 molecules LH

-Non-polymers , 5 types, 270 molecules

-Details

-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

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Movie

-
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

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Basic information

-
Structure visualization

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Downloads & links

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Download

-
Validation report

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Related structure data

-
Links

-
Assembly

-
Components

-
Antibody , 2 types, 2 molecules LH

-
Non-polymers , 5 types, 270 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi