PDB-4wdz: JC Polyomavirus VP1 five-fold pore mutant N221W

ID or keywords:

Entry

Database: PDB / ID: 4wdz

Title

JC Polyomavirus VP1 five-fold pore mutant N221W

Components

Major capsid protein VP1

Keywords

VIRAL PROTEIN / beta-sandwich / jelly-roll / viral major capsid protein / five-fold pore

Function / homology

Function and homology information

T=7 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / host cell nucleus / virion attachment to host cell / structural molecule activity
Similarity search - Function

Biological species

JC polyomavirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Stroh, L.J. / Stehle, T.

Citation

Journal: J.Virol. / Year: 2015
Title: Modulation of a Pore in the Capsid of JC Polyomavirus Reduces Infectivity and Prevents Exposure of the Minor Capsid Proteins.
Authors: Nelson, C.D. / Stroh, L.J. / Gee, G.V. / O'Hara, B.A. / Stehle, T. / Atwood, W.J.

History

Deposition	Sep 9, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Feb 18, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 18, 2015	Group: Database references
Revision 1.2	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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4wdz.cif.gz	518 KB	Display	PDBx/mmCIF format
PDB format	pdb4wdz.ent.gz	428.3 KB	Display	PDB format
PDBx/mmJSON format	4wdz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4wdz_validation.pdf.gz	473.6 KB	Display	wwPDB validaton report
Full document	4wdz_full_validation.pdf.gz	477 KB	Display
Data in XML	4wdz_validation.xml.gz	54.3 KB	Display
Data in CIF	4wdz_validation.cif.gz	77.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wd/4wdz ftp://data.pdbj.org/pub/pdb/validation_reports/wd/4wdz	HTTPS FTP

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Related structure data

Related structure data	4wdyC 4we0C 3nxgS 3nxd S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4x0y-d 4x11-d 4jce-d 4x14-d 4x17-d 4x15-d 4x0z-d 4x13-d 4x16-d 4we0-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	#47 - Nov 2003 Simian Virus 40 similarity (4) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (5)

Deposited unit

A: Major capsid protein VP1

B: Major capsid protein VP1

C: Major capsid protein VP1

D: Major capsid protein VP1

E: Major capsid protein VP1

hetero molecules

152 kDa, 5 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)	149.340, 95.980, 128.510
Angle α, β, γ (deg.)	90.00, 110.48, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	VAL	VAL	VAL	VAL	A	A	26 - 29	9 - 12
2	1	VAL	VAL	VAL	VAL	B	B	26 - 29	9 - 12
3	1	VAL	VAL	VAL	VAL	C	C	26 - 29	9 - 12
4	1	VAL	VAL	VAL	VAL	D	D	26 - 29	9 - 12
5	1	VAL	VAL	VAL	VAL	E	E	26 - 29	9 - 12
1	2	THR	THR	ASP	ASP	A	A	31 - 51	14 - 34
2	2	THR	THR	ASP	ASP	B	B	31 - 51	14 - 34
3	2	THR	THR	ASP	ASP	C	C	31 - 51	14 - 34
4	2	THR	THR	ASP	ASP	D	D	31 - 51	14 - 34
5	2	THR	THR	ASP	ASP	E	E	31 - 51	14 - 34
1	3	HIS	HIS	PHE	PHE	A	A	53 - 57	36 - 40
2	3	HIS	HIS	PHE	PHE	B	B	53 - 57	36 - 40
3	3	HIS	HIS	PHE	PHE	C	C	53 - 57	36 - 40
4	3	HIS	HIS	PHE	PHE	D	D	53 - 57	36 - 40
5	3	HIS	HIS	PHE	PHE	E	E	53 - 57	36 - 40
1	4	PRO	PRO	ILE	ILE	A	A	78 - 85	61 - 68
2	4	PRO	PRO	ILE	ILE	B	B	78 - 85	61 - 68
3	4	PRO	PRO	ILE	ILE	C	C	78 - 85	61 - 68
4	4	PRO	PRO	ILE	ILE	D	D	78 - 85	61 - 68
5	4	PRO	PRO	ILE	ILE	E	E	78 - 85	61 - 68
1	5	MET	MET	VAL	VAL	A	A	101 - 111	84 - 94
2	5	MET	MET	VAL	VAL	B	B	101 - 111	84 - 94
3	5	MET	MET	VAL	VAL	C	C	101 - 111	84 - 94
4	5	MET	MET	VAL	VAL	D	D	101 - 111	84 - 94
5	5	MET	MET	VAL	VAL	E	E	101 - 111	84 - 94
1	6	ALA	ALA	THR	THR	A	A	126 - 162	109 - 145
2	6	ALA	ALA	THR	THR	B	B	126 - 162	109 - 145
3	6	ALA	ALA	THR	THR	C	C	126 - 162	109 - 145
4	6	ALA	ALA	THR	THR	D	D	126 - 162	109 - 145
5	6	ALA	ALA	THR	THR	E	E	126 - 162	109 - 145
1	7	ASN	ASN	LEU	LEU	A	A	173 - 189	156 - 172
2	7	ASN	ASN	LEU	LEU	B	B	173 - 189	156 - 172
3	7	ASN	ASN	LEU	LEU	C	C	173 - 189	156 - 172
4	7	ASN	ASN	LEU	LEU	D	D	173 - 189	156 - 172
5	7	ASN	ASN	LEU	LEU	E	E	173 - 189	156 - 172
1	8	ALA	ALA	THR	THR	A	A	194 - 205	177 - 188
2	8	ALA	ALA	THR	THR	B	B	194 - 205	177 - 188
3	8	ALA	ALA	THR	THR	C	C	194 - 205	177 - 188
4	8	ALA	ALA	THR	THR	D	D	194 - 205	177 - 188
5	8	ALA	ALA	THR	THR	E	E	194 - 205	177 - 188
1	9	PHE	PHE	VAL	VAL	A	A	240 - 287	223 - 270
2	9	PHE	PHE	VAL	VAL	B	B	240 - 287	223 - 270
3	9	PHE	PHE	VAL	VAL	C	C	240 - 287	223 - 270
4	9	PHE	PHE	VAL	VAL	D	D	240 - 287	223 - 270
5	9	PHE	PHE	VAL	VAL	E	E	240 - 287	223 - 270
1	10	ILE	ILE	SER	SER	A	A	112 - 122	95 - 105
2	10	ILE	ILE	SER	SER	B	B	112 - 122	95 - 105
3	10	ILE	ILE	SER	SER	C	C	112 - 122	95 - 105
4	10	ILE	ILE	SER	SER	D	D	112 - 122	95 - 105
5	10	ILE	ILE	SER	SER	E	E	112 - 122	95 - 105

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(0.439988, 0.854047, 0.277514), (-0.856603, 0.306408, 0.415144), (0.26952, -0.420378, 0.866396)	11.23434, 20.21885, -5.60386
3	given	(-0.451411, 0.514804, 0.728838), (-0.527757, -0.812649, 0.247132), (0.719514, -0.273091, 0.63853)	31.4349, 14.57475, -15.56504
4	given	(-0.443877, -0.535489, 0.718488), (0.520866, -0.806623, -0.279389), (0.729159, 0.250221, 0.636959)	32.80703, -8.64556, -16.63044
5	given	(0.447828, -0.852525, 0.269539), (0.849033, 0.310943, -0.42715), (0.280345, 0.420137, 0.863071)	13.51019, -17.83764, -6.85143

#1: Protein	Major capsid protein VP1 / Major structural protein VP1 / Mad-1 VP1 Mass: 30147.967 Da / Num. of mol.: 5 / Fragment: UNP residues 23-290 / Mutation: N221W Source method: isolated from a genetically manipulated source Source: (gene. exp.) JC polyomavirus / Plasmid: 15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03089
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 873 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.86 Å³/Da / Density % sol: 57.02 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 0.2 M KSCN, 12% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 18, 2010
Radiation	Monochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. obs: 155280 / % possible obs: 98.8 % / Redundancy: 4.1 % / B_iso Wilson estimate: 30.7 Å² / Net I/σ(I): 11.7
Reflection shell	Resolution: 1.8→1.85 Å / Mean I/σ(I) obs: 1.5 / % possible all: 88.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0049	refinement
Coot		model building
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3NXG

3nxg

Resolution: 1.8→50 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.961 / SU B: 4.773 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18584	7790	5 %	RANDOM
R_work	0.15979	-	-	-
obs	0.16109	147490	98.82 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 26.921 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.16 Å²	-0 Å²	-0.03 Å²
2-	-	0.51 Å²	0 Å²
3-	-	-	-0.51 Å²

Refinement step

Cycle: 1 / Resolution: 1.8→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10033	0	112	873	11018

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	10433
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	9736
X-RAY DIFFRACTION	r_angle_refined_deg	1.269	1.957	14162
X-RAY DIFFRACTION	r_angle_other_deg	0.729	3	22422
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.763	5	1302
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.097	24.085	470
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.973	15	1677
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.922	15	64
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	1588
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	11812
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2408
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.706	5.109	5172
X-RAY DIFFRACTION	r_mcbond_other	1.705	5.108	5171
X-RAY DIFFRACTION	r_mcangle_it	2.193	6.858	6453
X-RAY DIFFRACTION	r_mcangle_other	2.193	6.859	6454
X-RAY DIFFRACTION	r_scbond_it	3.079	6.162	5261
X-RAY DIFFRACTION	r_scbond_other	3.08	6.162	5261
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.162	7.921	7699
X-RAY DIFFRACTION	r_long_range_B_refined	6.314	14.522	12062
X-RAY DIFFRACTION	r_long_range_B_other	6.314	14.525	12063
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2598 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Type	Rms dev position (Å)	Weight position
A	medium positional	0.24	0.5
B	medium positional	0.29	0.5
C	medium positional	0.26	0.5
D	medium positional	0.28	0.5
E	medium positional	0.27	0.5
A	medium thermal	1.38	2
B	medium thermal	1.2	2
C	medium thermal	1.17	2
D	medium thermal	1.19	2
E	medium thermal	1.18	2

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.361	503	-
R_work	0.342	9808	-
obs	-	-	88.49 %

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	0.8957	-0.0063	0.6665	0.5002	-0.1592	1.8582	-0.0659	0.0252	0.0625	0.0661	0.0085	-0.1066	-0.1081	0.2307	0.0574	0.0497	-0.003	-0.0176	0.0936	0.0188	0.1504	60.383	11.7285	18.846
2	0.5794	-0.1114	0.1471	0.7095	0.1293	0.6479	-0.0116	0.0548	-0.003	-0.0056	-0.0056	-0.0585	-0.0029	0.0862	0.0171	0.0128	-0.0202	-0.0241	0.0511	0.023	0.1041	57.7277	5.5872	18.58
3	4.1698	0.2552	3.9502	0.6759	0.377	5.1614	-0.1108	-0.0014	0.0804	0.0449	-0.0041	-0.0401	-0.1687	0.1036	0.1149	0.0155	-0.0124	-0.0024	0.0245	0.0193	0.0915	59.1416	12.132	24.2431
4	8.3814	0.0963	4.4584	0.9994	0.5587	4.7788	0.0302	-0.5582	-0.0568	0.0812	-0.0161	-0.0388	-0.174	-0.233	-0.014	0.2197	0.0002	-0.0275	0.127	0.0054	0.2089	43.7972	30.2567	52.0065
5	0.802	0.0687	-0.1209	0.2639	-0.1414	0.6354	-0.0172	-0.0027	0.1022	0.0159	0.0096	-0.0001	-0.143	-0.0174	0.0076	0.0577	0.0074	-0.0424	0.0274	0.007	0.135	37.8418	25.3383	25.1078
6	2.2959	0.8791	2.3328	0.9929	1.1177	4.1299	-0.0239	-0.073	0.0498	0.0579	0.0117	-0.024	-0.1205	0.0533	0.0122	0.0396	0.0145	-0.018	0.0304	0.0075	0.1297	38.0083	25.8885	35.3415
7	3.5703	2.5994	4.0151	3.4675	2.7921	8.2191	0.1491	-0.1175	-0.0978	0.347	-0.0119	-0.0971	0.2759	-0.0893	-0.1372	0.1489	0.0458	0.0226	0.16	-0.0027	0.1798	21.5879	5.6236	62.6403
8	0.4482	-0.0306	0.1576	0.897	-0.0543	0.4769	-0.0017	-0.0248	0.0638	0.0477	0.0083	0.0724	-0.0654	-0.133	-0.0066	0.019	0.0182	-0.0198	0.086	0.0049	0.1216	15.3722	11.4286	35.6591
9	0.7671	0.1201	0.9383	0.98	0.7672	4.776	-0.02	-0.0737	0.0248	0.1136	0.009	-0.0203	-0.1131	-0.0065	0.011	0.0244	0.0042	-0.0143	0.0473	0.0021	0.1261	19.1458	7.1096	45.8388
10	0.7051	-0.4632	1.1266	2.3345	1.3674	10.6172	-0.0208	-0.0628	-0.0547	0.1722	0.0065	-0.0222	0.2364	0.3067	0.0142	0.1057	-0.0335	-0.0158	0.1537	0.0254	0.187	34.87	-24.4167	55.8302
11	0.8336	-0.1066	-0.0774	0.3806	0.1709	0.6268	0.0087	-0.0297	-0.0526	0.0128	0.0167	0.0676	0.0842	-0.0795	-0.0253	0.0217	-0.0188	-0.0354	0.047	0.0114	0.1216	20.6567	-16.4208	33.3775
12	0.977	-0.3004	0.8331	0.7313	-0.7	5.4095	-0.0347	-0.1302	-0.0138	0.066	0.0405	0.0108	-0.0109	-0.0592	-0.0058	0.0132	-0.0046	-0.0141	0.0416	-0.0007	0.1181	27.9212	-19.3155	40.6172
13	2.7281	0.3762	0.2673	1.9581	-2.5402	10.865	-0.0203	-0.0988	-0.0403	0.2292	-0.1212	-0.1197	-0.2433	0.562	0.1415	0.1047	0.0528	-0.02	0.0898	-0.0318	0.1943	65.2589	-20.1261	41.6209
14	0.5364	0.2147	0.1082	0.4316	-0.0951	0.6875	0.0104	0.0514	-0.0676	-0.0507	-0.0073	-0.0109	0.0928	0.0403	-0.0031	0.0222	0.0135	-0.0252	0.0393	-0.0176	0.115	45.8533	-19.6844	21.0144
15	1.9185	-0.7647	2.1846	1.2889	-1.3543	3.7654	0.0154	-0.0336	-0.0418	0.0344	0.0048	0.0139	0.0294	0.0337	-0.0202	0.0029	0.0015	-0.0026	0.0257	-0.0166	0.0825	53.4037	-17.6248	27.2081

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	24 - 68
2	X-RAY DIFFRACTION	2	A	69 - 263
3	X-RAY DIFFRACTION	3	A	264 - 289
4	X-RAY DIFFRACTION	4	B	24 - 42
5	X-RAY DIFFRACTION	5	B	43 - 237
6	X-RAY DIFFRACTION	6	B	238 - 288
7	X-RAY DIFFRACTION	7	C	25 - 42
8	X-RAY DIFFRACTION	8	C	43 - 232
9	X-RAY DIFFRACTION	9	C	233 - 288
10	X-RAY DIFFRACTION	10	D	24 - 42
11	X-RAY DIFFRACTION	11	D	43 - 236
12	X-RAY DIFFRACTION	12	D	237 - 288
13	X-RAY DIFFRACTION	13	E	24 - 42
14	X-RAY DIFFRACTION	14	E	43 - 238
15	X-RAY DIFFRACTION	15	E	239 - 288

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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

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+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

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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

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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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