PDB-4wsv: The crystal structure of hemagglutinin from A/Taiwan/1/2013 in co...

ID or keywords:

Entry

Database: PDB / ID: 4wsv

Title

The crystal structure of hemagglutinin from A/Taiwan/1/2013 in complex with 6'SLN

Components

Hemagglutinin HA1 chain
Hemagglutinin HA2 chain

Keywords

VIRAL PROTEIN / Hemagglutinin / influenza virus / H6

Function / homology

Function and homology information

clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane
Similarity search - Function

Biological species

Influenza A virus H6N1 subtype

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 3.1 Å

Authors

Yang, H. / Carney, P.J. / Chang, J.C. / Villanueva, J.M. / Stevens, J.

Citation

Journal: J.Virol. / Year: 2015
Title: Structure and receptor binding preferences of recombinant hemagglutinins from avian and human h6 and h10 influenza a virus subtypes.
Authors: Yang, H. / Carney, P.J. / Chang, J.C. / Villanueva, J.M. / Stevens, J.

History

Deposition	Oct 28, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 25, 2015	Provider: repository / Type: Initial release
Revision 1.1	Apr 1, 2015	Group: Database references
Revision 1.2	Jul 29, 2020	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary Category: chem_comp / citation ...chem_comp / citation / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Dec 27, 2023	Group: Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4wsv.cif.gz	593 KB	Display	PDBx/mmCIF format
PDB format	pdb4wsv.ent.gz	495.2 KB	Display	PDB format
PDBx/mmJSON format	4wsv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4wsv_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4wsv_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4wsv_validation.xml.gz	54.3 KB	Display
Data in CIF	4wsv_validation.cif.gz	71.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ws/4wsv ftp://data.pdbj.org/pub/pdb/validation_reports/ws/4wsv	HTTPS FTP

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Related structure data

Related structure data	4wsrC 4wssC 4wstC 4wsuC 4wswC 4wsxC C: citing same article (ref.)
Similar structure data	4wsu-d 4xkf-d 2wr1-d 2wr5-d 4wsr-1 2wrf-1 4xkd-d 4lxv-1 5t0b-d 4m4y-d 5t0d-d 4xkg-d 4gxx-d 4mhi-1 4juh-d 6tzb-d 5xl1-1 2yp9-1 4juk-1 4zcj-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#76 - Apr 2006 Hemagglutinin similarity (6) #170 - Feb 2014 Broadly Neutralizing Antibodies similarity (5) #113 - May 2009 Influenza Neuraminidase similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (5) #62 - Feb 2005 Major Histocompatibility Complex similarity (5) #63 - Mar 2005 T-Cell Receptor similarity (5) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#76 - Apr 2006
Hemagglutinin
similarity (6)
#170 - Feb 2014
Broadly Neutralizing Antibodies
similarity (5)
#113 - May 2009
Influenza Neuraminidase
similarity (1)
#259 - Jul 2021
Designed Proteins and Citizen Science
similarity (5)
#62 - Feb 2005
Major Histocompatibility Complex
similarity (5)
#63 - Mar 2005
T-Cell Receptor
similarity (5)
#200 - Aug 2016
Quasisymmetry in Icosahedral Viruses
similarity (1)

Deposited unit

A: Hemagglutinin HA1 chain

C: Hemagglutinin HA1 chain

E: Hemagglutinin HA1 chain

B: Hemagglutinin HA2 chain

D: Hemagglutinin HA2 chain

F: Hemagglutinin HA2 chain

hetero molecules

177 kDa, 6 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)	186.438, 99.584, 134.216
Angle α, β, γ (deg.)	90.00, 125.96, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein

Hemagglutinin HA1 chain

Mass: 37434.273 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Influenza A virus H6N1 subtype / Production host:

Trichoplusia ni (cabbage looper) / References: UniProt: A0A0J9X248*PLUS

#2: Protein

Hemagglutinin HA2 chain

Mass: 20718.938 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Influenza A virus H6N1 subtype / Production host:

Trichoplusia ni (cabbage looper) / References: UniProt: A0A0J9X249*PLUS

#3: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#4: Sugar

ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID

Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₉NO₉

Identifier	Type	Program
DNeup5Aca	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-a-D-neuraminic acid	COMMON NAME	GMML 1.0
a-D-Neup5Ac	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
Neu5Ac	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.89 Å³/Da / Density % sol: 57.44 %
Crystal grow	Temperature: 293 K / Method: microbatch / pH: 8.5 Details: 0.01M nickel chloride, 0.1 M Tris-HCl pH 8.5 and 20% (w/v) PEG 2000MME

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 22, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3→50 Å / Num. obs: 37065 / % possible obs: 94.8 % / Redundancy: 3.1 % / Net I/σ(I): 13.1

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Processing

Software

Name: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement

Refinement

Resolution: 3.1→49.772 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.44 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.279	1862	5.03 %
R_work	0.2461	-	-
obs	0.2478	37033	94.71 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.1→49.772 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11757	0	166	0	11923

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	12217
X-RAY DIFFRACTION	f_angle_d	1.272	16556
X-RAY DIFFRACTION	f_dihedral_angle_d	15.9	4431
X-RAY DIFFRACTION	f_chiral_restr	0.049	1807
X-RAY DIFFRACTION	f_plane_restr	0.006	2140

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 (%)
3.0224-3.1041	0.3656	100	0.3388	2281	X-RAY DIFFRACTION	80
3.1041-3.1954	0.3976	135	0.3104	2808	X-RAY DIFFRACTION	98
3.1954-3.2985	0.2878	133	0.2818	2813	X-RAY DIFFRACTION	99
3.2985-3.4164	0.3243	169	0.2946	2831	X-RAY DIFFRACTION	100
3.4164-3.5531	0.335	148	0.2894	2827	X-RAY DIFFRACTION	100
3.5531-3.7148	0.4639	104	0.4067	1708	X-RAY DIFFRACTION	61
3.7148-3.9106	0.2689	140	0.2619	2774	X-RAY DIFFRACTION	97
3.9106-4.1555	0.2775	133	0.2241	2842	X-RAY DIFFRACTION	99
4.1555-4.4761	0.2337	165	0.1844	2826	X-RAY DIFFRACTION	100
4.4761-4.9262	0.215	137	0.1753	2864	X-RAY DIFFRACTION	100
4.9262-5.6382	0.2174	155	0.1924	2857	X-RAY DIFFRACTION	100
5.6382-7.1003	0.2768	165	0.2407	2868	X-RAY DIFFRACTION	100
7.1003-49.7786	0.267	178	0.2537	2872	X-RAY DIFFRACTION	99

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	1.3545	0.4434	-0.2587	-0.1591	0.2306	-0.2893	0.0415	0.3242	-0.0581	0.0287	-0.013	-0.1254	0.0739	0.0797	-0.002	0.3548	-0.0078	-0.0157	0.3335	0.0661	0.2687	-38.3245	23.1943	0.0226
2	0.9393	0.5994	-0.1398	1.2124	0.145	0.174	0.0026	0.2121	0.0256	-0.1078	-0.0021	0.1733	0.0794	-0.1841	-0.0004	0.5351	0.0199	-0.0541	0.6962	0.0275	0.4655	-70.5383	18.5081	-5.4469
3	0.4419	-0.2551	0.3333	0.897	-0.4775	-0.2486	0.1379	0.2993	-0.0738	0.0257	0.1691	0.1004	-0.0192	0.0263	-0	0.4727	0.0052	0.0388	0.7481	-0.0255	0.4648	-26.4131	24.8442	5.4818
4	0.8227	0.2071	0.1776	-0.4991	0.0557	-0.0948	-0.0167	-0.1965	-0.3992	0.0748	0.0224	-0.0891	0.1638	-0.006	-0.1649	0.4511	-0.0455	-0.0009	0.3655	0.0509	0.6007	-47.8576	0.1886	29.7975
5	2.3825	-0.7762	-0.9251	1.4719	-0.0162	0.6679	0.0591	0.0883	-0.0671	0.2021	-0.0572	0.1458	0.0794	-0.3317	0.0001	0.4386	-0.0578	-0.0192	0.4206	0.0218	0.4089	-81.4707	6.4825	20.5443
6	0.0214	-0.0544	0.2225	-0.0388	0.3013	0.0311	-0.1258	-0.2761	-0.8842	0.0842	0.0954	0.0271	0.0718	-0.034	0.0012	0.552	-0.1287	-0.0629	0.5934	0.0931	0.5433	-68.2402	6.0481	29.8528
7	0.1233	0.0051	0.26	0.2479	0.4303	-0.0453	0.2755	0.4118	-0.6494	-0.1566	0.0572	-0.3855	-0.1515	0.1259	0.0345	0.4653	-0.1047	-0.1377	0.4532	0.0969	0.6857	-34.684	0.6771	31.2637
8	1.0012	0.5134	1.1411	0.3528	-0.0642	0.4049	-0.1726	-0.2609	0.1824	0.2305	0.0786	0.1365	-0.127	-0.055	-0.0004	0.4303	0.0553	0.1171	0.4118	-0.0731	0.3509	-44.6152	37.6705	37.7799
9	0.9347	0.7505	0.7243	0.1074	0.4526	0.9524	0.0968	0.1325	0.0864	-0.0491	-0.1018	0.1661	-0.0752	-0.0771	0	0.3566	0.0481	0.0041	0.3799	0.0359	0.4607	-76.1164	38.7688	18.2677
10	0.5364	0.3479	0.3031	-0.0143	-0.1212	-0.1414	-0.1254	0.2088	0.0871	0.244	0.0441	-0.1196	0.0137	0.1872	-0.0006	0.4242	0.0109	-0.0823	0.5345	-0.1674	0.7051	-36.8306	36.1578	38.5667
11	0.1989	-0.1679	-0.1682	1.1152	-0.2832	0.8341	-0.0122	0.3392	-0.0767	0.408	0.272	-1.208	-0.3522	0.0906	-0.1156	0.1613	0.0627	0.0836	0.4407	-0.159	0.103	4.119	26.3106	20.9069
12	0.1318	-0.3021	0.0958	1.0349	0.4122	0.4265	0.0289	0.6919	-1.2165	-0.0713	-0.1154	-0.3119	0.0473	0.1498	-0.0339	0.3893	-0.0209	0.0225	0.4905	-0.03	0.3561	1.9279	17.0346	16.5993
13	0.6794	-0.8601	-0.87	0.3151	0.1654	0.4086	-0.0979	-0.0732	-0.5449	0.057	0.0633	0.047	-0.0777	-0.1655	0.0013	0.3935	-0.0148	0.0306	0.3312	-0.0023	0.3091	-22.7029	22.9838	21.1789
14	0.408	-0.0403	0.1849	-0.0836	0.0191	0.4758	-0.4699	-0.564	-0.7201	-0.2031	0.486	0.579	0.1041	0.2892	0.0048	0.4334	0.0278	-0.0095	0.6973	0.1199	0.714	22.8043	17.9198	26.6426
15	2.2782	1.5433	-1.6069	1.3017	-0.692	2.0696	-0.9323	-0.2097	-1.2276	-0.8903	0.261	-0.4394	0.3922	0.6912	-0.1351	0.1446	-0.0098	-0.0514	0.5264	0.1147	0.3593	-1.044	4.9351	37.9661
16	4.1581	-0.811	2.8998	0.0719	-0.5115	2.8363	-0.7628	-2.7337	0.1629	0.5019	0.2546	-0.0415	-0.0117	-1.1215	-0.3226	0.5057	-0.0868	0.0305	0.437	0.4305	0.5202	-7.2393	6.6892	46.1765
17	0.4554	-0.7661	0.0215	0.5913	-0.5505	0.3882	0.1003	-0.2657	-0.0745	0.0239	-0.0512	0.0553	0.0333	-0.1745	-0.0003	0.4459	-0.0033	-0.0353	0.3781	0.0208	0.3516	-25.1347	13.7409	28.7519
18	0.3798	-0.2014	0.1651	0.1362	-0.0176	0.0899	0.3967	-0.0087	0.432	0.3185	-0.013	-1.3372	-0.4404	0.4321	0.0901	0.7895	0.1067	-0.0956	0.5841	0.2251	0.5601	15.7769	7.2474	44.8885
19	0.6591	0.3186	0.174	0.1742	0.1514	0.0292	-0.3671	-1.5797	0.19	1.153	-0.2614	-0.7895	-1.0278	0.4688	-0.1034	0.7917	-0.014	-0.3563	0.8394	-0.1438	0.7692	15.2119	11.2532	54.1796
20	0.7244	-0.0507	0.4702	1.4906	-0.286	0.483	-0.0289	-0.6838	0.1961	0.7342	0.1755	0.1823	0.1712	-0.496	0.0429	0.2959	-0.0692	-0.0469	0.2741	-0.0873	0.3366	-3.977	30.4332	47.0905
21	1.0605	0.7214	1.3692	-0.4118	-0.0117	0.1876	-0.5735	1.219	1.0311	0.2007	0.1852	0.1498	-0.4701	0.9123	0.0049	0.5911	-0.0731	0.0209	0.367	-0.0446	0.5651	-5.5425	38.1992	40.3861
22	0.25	1.1723	0.5862	0.1849	0.3758	0.5896	-0.1642	0.117	0.5746	-0.0086	0.0291	0.2175	-0.014	-0.1046	-0.0003	0.4086	-0.0205	-0.015	0.3796	-0.0544	0.6111	-26.3698	25.3108	32.6086
23	0.512	0.0329	-0.003	0.2857	-0.2407	0.2085	-0.2788	1.0017	-0.2998	-0.1455	0.5199	-0.3454	-0.3125	1.0145	0.0011	0.636	-0.1006	-0.0165	0.7726	-0.0195	0.4862	13.9412	35.3798	46.3338
24	1.0467	0.6989	-1.5034	1.4772	-0.6676	2.1548	-0.1689	0.6869	0.5198	-0.5769	0.131	0.3329	-0.2858	-0.1077	0.9882	0.4336	-0.1142	-0.0812	0.6652	-0.139	0.7765	25.5723	34.0092	45.2869

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 121 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 122 through 269 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 270 through 324 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 0 through 121 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 122 through 245 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 246 through 269 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 270 through 324 )
8	X-RAY DIFFRACTION	8	chain 'E' and (resid 0 through 97 )
9	X-RAY DIFFRACTION	9	chain 'E' and (resid 98 through 269 )
10	X-RAY DIFFRACTION	10	chain 'E' and (resid 270 through 324 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1 through 22 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 23 through 58 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 59 through 129 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 130 through 168 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 1 through 22 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 23 through 58 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 59 through 129 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 130 through 145 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 146 through 168 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 1 through 22 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 23 through 58 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 59 through 129 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 130 through 159 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 160 through 168 )

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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

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

+
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