PDB-4we0: JC Polyomavirus VP1 five-fold pore mutant P223M

ID or keywords:

Entry

Database: PDB / ID: 4we0

Title

JC Polyomavirus VP1 five-fold pore mutant P223M

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 / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function

Biological species

JC polyomavirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 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

-
Download

PDBx/mmCIF format	4we0.cif.gz	507.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4we0.ent.gz	421.3 KB	Display	PDB format
PDBx/mmJSON format	4we0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4we0_validation.pdf.gz	472.8 KB	Display	wwPDB validaton report
Full document	4we0_full_validation.pdf.gz	475.4 KB	Display
Data in XML	4we0_validation.xml.gz	49 KB	Display
Data in CIF	4we0_validation.cif.gz	69 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/we/4we0 ftp://data.pdbj.org/pub/pdb/validation_reports/we/4we0	HTTPS FTP

-
Related structure data

Related structure data	4wdyC 4wdzC 3nxgS 3nxd S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6y5z-d 4jce-d 4jcd-d 4x12-d 4x13-d 4x0y-d 4x16-d 4jcf-d 3nxd-d 4wdz-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

-
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

151 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	149.720, 95.630, 128.510
Angle α, β, γ (deg.)	90.00, 110.40, 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	(0.441507, 0.853742, 0.276038), (-0.855906, 0.308413, 0.415098), (0.269253, -0.419531, 0.866889)	11.33337, 20.28363, -5.69503
3	given	(-0.449732, 0.514494, 0.730094), (-0.528187, -0.812374, 0.247117), (0.72025, -0.27449, 0.637099)	31.66548, 14.62503, -15.68106
4	given	(-0.443381, -0.536085, 0.71835), (0.519955, -0.806636, -0.281043), (0.73011, 0.2489, 0.636387)	33.07141, -8.74875, -16.81253
5	given	(0.448001, -0.852805, 0.268362), (0.848497, 0.311, -0.428172), (0.281686, 0.419526, 0.862931)	13.58788, -18.00196, -6.96701

#1: Protein	Major capsid protein VP1 / Major structural protein VP1 Mass: 30109.939 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) JC polyomavirus / Plasmid: pET15b / 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.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 530 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.86 Å³/Da / Density % sol: 57.05 %
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

-
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: 2.1→50 Å / Num. obs: 98969 / % possible obs: 99.8 % / Redundancy: 3.8 % / B_iso Wilson estimate: 29.8 Å² / Net I/σ(I): 9.2
Reflection shell	Resolution: 2.1→2.15 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.7 / % possible all: 99.8

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3NXG

3nxg

Resolution: 2.1→50 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.935 / SU B: 10.489 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21775	4940	5 %	RANDOM
R_work	0.18008	-	-	-
obs	0.18195	94028	99.83 %	-

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: 28.892 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.49 Å²	0 Å²	0.2 Å²
2-	-	-0.22 Å²	0 Å²
3-	-	-	-0.33 Å²

Refinement step

Cycle: 1 / Resolution: 2.1→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10031	0	38	530	10599

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	10314
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	9641
X-RAY DIFFRACTION	r_angle_refined_deg	1.307	1.956	13997
X-RAY DIFFRACTION	r_angle_other_deg	0.734	3	22207
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.444	5	1286
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.025	24.268	471
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.625	15	1698
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.949	15	62
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	1572
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	11721
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2373
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	1.697	4.247	5150
X-RAY DIFFRACTION	r_mcbond_other	1.697	4.246	5149
X-RAY DIFFRACTION	r_mcangle_it	2.289	5.701	6422
X-RAY DIFFRACTION	r_mcangle_other	2.289	5.702	6423
X-RAY DIFFRACTION	r_scbond_it	3.237	5.291	5164
X-RAY DIFFRACTION	r_scbond_other	3.231	5.291	5164
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	4.501	6.767	7572
X-RAY DIFFRACTION	r_long_range_B_refined	6.202	11.784	11419
X-RAY DIFFRACTION	r_long_range_B_other	6.202	11.784	11419
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: 2623 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Type	Rms dev position (Å)	Weight position
A	medium positional	0.27	0.5
B	medium positional	0.24	0.5
C	medium positional	0.23	0.5
D	medium positional	0.29	0.5
E	medium positional	0.26	0.5
A	medium thermal	1.86	2
B	medium thermal	1.83	2
C	medium thermal	1.66	2
D	medium thermal	1.6	2
E	medium thermal	1.65	2

LS refinement shell

Resolution: 2.1→2.154 Å

	R_factor	Num. reflection	% reflection
R_free	0.31	362	5 %
R_work	0.277	6891	-
obs	-	-	99.37 %

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	0.9959	-0.0825	0.8738	0.5757	-0.1161	3.0894	-0.0696	0.1002	0.0788	0.0947	0.0084	-0.0807	-0.0759	0.2826	0.0612	0.0618	-0.0006	-0.0444	0.2089	0.0209	0.1419	60.6072	11.4717	18.7366
2	0.4334	-0.2129	0.0915	0.9727	0.1306	0.7502	-0.0161	0.0844	-0.0008	-0.0281	0.0166	-0.0372	-0.0076	0.0722	-0.0005	0.0393	-0.0259	-0.0586	0.1913	0.0285	0.0991	58.0032	5.5917	18.4646
3	4.5558	0.1377	4.587	0.8228	0.0852	6.2861	-0.2105	0.0448	0.1031	0.0871	0.0329	-0.0614	-0.394	0.1137	0.1775	0.0428	-0.0229	-0.031	0.1143	0.0178	0.0842	59.0899	12.2123	23.9029
4	8.2612	-1.3547	4.2433	1.7307	-0.2097	5.1321	0.0909	-0.6172	0.1766	0.1458	-0.0212	-0.093	-0.3156	-0.3023	-0.0697	0.2421	0.0075	-0.0415	0.2011	-0.0004	0.1909	44.3045	30.5522	52.424
5	1.0324	-0.0288	-0.105	0.0969	-0.2381	1.141	-0.0249	0.0311	0.1205	0.0044	-0.0026	0.0151	-0.1522	-0.0618	0.0276	0.08	0.012	-0.0904	0.1508	0.017	0.1396	37.9763	25.3719	25.1666
6	2.5301	1.0921	2.5121	1.167	1.4764	4.4885	-0.049	-0.1221	0.0205	0.0275	-0.0127	-0.02	-0.1781	-0.0187	0.0617	0.0535	0.0266	-0.0569	0.1246	0.0214	0.1144	38.1696	25.9292	35.3769
7	4.4467	3.4121	3.5025	3.4771	2.3252	7.083	0.3019	-0.2015	-0.301	0.4969	-0.0328	-0.1377	0.3923	-0.2352	-0.2691	0.1986	0.0413	-0.0434	0.2652	0.0066	0.2009	21.8056	5.3777	63.3445
8	0.6116	0.0595	0.2366	1.4227	-0.0552	0.435	-0.0084	0.0347	0.054	-0.0135	-0.0004	0.0743	-0.055	-0.1204	0.0088	0.0367	0.0239	-0.0544	0.2396	0.006	0.1127	15.4507	11.4036	35.5027
9	1.15	0.1478	1.4998	0.944	0.6668	5.5843	0.0223	-0.0803	0.0383	0.0998	0.0126	-0.0276	-0.0209	-0.0643	-0.035	0.0295	-0.0005	-0.0428	0.1473	0.0108	0.1164	19.3277	7.0062	45.8706
10	1.5697	-0.6766	2.8529	3.0292	2.6197	10.8715	0.0118	0.058	-0.0077	0.2676	-0.1054	-0.0329	0.4878	0.174	0.0936	0.1656	-0.0488	-0.0057	0.2444	0.0746	0.1799	35.3251	-24.6692	56.3847
11	1.0396	-0.229	-0.0302	0.5296	0.2938	0.9773	-0.0025	0.0198	-0.0472	-0.0339	0.0228	0.0941	0.0786	-0.1014	-0.0203	0.0503	-0.029	-0.0763	0.1708	0.0134	0.1331	20.7676	-16.4989	33.1908
12	0.9611	-0.256	1.0101	0.7973	-1.015	6.4857	-0.0489	-0.0826	0.0123	0.0602	0.0293	0.0176	0.0158	-0.0381	0.0196	0.0263	0.0003	-0.0446	0.1225	0.003	0.1205	28.1975	-19.4293	40.5999
13	2.377	-0.0796	0.8069	0.3842	-0.9163	9.6214	-0.0759	-0.0072	0.0058	0.1601	-0.1202	-0.1687	-0.4061	0.3602	0.1961	0.1465	0.0248	-0.0619	0.1728	-0.0195	0.1881	65.6065	-20.1331	41.6931
14	0.7387	0.3076	0.1728	0.4646	-0.1227	1.02	0.0039	0.0828	-0.0496	-0.0772	0.0083	0.0046	0.0718	0.0154	-0.0122	0.0536	0.02	-0.0642	0.1662	-0.0293	0.1048	46.1376	-19.8211	20.8891
15	2.297	-0.8329	2.6424	1.3745	-1.3372	4.1639	0.0234	0.0218	-0.0144	0.0397	-0.0674	0.035	0.0201	0.1159	0.044	0.0182	-0.0013	-0.0319	0.1313	-0.0184	0.0826	53.7505	-17.7961	27.3652

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

-
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