PDB-4u62: Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in ...

ID or keywords:

Entry

Database: PDB / ID: 4u62

Title

Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with 3'-sialyllactose

Components

Structural protein VP1

Structure

Keywords

VIRAL PROTEIN /

viral coat protein /

jelly-roll fold /

glycan binding

Function / homology

Function and homology information

T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity
Similarity search - Function

Biological species

Trichodysplasia spinulosa-associated polyomavirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Stroh, L.J. / Stehle, T.

Citation

Journal: Plos Pathog. / Year: 2015
Title: Trichodysplasia spinulosa-Associated Polyomavirus Uses a Displaced Binding Site on VP1 to Engage Sialylated Glycolipids.
Authors: Stroh, L.J. / Gee, G.V. / Blaum, B.S. / Dugan, A.S. / Feltkamp, M.C. / Atwood, W.J. / Stehle, T.

History

Deposition	Jul 26, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Aug 5, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 2, 2015	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_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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	4u62.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb4u62.ent.gz	893.5 KB	Display	PDB format
PDBx/mmJSON format	4u62.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u6/4u62 ftp://data.pdbj.org/pub/pdb/validation_reports/u6/4u62	HTTPS FTP

-
Related structure data

Related structure data	4u5zSC 4u60C 4u61C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3bwq-d 4poq-2 4pos-1 4u61-1 4poq-1 4fmi-1 6hku-2 4u61-2 4mbx-2 4por-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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) #113 - May 2009 Influenza Neuraminidase similarity (1)

Deposited unit

A: Structural protein VP1

B: Structural protein VP1

C: Structural protein VP1

D: Structural protein VP1

E: Structural protein VP1

F: Structural protein VP1

G: Structural protein VP1

H: Structural protein VP1

I: Structural protein VP1

J: Structural protein VP1

hetero molecules

312 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Structural protein VP1

B: Structural protein VP1

C: Structural protein VP1

D: Structural protein VP1

E: Structural protein VP1

hetero molecules

defined by author&software
156 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: Structural protein VP1

G: Structural protein VP1

H: Structural protein VP1

I: Structural protein VP1

J: Structural protein VP1

hetero molecules

defined by author&software
156 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	66.240, 152.840, 147.240
Angle α, β, γ (deg.)	90.00, 92.34, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J

NCS domain segments:

Ens-ID: 1 / Refine code: 5

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	ILE	ILE	ALA	ALA	A	A	45 - 94	22 - 71
2	1	ILE	ILE	ALA	ALA	B	B	45 - 94	22 - 71
3	1	ILE	ILE	ALA	ALA	C	C	45 - 94	22 - 71
4	1	ILE	ILE	ALA	ALA	D	D	45 - 94	22 - 71
5	1	ILE	ILE	ALA	ALA	E	E	45 - 94	22 - 71
6	1	ILE	ILE	ALA	ALA	F	F	45 - 94	22 - 71
7	1	ILE	ILE	ALA	ALA	G	G	45 - 94	22 - 71
8	1	ILE	ILE	ALA	ALA	H	H	45 - 94	22 - 71
9	1	ILE	ILE	ALA	ALA	I	I	45 - 94	22 - 71
10	1	ILE	ILE	ALA	ALA	J	J	45 - 94	22 - 71
1	2	TRP	TRP	MET	MET	A	A	113 - 133	90 - 110
2	2	TRP	TRP	MET	MET	B	B	113 - 133	90 - 110
3	2	TRP	TRP	MET	MET	C	C	113 - 133	90 - 110
4	2	TRP	TRP	MET	MET	D	D	113 - 133	90 - 110
5	2	TRP	TRP	MET	MET	E	E	113 - 133	90 - 110
6	2	TRP	TRP	MET	MET	F	F	113 - 133	90 - 110
7	2	TRP	TRP	MET	MET	G	G	113 - 133	90 - 110
8	2	TRP	TRP	MET	MET	H	H	113 - 133	90 - 110
9	2	TRP	TRP	MET	MET	I	I	113 - 133	90 - 110
10	2	TRP	TRP	MET	MET	J	J	113 - 133	90 - 110
1	3	PRO	PRO	LEU	LEU	A	A	147 - 240	124 - 217
2	3	PRO	PRO	LEU	LEU	B	B	147 - 240	124 - 217
3	3	PRO	PRO	LEU	LEU	C	C	147 - 240	124 - 217
4	3	PRO	PRO	LEU	LEU	D	D	147 - 240	124 - 217
5	3	PRO	PRO	LEU	LEU	E	E	147 - 240	124 - 217
6	3	PRO	PRO	LEU	LEU	F	F	147 - 240	124 - 217
7	3	PRO	PRO	LEU	LEU	G	G	147 - 240	124 - 217
8	3	PRO	PRO	LEU	LEU	H	H	147 - 240	124 - 217
9	3	PRO	PRO	LEU	LEU	I	I	147 - 240	124 - 217
10	3	PRO	PRO	LEU	LEU	J	J	147 - 240	124 - 217
1	4	LEU	LEU	LEU	LEU	A	A	250 - 288	227 - 265
2	4	LEU	LEU	LEU	LEU	B	B	250 - 288	227 - 265
3	4	LEU	LEU	LEU	LEU	C	C	250 - 288	227 - 265
4	4	LEU	LEU	LEU	LEU	D	D	250 - 288	227 - 265
5	4	LEU	LEU	LEU	LEU	E	E	250 - 288	227 - 265
6	4	LEU	LEU	LEU	LEU	F	F	250 - 288	227 - 265
7	4	LEU	LEU	LEU	LEU	G	G	250 - 288	227 - 265
8	4	LEU	LEU	LEU	LEU	H	H	250 - 288	227 - 265
9	4	LEU	LEU	LEU	LEU	I	I	250 - 288	227 - 265
10	4	LEU	LEU	LEU	LEU	J	J	250 - 288	227 - 265

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(0.994393, 0.072429, 0.077052), (0.050533, 0.314596, -0.947879), (-0.092894, 0.946458, 0.309172)	2.78722, -43.16415, -79.32949
3	given	(0.983377, 0.177664, 0.037486), (0.165715, -0.79376, -0.58522), (-0.074218, 0.581704, -0.810007)	-3.43686, 18.89888, -145.10034
4	given	(0.98252, 0.175882, -0.060992), (0.177931, -0.790948, 0.585441), (0.054727, -0.58606, -0.808417)	-10.23467, 100.14999, -106.013
5	given	(0.993462, 0.070127, -0.090082), (0.063568, 0.315624, 0.946753), (0.094825, -0.946289, 0.309103)	-8.75341, 88.36788, -16.42954
6	given	(-0.982011, -0.183009, -0.046488), (-0.174504, 0.78557, 0.593657), (-0.072125, 0.59109, -0.803375)	-61.60261, 101.75751, -192.4332
7	given	(-0.993992, -0.077216, -0.077571), (-0.048837, -0.321366, 0.945695), (-0.097951, 0.943802, 0.315665)	-67.52795, 167.53665, -37.14997
8	given	(-0.999921, -0.004691, 0.011682), (0.004592, -0.999954, -0.008463), (0.011721, -0.008409, 0.999896)	-55.51758, 39.88809, 73.76595
9	given	(-0.992446, -0.084126, 0.089292), (-0.059666, -0.30497, -0.950491), (0.107193, -0.948639, 0.297647)	-43.71264, -103.32271, -13.72179
10	given	(-0.980973, -0.184887, 0.059226), (-0.184559, 0.79344, -0.579993), (0.060241, -0.579888, -0.812466)	-46.46658, -65.99577, -177.18538

#1: Protein

Structural protein VP1 /

Structure

Mass: 30994.908 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Trichodysplasia spinulosa-associated polyomavirus
Gene: VP1 / Plasmid: pET28b / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E2ESL7

#2: Chemical

ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL /

Glycerol

Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃

#3: Sugar

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

Sialic acid

Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 3 / 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

#4: Chemical

ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL /

Ethylene glycol

Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂

#5: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 2355 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.81 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM Na-malonate pH 5.0, 10% PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.55→40 Å / Num. obs: 412698 / % possible obs: 97.8 % / Redundancy: 3.8 % / Net I/σ(I): 13.4
Reflection shell	Resolution: 1.55→1.59 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.2 / % possible all: 93.5

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4U5Z

4u5z

Resolution: 1.55→40 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.966 / SU B: 2.913 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18028	20677	5 %	RANDOM
R_work	0.15529	-	-	-
obs	0.15654	392021	97.78 %	-

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: 27.463 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.94 Å²	0 Å²	0.17 Å²
2-	-	-0.66 Å²	0 Å²
3-	-	-	-0.29 Å²

Refinement step

Cycle: 1 / Resolution: 1.55→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20842	0	109	2355	23306

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.02	21448
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	19921
X-RAY DIFFRACTION	r_angle_refined_deg	1.356	1.973	29186
X-RAY DIFFRACTION	r_angle_other_deg	0.745	3	45994
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.17	5	2703
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.753	24.936	936
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.194	15	3521
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.867	15	96
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	3305
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	24449
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4714
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	1.573	4.67	10788
X-RAY DIFFRACTION	r_mcbond_other	1.567	4.669	10787
X-RAY DIFFRACTION	r_mcangle_it	2.046	5.238	13460
X-RAY DIFFRACTION	r_mcangle_other	2.047	5.238	13461
X-RAY DIFFRACTION	r_scbond_it	2.89	5.484	10660
X-RAY DIFFRACTION	r_scbond_other	2.891	5.484	10660
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.799	5.966	15714
X-RAY DIFFRACTION	r_long_range_B_refined	6.053	10.573	25377
X-RAY DIFFRACTION	r_long_range_B_other	6.053	10.573	25378
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 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
A	1184	medium positional	0.09	0.5
B	1184	medium positional	0.06	0.5
C	1184	medium positional	0.09	0.5
D	1184	medium positional	0.15	0.5
E	1184	medium positional	0.13	0.5
F	1184	medium positional	0.07	0.5
G	1184	medium positional	0.1	0.5
H	1184	medium positional	0.09	0.5
I	1184	medium positional	0.08	0.5
J	1184	medium positional	0.09	0.5
A	1760	loose positional	0.33	5
B	1760	loose positional	0.33	5
C	1760	loose positional	0.33	5
D	1760	loose positional	0.36	5
E	1760	loose positional	0.46	5
F	1760	loose positional	0.32	5
G	1760	loose positional	0.39	5
H	1760	loose positional	0.3	5
I	1760	loose positional	0.32	5
J	1760	loose positional	0.32	5
A	1184	medium thermal	1.03	2
B	1184	medium thermal	1.19	2
C	1184	medium thermal	1.32	2
D	1184	medium thermal	1.12	2
E	1184	medium thermal	1.11	2
F	1184	medium thermal	1.17	2
G	1184	medium thermal	1.17	2
H	1184	medium thermal	1.12	2
I	1184	medium thermal	0.82	2
J	1184	medium thermal	1.13	2
A	1760	loose thermal	1.53	10
B	1760	loose thermal	1.56	10
C	1760	loose thermal	1.68	10
D	1760	loose thermal	1.53	10
E	1760	loose thermal	1.92	10
F	1760	loose thermal	1.41	10
G	1760	loose thermal	1.61	10
H	1760	loose thermal	1.51	10
I	1760	loose thermal	1.18	10
J	1760	loose thermal	1.54	10

LS refinement shell

Resolution: 1.55→1.59 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.266	1427	-
R_work	0.249	27691	-
obs	-	-	93.54 %

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	6.1494	0.1071	-1.1146	0.7488	0.1251	0.9324	0.0828	0.3042	0.1395	-0.0404	-0.0319	0.1204	-0.1069	-0.0817	-0.0509	0.1229	-0.0084	0.0018	0.0227	0.0099	0.047	-27.4158	60.1335	-75.3947
2	0.616	-0.1367	0.0219	0.6941	0.0435	0.5646	0.024	0.0102	0.0419	0.0086	-0.039	-0.0595	-0.1162	0.037	0.015	0.0592	-0.0305	0.0002	0.0252	0.0096	0.0159	-16.0626	56.15	-68.8331
3	0.7728	0.1149	-0.0607	1.2103	-0.0395	0.7127	-0.0186	0.0895	-0.0189	-0.258	-0.0425	-0.049	-0.0185	0.0151	0.0611	0.1082	0.0044	0.0371	0.0253	0.0012	0.0235	-15.2202	39.6401	-93.0286
4	6.4602	-0.1584	1.402	1.0188	0.0538	1.175	0.1481	0.2311	-0.0905	-0.2382	-0.1176	0.0104	0.08	-0.038	-0.0305	0.1047	0.0134	0.0162	0.0308	-0.0089	0.0121	-22.551	34.5983	-94.3301
5	0.8911	-0.2902	-0.0302	1.7395	-0.2168	1.2082	0.0917	0.0593	-0.2682	-0.2215	-0.0504	-0.0821	0.2016	-0.0428	-0.0414	0.1758	0.0388	0.0466	0.0173	0.0084	0.1396	-11.1695	6.5387	-84.3165
6	0.4862	0.0693	0.0131	1.0265	0.0266	1.0727	0.0307	0.0176	-0.0368	-0.191	-0.0429	-0.123	0.1573	-0.0191	0.0122	0.1081	0.0207	0.0597	0.0097	0.0142	0.0478	-13.2316	13.2729	-83.5239
7	6.1179	-0.5365	-1.6435	0.6227	-0.7196	4.0898	0.2033	-0.3437	-0.5548	0	-0.293	0.4101	0.3717	-0.6676	0.0898	0.235	-0.2526	0.1179	0.6726	-0.3722	0.449	-34.6127	7.0064	-52.2927
8	0.2956	0.0759	0.007	1.4212	0.4621	0.9661	0.0142	-0.0639	-0.0789	0.144	-0.0533	-0.1138	0.3134	0.0027	0.0391	0.1356	-0.0136	-0.016	0.0507	0.041	0.0576	-10.7274	12.3909	-54.9395
9	0.56	0.1792	0.0146	0.8478	-0.1918	0.8287	0.0401	-0.1177	0.054	0.1606	-0.0188	-0.035	-0.0381	0.023	-0.0214	0.0579	-0.0342	-0.0263	0.0575	0.0078	0.0256	-13.4922	40.5544	-44.5641
10	1.2538	-0.25	-0.1534	0.8435	-0.1512	0.8894	0.0271	-0.0502	-0.0426	0.1145	-0.0023	-0.0004	0.0211	-0.0665	-0.0248	0.0401	-0.0304	-0.0128	0.0375	0.0155	0.0068	-19.15	38.4365	-47.393
11	1.7311	0.2293	0.4343	1.6592	-0.4782	1.4933	0.0835	0.0068	0.1928	0.4644	-0.0879	-0.0354	-0.4442	0.1195	0.0044	0.4228	-0.0536	0.0141	0.0374	-0.0239	0.0479	-47.1648	30.9211	-125.2277
12	0.3163	-0.0412	0.0393	1.6452	-0.6	1.0904	0.0118	-0.0487	0.0686	0.4343	-0.0947	-0.0576	-0.4138	0.1292	0.0829	0.3089	-0.0822	-0.0264	0.0461	-0.0054	0.021	-44.7089	28.1235	-128.8254
13	1.1204	0.1137	-0.2241	1.6099	-0.3034	1.2867	0.1129	-0.2594	-0.1793	0.2491	-0.1607	-0.2896	0.0706	0.3121	0.0478	0.2146	-0.0151	-0.0375	0.1288	0.0569	0.08	-36.381	-5.5496	-117.4167
14	0.3883	0.0644	-0.0966	1.0369	-0.1414	1.1942	0.0545	-0.1163	-0.0438	0.3082	-0.0896	-0.0545	-0.1017	0.1609	0.035	0.1906	-0.054	-0.0161	0.0661	0.0226	0.0096	-42.7115	2.3384	-119.7405
15	5.5279	-0.055	1.0312	0.6688	-0.1828	0.7214	0.0153	0.2912	-0.1095	-0.054	-0.0018	-0.138	0.0846	0.1008	-0.0134	0.1875	0.0343	-0.0012	0.0249	-0.0174	0.0981	-30.1574	-19.3183	-149.0279
16	0.4888	-0.2162	0.0142	0.6102	-0.1232	0.474	-0.003	0.0069	-0.0633	0.0419	-0.0183	0.007	0.1486	0.0388	0.0213	0.112	0.0021	-0.0206	0.0272	0.0033	0.0544	-41.0467	-15.2447	-142.2529
17	7.8963	-2.2916	0.3564	3.5398	-0.3469	1.667	0.0743	0.2089	0.3245	-0.0871	-0.0158	-0.6721	-0.032	0.3927	-0.0585	0.1229	-0.0151	0.0451	0.307	-0.0376	0.1505	-18.2486	6.9938	-170.7504
18	0.6014	-0.0913	0.0242	1.4982	-0.0243	0.9276	0.0209	0.1247	-0.0249	-0.1589	-0.0223	-0.0328	0.1299	0.0769	0.0014	0.0657	0.0061	-0.0181	0.0449	-0.0008	0.0167	-44.2232	1.9145	-165.5896
19	1.6826	0.4955	0.1154	2.3722	0.2814	1.3459	0.0209	0.1474	0.2527	0.0635	-0.0191	-0.1122	-0.2434	0.1371	-0.0018	0.1436	-0.038	-0.0305	0.0349	0.0335	0.0632	-45.2972	34.0389	-155.8474
20	0.3941	0.0989	0.0178	1.309	-0.1142	1.0204	0.02	0.0382	0.0462	0.0477	-0.0366	-0.0565	-0.1814	0.0784	0.0165	0.0842	-0.0275	-0.0331	0.0219	0.0181	0.0293	-44.62	28.5099	-156.8803

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	32 - 65
2	X-RAY DIFFRACTION	2	A	66 - 303
3	X-RAY DIFFRACTION	3	B	32 - 279
4	X-RAY DIFFRACTION	4	B	280 - 303
5	X-RAY DIFFRACTION	5	C	33 - 101
6	X-RAY DIFFRACTION	6	C	102 - 303
7	X-RAY DIFFRACTION	7	D	24 - 50
8	X-RAY DIFFRACTION	8	D	51 - 303
9	X-RAY DIFFRACTION	9	E	33 - 198
10	X-RAY DIFFRACTION	10	E	199 - 303
11	X-RAY DIFFRACTION	11	F	24 - 88
12	X-RAY DIFFRACTION	12	F	89 - 303
13	X-RAY DIFFRACTION	13	G	33 - 72
14	X-RAY DIFFRACTION	14	G	73 - 303
15	X-RAY DIFFRACTION	15	H	32 - 65
16	X-RAY DIFFRACTION	16	H	66 - 303
17	X-RAY DIFFRACTION	17	I	33 - 50
18	X-RAY DIFFRACTION	18	I	51 - 303
19	X-RAY DIFFRACTION	19	J	33 - 81
20	X-RAY DIFFRACTION	20	J	82 - 303

-
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