PDB-4mj1: unliganded BK Polyomavirus VP1 pentamer

ID or keywords:

Entry

Database: PDB / ID: 4mj1

Title

unliganded BK Polyomavirus VP1 pentamer

Components

VP1 capsid protein

Keywords

VIRAL PROTEIN / antiparallel beta sandwich / jelly-roll topology /

polyomavirus / receptor switch / virus major capsid protein / attachment to host-cell surface receptors

Function / homology

Function and homology information

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

Biological species

BK polyomavirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Neu, U. / Stroh, L.J. / Stehle, T.

Citation

Journal: Plos Pathog. / Year: 2013
Title: A Structure-Guided Mutation in the Major Capsid Protein Retargets BK Polyomavirus.
Authors: Neu, U. / Allen, S.A. / Blaum, B.S. / Liu, Y. / Frank, M. / Palma, A.S. / Stroh, L.J. / Feizi, T. / Peters, T. / Atwood, W.J. / Stehle, T.

History

Deposition	Sep 3, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 6, 2013	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_ref_seq_dif / struct_site 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4mj1.cif.gz	533.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4mj1.ent.gz	441.9 KB	Display	PDB format
PDBx/mmJSON format	4mj1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mj/4mj1 ftp://data.pdbj.org/pub/pdb/validation_reports/mj/4mj1	HTTPS FTP

-
Related structure data

Related structure data	4mj0C 3bwqS 3bwr 3nxd S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4jce-d 4x0y-d 6y63-1 3nxg-d 6y61-1 4x11-d 6y61-2 4fmi-1 4wdy-d 6y64-1 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: VP1 capsid protein

B: VP1 capsid protein

C: VP1 capsid protein

D: VP1 capsid protein

E: VP1 capsid protein

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)	144.900, 152.290, 62.720
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

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	ASN	ASN	ASP	ASP	A	A	52 - 59	27 - 34
2	1	ASN	ASN	ASP	ASP	B	B	52 - 59	27 - 34
3	1	ASN	ASN	ASP	ASP	C	C	52 - 59	27 - 34
4	1	ASN	ASN	ASP	ASP	D	D	52 - 59	27 - 34
5	1	ASN	ASN	ASP	ASP	E	E	52 - 59	27 - 34
1	2	ASN	ASN	LEU	LEU	A	A	61 - 69	36 - 44
2	2	ASN	ASN	LEU	LEU	B	B	61 - 69	36 - 44
3	2	ASN	ASN	LEU	LEU	C	C	61 - 69	36 - 44
4	2	ASN	ASN	LEU	LEU	D	D	61 - 69	36 - 44
5	2	ASN	ASN	LEU	LEU	E	E	61 - 69	36 - 44
1	3	SER	SER	ASP	ASP	A	A	70 - 78	45 - 53
2	3	SER	SER	ASP	ASP	B	B	70 - 78	45 - 53
3	3	SER	SER	ASP	ASP	C	C	70 - 78	45 - 53
4	3	SER	SER	ASP	ASP	D	D	70 - 78	45 - 53
5	3	SER	SER	ASP	ASP	E	E	70 - 78	45 - 53
1	4	MET	MET	ALA	ALA	A	A	84 - 91	59 - 66
2	4	MET	MET	ALA	ALA	B	B	84 - 91	59 - 66
3	4	MET	MET	ALA	ALA	C	C	84 - 91	59 - 66
4	4	MET	MET	ALA	ALA	D	D	84 - 91	59 - 66
5	4	MET	MET	ALA	ALA	E	E	84 - 91	59 - 66
1	5	THR	THR	SER	SER	A	A	117 - 124	92 - 99
2	5	THR	THR	SER	SER	B	B	117 - 124	92 - 99
3	5	THR	THR	SER	SER	C	C	117 - 124	92 - 99
4	5	THR	THR	SER	SER	D	D	117 - 124	92 - 99
5	5	THR	THR	SER	SER	E	E	117 - 124	92 - 99
1	6	LEU	LEU	GLN	GLN	A	A	126 - 133	101 - 108
2	6	LEU	LEU	GLN	GLN	B	B	126 - 133	101 - 108
3	6	LEU	LEU	GLN	GLN	C	C	126 - 133	101 - 108
4	6	LEU	LEU	GLN	GLN	D	D	126 - 133	101 - 108
5	6	LEU	LEU	GLN	GLN	E	E	126 - 133	101 - 108
1	7	VAL	VAL	HIS	HIS	A	A	135 - 136	110 - 111
2	7	VAL	VAL	HIS	HIS	B	B	135 - 136	110 - 111
3	7	VAL	VAL	HIS	HIS	C	C	135 - 136	110 - 111
4	7	VAL	VAL	HIS	HIS	D	D	135 - 136	110 - 111
5	7	VAL	VAL	HIS	HIS	E	E	135 - 136	110 - 111
1	8	HIS	HIS	LEU	LEU	A	A	138 - 159	113 - 134
2	8	HIS	HIS	LEU	LEU	B	B	138 - 159	113 - 134
3	8	HIS	HIS	LEU	LEU	C	C	138 - 159	113 - 134
4	8	HIS	HIS	LEU	LEU	D	D	138 - 159	113 - 134
5	8	HIS	HIS	LEU	LEU	E	E	138 - 159	113 - 134
1	9	MET	MET	LEU	LEU	A	A	161 - 165	136 - 140
2	9	MET	MET	LEU	LEU	B	B	161 - 165	136 - 140
3	9	MET	MET	LEU	LEU	C	C	161 - 165	136 - 140
4	9	MET	MET	LEU	LEU	D	D	161 - 165	136 - 140
5	9	MET	MET	LEU	LEU	E	E	161 - 165	136 - 140
1	10	ASN	ASN	THR	THR	A	A	167 - 170	142 - 145
2	10	ASN	ASN	THR	THR	B	B	167 - 170	142 - 145
3	10	ASN	ASN	THR	THR	C	C	167 - 170	142 - 145
4	10	ASN	ASN	THR	THR	D	D	167 - 170	142 - 145
5	10	ASN	ASN	THR	THR	E	E	167 - 170	142 - 145
1	11	GLY	GLY	PRO	PRO	A	A	175 - 179	150 - 154
2	11	GLY	GLY	PRO	PRO	B	B	175 - 179	150 - 154
3	11	GLY	GLY	PRO	PRO	C	C	175 - 179	150 - 154
4	11	GLY	GLY	PRO	PRO	D	D	175 - 179	150 - 154
5	11	GLY	GLY	PRO	PRO	E	E	175 - 179	150 - 154
1	12	PRO	PRO	ALA	ALA	A	A	182 - 184	157 - 159
2	12	PRO	PRO	ALA	ALA	B	B	182 - 184	157 - 159
3	12	PRO	PRO	ALA	ALA	C	C	182 - 184	157 - 159
4	12	PRO	PRO	ALA	ALA	D	D	182 - 184	157 - 159
5	12	PRO	PRO	ALA	ALA	E	E	182 - 184	157 - 159
1	13	SER	SER	GLN	GLN	A	A	186 - 187	161 - 162
2	13	SER	SER	GLN	GLN	B	B	186 - 187	161 - 162
3	13	SER	SER	GLN	GLN	C	C	186 - 187	161 - 162
4	13	SER	SER	GLN	GLN	D	D	186 - 187	161 - 162
5	13	SER	SER	GLN	GLN	E	E	186 - 187	161 - 162
1	14	ASN	ASN	ALA	ALA	A	A	190 - 195	165 - 170
2	14	ASN	ASN	ALA	ALA	B	B	190 - 195	165 - 170
3	14	ASN	ASN	ALA	ALA	C	C	190 - 195	165 - 170
4	14	ASN	ASN	ALA	ALA	D	D	190 - 195	165 - 170
5	14	ASN	ASN	ALA	ALA	E	E	190 - 195	165 - 170
1	15	LEU	LEU	SER	SER	A	A	197 - 213	172 - 188
2	15	LEU	LEU	SER	SER	B	B	197 - 213	172 - 188
3	15	LEU	LEU	SER	SER	C	C	197 - 213	172 - 188
4	15	LEU	LEU	SER	SER	D	D	197 - 213	172 - 188
5	15	LEU	LEU	SER	SER	E	E	197 - 213	172 - 188
1	16	GLU	GLU	GLY	GLY	A	A	216 - 227	191 - 202
2	16	GLU	GLU	GLY	GLY	B	B	216 - 227	191 - 202
3	16	GLU	GLU	GLY	GLY	C	C	216 - 227	191 - 202
4	16	GLU	GLU	GLY	GLY	D	D	216 - 227	191 - 202
5	16	GLU	GLU	GLY	GLY	E	E	216 - 227	191 - 202
1	17	PRO	PRO	ASN	ASN	A	A	231 - 238	206 - 213
2	17	PRO	PRO	ASN	ASN	B	B	231 - 238	206 - 213
3	17	PRO	PRO	ASN	ASN	C	C	231 - 238	206 - 213
4	17	PRO	PRO	ASN	ASN	D	D	231 - 238	206 - 213
5	17	PRO	PRO	ASN	ASN	E	E	231 - 238	206 - 213
1	18	LEU	LEU	ASP	ASP	A	A	244 - 246	219 - 221
2	18	LEU	LEU	ASP	ASP	B	B	244 - 246	219 - 221
3	18	LEU	LEU	ASP	ASP	C	C	244 - 246	219 - 221
4	18	LEU	LEU	ASP	ASP	D	D	244 - 246	219 - 221
5	18	LEU	LEU	ASP	ASP	E	E	244 - 246	219 - 221
1	19	GLY	GLY	LEU	LEU	A	A	251 - 253	226 - 228
2	19	GLY	GLY	LEU	LEU	B	B	251 - 253	226 - 228
3	19	GLY	GLY	LEU	LEU	C	C	251 - 253	226 - 228
4	19	GLY	GLY	LEU	LEU	D	D	251 - 253	226 - 228
5	19	GLY	GLY	LEU	LEU	E	E	251 - 253	226 - 228
1	20	SER	SER	SER	SER	A	A	258 - 273	233 - 248
2	20	SER	SER	SER	SER	B	B	258 - 273	233 - 248
3	20	SER	SER	SER	SER	C	C	258 - 273	233 - 248
4	20	SER	SER	SER	SER	D	D	258 - 273	233 - 248
5	20	SER	SER	SER	SER	E	E	258 - 273	233 - 248
1	21	GLN	GLN	LYS	LYS	A	A	277 - 287	252 - 262
2	21	GLN	GLN	LYS	LYS	B	B	277 - 287	252 - 262
3	21	GLN	GLN	LYS	LYS	C	C	277 - 287	252 - 262
4	21	GLN	GLN	LYS	LYS	D	D	277 - 287	252 - 262
5	21	GLN	GLN	LYS	LYS	E	E	277 - 287	252 - 262
1	22	PHE	PHE	ASP	ASP	A	A	75 - 78	50 - 53
2	22	PHE	PHE	ASP	ASP	B	B	75 - 78	50 - 53
3	22	PHE	PHE	ASP	ASP	C	C	75 - 78	50 - 53
4	22	PHE	PHE	ASP	ASP	D	D	75 - 78	50 - 53
5	22	PHE	PHE	ASP	ASP	E	E	75 - 78	50 - 53

#1: Protein	VP1 capsid protein Mass: 30261.039 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BK polyomavirus / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q85235, UniProt: P03088*PLUS
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 864 / 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: 2.29 Å³/Da / Density % sol: 46.21 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 16-18 % PEG 3,350, 0.1 M HEPES pH 7.5, 0.25 M LiCl , VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
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: Jan 28, 2009
Radiation	Monochromator: Bartels monochromator (DCCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. all: 94566 / Num. obs: 94342 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / B_iso Wilson estimate: 27.1 Å² / Net I/σ(I): 11.01
Reflection shell	Resolution: 2→2.05 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 6939 / % possible all: 98.4

-
Processing

Software

Name	Version	Classification
RemDAq		data collection
PHASER		phasing
REFMAC	5.5.0102	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BWQ

3bwq

Resolution: 2→47.42 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.941 / SU B: 7.547 / SU ML: 0.094 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19876	3296	3.5 %	RANDOM
R_work	0.16091	-	-	-
all	0.16224	94340	-	-
obs	0.16224	91044	99.78 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 18.461 Å²

Refinement step

Cycle: LAST / Resolution: 2→47.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9843	0	35	864	10742

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	10227
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	6848
X-RAY DIFFRACTION	r_angle_refined_deg	1.246	1.958	13934
X-RAY DIFFRACTION	r_angle_other_deg	0.819	3	16768
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.254	5	1312
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.435	24.602	465
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.537	15	1640
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.149	15	58
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	1550
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	11507
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1984
X-RAY DIFFRACTION	r_mcbond_it	1.293	4	6441
X-RAY DIFFRACTION	r_mcbond_other	0.587	4	2601
X-RAY DIFFRACTION	r_mcangle_it	1.865	5	10448
X-RAY DIFFRACTION	r_scbond_it	2.328	6	3786
X-RAY DIFFRACTION	r_scangle_it	3.188	7	3465

Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2205 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Type	Rms dev position (Å)	Weight position
A	medium positional	0.16	0.5
B	medium positional	0.13	0.5
C	medium positional	0.13	0.5
D	medium positional	0.13	0.5
E	medium positional	0.13	0.5
A	medium thermal	0.6	2
B	medium thermal	0.6	2
C	medium thermal	0.62	2
D	medium thermal	0.7	2
E	medium thermal	0.67	2

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.251	249	-
R_work	0.22	6567	-
obs	-	6816	98.45 %

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	1.1426	0.0804	-0.0391	1.0207	0.0809	1.326	0.0414	-0.0421	0.1926	0.0011	0.014	0.0265	-0.2752	0.0162	-0.0555	0.1234	0.0397	0.0238	0.0406	-0.0132	0.1106	28.2752	49.0213	22.5809
2	1.8059	-0.6424	1.896	1.3485	-1.365	5.2198	-0.0044	-0.1396	0.0534	-0.0076	0.0771	0.0468	0.0424	-0.121	-0.0726	0.0362	-0.0193	0.0478	0.0235	-0.0325	0.0852	38.8279	46.4184	19.9992
3	2.1368	0.4937	-0.4766	0.9842	-0.1916	1.6443	0.0116	-0.0064	0.0602	0.0376	0.0529	0.104	-0.0758	-0.1618	-0.0645	0.07	0.0194	0.0215	0.0258	0.0007	0.0456	22.2305	40.6975	19.7682
4	1.2174	-0.3889	0.4642	1.4839	-1.3174	4.9574	0.038	0.1009	0.0732	-0.1048	-0.0018	0.0425	-0.0203	0.0227	-0.0362	0.0475	-0.0069	0.0284	0.0117	-0.0062	0.0849	32.1654	46.289	12.2484
5	1.8687	-0.4257	-0.0512	1.5466	-0.0364	0.9745	-0.0136	-0.1052	0.1741	0.0849	0.0384	-0.25	-0.0739	0.2381	-0.0248	0.0848	-0.0452	-0.0263	0.1049	-0.0277	0.1396	60.4462	44.0248	26.5536
6	1.2108	0.3842	-0.4589	2.9232	-2.1003	3.5163	0.0848	0.0559	0.1038	-0.0038	0.073	-0.0324	0.0461	0.0184	-0.1578	0.0085	-0.0018	0.0064	0.0957	-0.058	0.101	62.5142	35.6808	18.1827
7	1.3817	-0.4345	-0.3653	1.3678	0.2617	1.5226	0.022	-0.0837	0.1578	0.083	0.0244	-0.0544	-0.1436	0.0225	-0.0464	0.0558	-0.0227	-0.0077	0.07	-0.0245	0.08	51.3353	46.8779	22.4247
8	1.5503	0.0995	-0.7818	1.6091	-1.1087	4.7824	0.0131	0.1712	0.0862	-0.1405	-0.0124	-0.0725	0.0232	0.0864	-0.0007	0.0326	-0.0215	0.0045	0.071	-0.0279	0.1028	59.3328	41.742	13.0212
9	1.4128	0.5614	0.5468	2.132	-0.3145	0.7113	0.1335	-0.0963	-0.2506	0.2423	0.0024	-0.3527	0.1698	0.1441	-0.1359	0.1345	0.0659	-0.0848	0.1596	-0.0116	0.2305	65.7587	11.1296	26.4076
10	2.7044	1.2191	-1.8612	1.8097	-1.1943	4.5098	0.032	-0.0625	-0.2176	-0.0391	0.0145	-0.2301	0.003	0.2233	-0.0465	0.0649	0.0226	-0.0589	0.0281	-0.028	0.1363	55.0771	7.6944	18.822
11	1.9871	1.0463	0.8408	1.9644	0.7053	1.472	-0.0266	0.0584	-0.067	-0.0939	0.0548	-0.2559	-0.0433	0.199	-0.0282	0.051	0.0122	0.0062	0.0628	-0.0007	0.1474	66.3239	21.5539	16.9732
12	2.398	0.2018	-1.9901	1.4158	0.4874	6.9981	-0.0099	0.2079	-0.1269	-0.0679	0.0124	-0.223	0.0157	-0.1723	-0.0026	0.0396	-0.0027	-0.011	0.0299	-0.0162	0.1507	59.8657	11.1543	15.7712
13	3.8506	0.4319	-7.9181	1.4149	-0.1408	31.4213	-0.136	0.8937	-0.0488	-0.4472	0.0515	0.1414	0.2151	-2.3279	0.0845	0.259	-0.0253	-0.0378	0.2964	-0.0184	0.1732	27.9344	-0.8335	-5.6929
14	1.4088	-0.4187	-0.3872	0.9231	0.0528	0.394	0.0023	-0.078	-0.2055	0.0666	0.0226	-0.0662	0.1449	-0.0719	-0.0248	0.1223	-0.035	-0.042	0.0459	0.0394	0.1051	37.9099	-0.937	18.859
15	1.8535	-0.3683	0.5479	1.1053	-0.039	1.4018	0.0572	0.0906	-0.0316	0.0108	-0.0018	-0.1848	0.0682	0.126	-0.0554	0.0669	-0.0186	-0.0027	0.0231	-0.006	0.1067	46.4146	1.9241	11.7471
16	1.3132	-0.3151	-0.1332	1.9186	1.5857	4.9943	0.0158	0.0831	-0.1029	-0.201	-0.0281	-0.0454	-0.1701	-0.0576	0.0123	0.0407	-0.0106	-0.018	0.0151	0.0149	0.0739	35.6818	0.968	10.1431
17	0.8307	-0.2147	-0.3897	1.0147	0.3478	3.5941	0.0056	0.0398	0.0334	-0.0287	-0.0259	0.1037	-0.1972	-0.5613	0.0203	0.0562	0.0077	0.0087	0.1215	0.031	0.0896	13.6088	22.931	14.7725
18	1.328	-0.4311	0.2107	1.3459	-1.9784	5.4159	0.0498	-0.0059	-0.0867	-0.059	0.0956	0.1382	0.1668	-0.6152	-0.1454	0.0357	-0.0252	-0.0068	0.0996	-0.0019	0.0543	11.7169	16.828	10.7903
19	0.5679	-0.1147	-0.0038	1.4612	0.359	1.0754	0.0279	-0.0432	-0.0709	0.0618	0.027	0.02	0.0941	-0.0668	-0.0549	0.0316	-0.0021	0.0023	0.0676	0.0287	0.0404	20.842	16.0221	18.8721
20	1.0556	0.1003	1.0166	0.7363	-0.2024	6.3736	0.0021	0.0997	-0.041	-0.0557	0.0228	-0.0105	-0.1011	-0.0826	-0.025	0.0171	0.015	0.0213	0.0291	0.0207	0.0474	17.2146	22.0983	9.1764

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	33 - 93
2	X-RAY DIFFRACTION	2	A	94 - 144
3	X-RAY DIFFRACTION	3	A	145 - 239
4	X-RAY DIFFRACTION	4	A	240 - 296
5	X-RAY DIFFRACTION	5	B	34 - 91
6	X-RAY DIFFRACTION	6	B	92 - 141
7	X-RAY DIFFRACTION	7	B	142 - 240
8	X-RAY DIFFRACTION	8	B	241 - 297
9	X-RAY DIFFRACTION	9	C	43 - 91
10	X-RAY DIFFRACTION	10	C	92 - 144
11	X-RAY DIFFRACTION	11	C	145 - 262
12	X-RAY DIFFRACTION	12	C	263 - 295
13	X-RAY DIFFRACTION	13	D	32 - 50
14	X-RAY DIFFRACTION	14	D	51 - 178
15	X-RAY DIFFRACTION	15	D	179 - 254
16	X-RAY DIFFRACTION	16	D	255 - 297
17	X-RAY DIFFRACTION	17	E	32 - 73
18	X-RAY DIFFRACTION	18	E	74 - 116
19	X-RAY DIFFRACTION	19	E	117 - 245
20	X-RAY DIFFRACTION	20	E	246 - 297

-
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