PDB-4kdq: Crystal structure of the hemagglutinin of A/Xinjiang/1/2006 virus

ID or keywords:

Entry

Database: PDB / ID: 4kdq

Title

Crystal structure of the hemagglutinin of A/Xinjiang/1/2006 virus

Components

(Hemagglutinin

) x 2

Keywords

VIRAL PROTEIN /

homotrimer / virus attachment and membrane fusion

Function / homology

Function and homology information

viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 / virion membrane
Similarity search - Function

Biological species

Influenza A virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.604 Å

Authors

Lu, X. / Shi, Y. / Zhang, W. / Zhang, Y. / Qi, J. / Gao, G.F.

Citation

Journal: Protein Cell / Year: 2013
Title: Structure and receptor-binding properties of an airborne transmissible avian influenza A virus hemagglutinin H5 (VN1203mut).
Authors: Lu, X. / Shi, Y. / Zhang, W. / Zhang, Y. / Qi, J. / Gao, G.F.

History

Deposition	Apr 25, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 24, 2013	Provider: repository / Type: Initial release
Revision 1.1	Sep 4, 2013	Group: Database references
Revision 1.2	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Mar 13, 2024	Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4kdq.cif.gz	593.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4kdq.ent.gz	498.7 KB	Display	PDB format
PDBx/mmJSON format	4kdq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	4kdmC 4kdnC 4kdoC C: citing same article (ref.)
Similar structure data	4k65-1 4k66-2 4k62-1 3znl-d 4k62-3 4k65-2 4k65-4 4k66-1 4cqw-d 4k62-2 4yy1-2 4k63-2 4mhi-3 5vmc-d 4k67-4 3zp0-1 1jso-2 4yy0-d 4bgx-1 4yy7-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#76 - Apr 2006 Hemagglutinin similarity (5) #170 - Feb 2014 Broadly Neutralizing Antibodies similarity (5) #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

C: Hemagglutinin

E: Hemagglutinin

B: Hemagglutinin

D: Hemagglutinin

F: Hemagglutinin

hetero molecules

167 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)	72.049, 72.049, 365.862
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

#1: Protein

Hemagglutinin /

Mass: 36298.949 Da / Num. of mol.: 3 / Fragment: Residues 17-336
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Influenza A virus / Strain: (A/Xinjiang/1/2006(H5N1)) / Gene: HA / Production host:

Spodoptera frugiperda (fall armyworm) / References: UniProt: C5HMM2

#2: Protein

Hemagglutinin /

Mass: 18925.811 Da / Num. of mol.: 3 / Fragment: Residues 347-510
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Influenza A virus / Strain: (A/chicken/Guangdong/174/04(H5N1)) / Gene: HA / Production host:

Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6J0Q2

#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 /

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
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: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.31 Å³/Da / Density % sol: 62.83 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10% PEG 6,000, 5% MPD, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2012
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.6→50 Å / Num. all: 65515 / Num. obs: 65515 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell	Resolution: 2.6→2.69 Å / % possible all: 100

-
Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.604→36.886 Å / SU ML: 0.39 / σ(F): 1.98 / Phase error: 28.36 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2623	3292	5.07 %
R_work	0.2332	-	-
all	0.2346	64905	-
obs	0.2346	64905	99.75 %

Solvent computation

Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 31.151 Å² / k_sol: 0.275 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	7.7308 Å²	-0 Å²	-0 Å²
2-	-	7.7308 Å²	0 Å²
3-	-	-	-15.4616 Å²

Refinement step

Cycle: LAST / Resolution: 2.604→36.886 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11634	0	98	73	11805

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	12018
X-RAY DIFFRACTION	f_angle_d	1.024	16257
X-RAY DIFFRACTION	f_dihedral_angle_d	17.76	4442
X-RAY DIFFRACTION	f_chiral_restr	0.071	1744
X-RAY DIFFRACTION	f_plane_restr	0.004	2128

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 (%)
2.6035-2.6407	0.3578	122	0.3361	2516	X-RAY DIFFRACTION	97
2.6407-2.6801	0.3429	131	0.3107	2618	X-RAY DIFFRACTION	100
2.6801-2.722	0.3419	138	0.3009	2539	X-RAY DIFFRACTION	100
2.722-2.7666	0.3104	174	0.3047	2590	X-RAY DIFFRACTION	100
2.7666-2.8143	0.3221	123	0.2957	2472	X-RAY DIFFRACTION	100
2.8143-2.8654	0.3327	148	0.2952	2612	X-RAY DIFFRACTION	100
2.8654-2.9205	0.333	143	0.2899	2555	X-RAY DIFFRACTION	100
2.9205-2.9801	0.3789	145	0.2899	2608	X-RAY DIFFRACTION	100
2.9801-3.0449	0.3479	112	0.2875	2534	X-RAY DIFFRACTION	100
3.0449-3.1157	0.3366	146	0.2751	2623	X-RAY DIFFRACTION	100
3.1157-3.1935	0.2932	139	0.2612	2526	X-RAY DIFFRACTION	100
3.1935-3.2798	0.2799	146	0.2593	2638	X-RAY DIFFRACTION	100
3.2798-3.3763	0.3098	144	0.2623	2511	X-RAY DIFFRACTION	100
3.3763-3.4852	0.3153	138	0.2683	2555	X-RAY DIFFRACTION	100
3.4852-3.6096	0.2849	127	0.254	2617	X-RAY DIFFRACTION	100
3.6096-3.754	0.2542	143	0.2327	2563	X-RAY DIFFRACTION	100
3.754-3.9247	0.2526	126	0.2276	2536	X-RAY DIFFRACTION	100
3.9247-4.1314	0.1871	138	0.1994	2601	X-RAY DIFFRACTION	100
4.1314-4.3898	0.2071	135	0.1877	2559	X-RAY DIFFRACTION	100
4.3898-4.7281	0.2324	138	0.1839	2580	X-RAY DIFFRACTION	100
4.7281-5.2028	0.221	133	0.1955	2577	X-RAY DIFFRACTION	100
5.2028-5.9529	0.2071	141	0.2075	2575	X-RAY DIFFRACTION	100
5.9529-7.4897	0.2702	135	0.2102	2547	X-RAY DIFFRACTION	100
7.4897-36.8897	0.2267	127	0.2129	2561	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	0.4795	0.2029	0.3942	0.6514	0.1096	1.4438	0.0907	-0.1158	0.2053	0.1636	-0.1269	-0.0724	-0.2924	0.0406	0.0773	0.6556	-0.0147	-0.0215	0.2052	0.0038	0.4495	-0.1643	30.7572	-0.9475
2	2.2112	-0.2781	1.2484	1.5874	0.5494	1.9532	0.1352	0.4119	0.0757	-0.3495	-0.1821	0.015	-0.1429	0.3013	0.0176	0.5471	0.176	0.0233	0.2686	0.0784	0.3493	-6.3818	21.9364	-35.3851
3	0.7956	0.0834	0.2539	0.4242	0.1085	2.3493	-0.0476	-0.1697	0.3114	0.4519	-0.152	-0.2422	-0.16	-0.0144	0.0105	0.8527	-0.0828	-0.0392	0.2926	0.0165	0.4792	1.4957	30.949	7.472
4	0.2272	-0.0572	0.1198	0.0169	-0.0877	1.1506	0.1871	-0.0587	-0.144	0.2796	-0.19	-0.1497	0.0851	0.3688	-0.0423	0.6683	-0.0092	-0.1672	0.2415	0.0798	0.4016	-3.8611	-7.0119	2.3083
5	1.7271	-0.1781	0.0864	2.2555	-0.6848	1.1502	0.2747	0.2626	-0.1941	-0.2135	-0.168	0.0746	0.1237	-0.0301	0.0668	0.4333	0.1879	-0.0732	0.2081	-0.0404	0.3428	-20.8952	-9.0791	-29.4437
6	0.644	-0.0906	0.7328	0.7023	0.5698	1.485	0.2002	-0.3831	-0.159	0.3636	-0.1961	-0.1395	0.2117	0.2028	-0.0342	0.7739	-0.1893	-0.2249	0.436	0.0939	0.4303	-1.421	-5.6731	10.4301
7	0.9963	-0.1912	0.8273	0.4188	-0.4073	1.0424	0.1151	-0.6262	0.0961	0.3565	-0.1305	0.2448	-0.1644	-0.2849	0.0516	0.7744	0.0289	0.1419	0.6188	-0.0523	0.5363	-33.9401	15.6423	9.4481
8	0.7181	-0.2472	-0.2081	1.1034	0.0201	0.6573	0.1147	0.1435	0.2012	-0.0274	-0.0181	0.1367	-0.2102	-0.2198	0.2894	0.4469	0.4327	-0.0357	0.0294	-0.0264	0.4247	-39.7938	19.7467	-25.9239
9	0.8842	-0.0648	0.7312	0.5799	0.0202	2.0077	0.2763	-0.5687	0.0901	0.4034	-0.3137	0.299	0.0862	-0.3274	-0.0033	0.896	-0.1208	0.0908	0.8385	-0.011	0.489	-31.0168	15.759	17.5061
10	1.6023	0.0825	0.8533	1.2199	0.23	0.4837	-0.399	-0.1874	0.5051	0.1198	-0.1633	-0.1509	-0.5466	-0.3004	0.0417	1.2828	-0.3814	-0.1204	0.7323	-0.0863	0.5437	11.232	30.8297	45.7139
11	3.2169	0.0592	0.9182	2.3729	-0.0967	2.6652	0.8883	0.3252	-0.2856	-0.0303	-0.1549	-0.4972	-0.0525	0.3174	-0.1247	1.0088	-0.1071	-0.0289	0.6979	0.0243	0.6239	10.5589	19.8108	27.3006
12	0.8268	0.4138	-1.6121	1.275	-0.9731	3.1716	0.0697	-0.105	0.5352	0.9429	-0.4985	-0.3232	-0.5103	0.7442	0.3278	0.7918	-0.05	-0.1222	0.209	0.042	0.5299	-8.5703	19.6455	-3.5678
13	0.512	0.2961	0.351	0.4027	0.5941	1.1435	0.2251	-0.4511	0.0921	0.3852	-0.176	-0.0805	-0.3694	0.0402	0.3542	0.9657	-0.3075	-0.0242	0.5249	-0.0146	0.4403	-1.9503	20.8672	28.9142
14	0.4886	-0.1094	0.1284	0.2386	-0.1336	0.089	0.2893	-0.773	-0.1162	0.2915	-0.2098	-0.0465	-0.0409	0.0214	-0.0665	1.224	-0.5094	-0.3193	1.0538	0.0729	0.5706	19.9141	22.9976	58.3344
15	0.6985	-0.5732	0.1263	0.9255	-0.6463	1.5056	-0.1838	0.2302	-0.0154	-0.3753	0.3075	0.0802	0.3783	0.3889	0.0039	1.4056	-0.2163	-0.1709	0.8254	0.0448	0.5037	7.8585	-0.9025	48.8208
16	1.7079	-0.4817	-0.8144	2.055	-0.6818	2.2614	0.4541	0.2417	-0.3555	0.4486	-0.1048	-0.2172	0.1691	-0.7124	-0.1482	0.9999	-0.4445	-0.078	0.838	0.0647	0.5164	-7.5769	-1.2433	33.9039
17	0.3963	-0.0821	0.1184	0.017	-0.0246	0.0352	0.0751	-0.8647	0.3414	0.5942	-0.0528	-0.1454	0.3027	-0.2516	0.0431	1.3059	-0.218	-0.0749	0.8946	-0.0379	0.9017	-11.8072	2.375	6.8448
18	0.4803	-0.2238	1.0105	0.1087	-0.473	2.1347	0.1664	-0.2195	-0.08	0.3091	-0.1285	-0.0962	0.108	0.1418	0.0055	0.8822	-0.1784	-0.0716	0.4151	0.0881	0.3859	-2.2547	8.8323	25.5381
19	1.255	0.5018	-0.5099	0.6069	-0.5876	0.6403	-0.0009	0.1808	0.1525	0.0945	-0.0111	-0.0493	-0.2526	0.1611	0.2428	1.5427	-0.4959	-0.2487	0.738	0.1538	0.549	7.4046	1.4027	65.4338
20	1.4587	-0.6294	-0.0047	0.5833	0.2962	0.2772	-0.3257	-0.182	-0.2349	0.1318	0.1304	0.1863	0.3073	-0.2702	0.0146	1.259	-0.4057	-0.0611	1.0047	0.0894	0.4295	-0.542	-0.8506	64.7945
21	0.741	-0.2605	0.1104	0.7485	0.5438	0.532	0.0582	-0.923	0.0435	0.5876	0.0705	0.1308	-0.5632	-0.7492	0.0193	1.3973	-0.1072	0.0901	1.076	-0.0972	0.4299	-17.4012	21.3132	47.2943
22	1.8567	1.0158	1.5207	0.5976	1.1857	4.2265	0.1479	-0.5404	0.2417	0.4546	-0.525	0.255	-0.4015	-0.5624	0.128	0.8434	0.026	0.0578	0.3477	-0.1124	0.5221	-22.7887	14.4848	0.7331
23	0.3222	-0.1033	0.8843	0.8843	0.9684	4.5628	0.1908	-0.4827	0.0403	0.5424	-0.1779	-0.0078	0.1127	-0.2547	0.0107	0.8529	-0.216	0.0439	0.554	-0.0574	0.3287	-12.4184	14.8075	28.5928
24	0.3437	0.0137	0.3656	0.7043	0.2993	0.6281	-0.1835	-0.7539	0.3015	0.4959	-0.0431	0.0477	-0.5949	-0.3727	-0.2052	1.9365	0.0216	-0.0946	1.7839	-0.251	0.5212	-9.033	25.58	65.4757

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 1:108)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 109:267)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 268:321)
4	X-RAY DIFFRACTION	4	chain 'C' and (resseq 1:108)
5	X-RAY DIFFRACTION	5	chain 'C' and (resseq 109:267)
6	X-RAY DIFFRACTION	6	chain 'C' and (resseq 268:321)
7	X-RAY DIFFRACTION	7	chain 'E' and (resseq 1:108)
8	X-RAY DIFFRACTION	8	chain 'E' and (resseq 109:267)
9	X-RAY DIFFRACTION	9	chain 'E' and (resseq 268:321)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 1:37)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 38:58)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 59:74)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 75:137)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 138:164)
15	X-RAY DIFFRACTION	15	chain 'D' and (resseq 1:37)
16	X-RAY DIFFRACTION	16	chain 'D' and (resseq 38:58)
17	X-RAY DIFFRACTION	17	chain 'D' and (resseq 59:68)
18	X-RAY DIFFRACTION	18	chain 'D' and (resseq 69:137)
19	X-RAY DIFFRACTION	19	chain 'D' and (resseq 138:145)
20	X-RAY DIFFRACTION	20	chain 'D' and (resseq 146:164)
21	X-RAY DIFFRACTION	21	chain 'F' and (resseq 1:58)
22	X-RAY DIFFRACTION	22	chain 'F' and (resseq 59:74)
23	X-RAY DIFFRACTION	23	chain 'F' and (resseq 75:129)
24	X-RAY DIFFRACTION	24	chain 'F' and (resseq 130:164)

-
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