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- PDB-6hku: Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in ... -

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Basic information

Entry
Database: PDB / ID: 6hku
TitleTrichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with sialylated precision glycooligomers
ComponentsCapsid protein VP1
KeywordsVIRAL PROTEIN / SIALIC ACID DERIVATIVE
Function / homology
Function and homology information


T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity / metal ion binding
Similarity search - Function
Capsid protein VP1,Polyomavirus / Polyomavirus Vp1; Chain A / Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid / Sandwich / Mainly Beta
Similarity search - Domain/homology
3'-sialyl-alpha-lactose / N-acetyl-alpha-neuraminic acid / Capsid protein VP1
Similarity search - Component
Biological speciesTrichodysplasia spinulosa-associated polyomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å
AuthorsRustmeier, N.H. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
FOR2327 Germany
CitationJournal: Macromol Biosci / Year: 2019
Title: Divalent Sialylated Precision Glycooligomers Binding to Polyomaviruses and the Effect of Different Linkers.
Authors: Baier, M. / Rustmeier, N.H. / Harr, J. / Cyrus, N. / Reiss, G.J. / Grafmuller, A. / Blaum, B.S. / Stehle, T. / Hartmann, L.
History
DepositionSep 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn / 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_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
E: Capsid protein VP1
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
J: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,38518
Polymers302,21010
Non-polymers3,1758
Water42,3172349
1
A: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
E: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,4499
Polymers151,1055
Non-polymers1,3444
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24550 Å2
ΔGint-139 kcal/mol
Surface area48050 Å2
MethodPISA
2
F: Capsid protein VP1
G: Capsid protein VP1
H: Capsid protein VP1
I: Capsid protein VP1
J: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,9369
Polymers151,1055
Non-polymers1,8314
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24900 Å2
ΔGint-135 kcal/mol
Surface area48690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.277, 146.160, 150.413
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110B
210C
111B
211D
112B
212E
113B
213F
114B
214G
115B
215H
116B
216I
117B
217J
118C
218D
119C
219E
120C
220F
121C
221G
122C
222H
123C
223I
124C
224J
125D
225E
126D
226F
127D
227G
128D
228H
129D
229I
130D
230J
131E
231F
132E
232G
133E
233H
134E
234I
135E
235J
136F
236G
137F
237H
138F
238I
139F
239J
140G
240H
141G
241I
142G
242J
143H
243I
144H
244J
145I
245J

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNASNASNAA32 - 3031 - 272
21ASNASNASNASNBB32 - 3031 - 272
12ASNASNASNASNAA32 - 3031 - 272
22ASNASNASNASNCC32 - 3031 - 272
13ASNASNASNASNAA32 - 3031 - 272
23ASNASNASNASNDD32 - 3031 - 272
14ILEILEARGARGAA33 - 3022 - 271
24ILEILEARGARGEE33 - 3022 - 271
15ILEILEARGARGAA33 - 3022 - 271
25ILEILEARGARGFF33 - 3022 - 271
16ILEILEARGARGAA33 - 3022 - 271
26ILEILEARGARGGG33 - 3022 - 271
17ASNASNASNASNAA32 - 3031 - 272
27ASNASNASNASNHH32 - 3031 - 272
18ASNASNASNASNAA32 - 3031 - 272
28ASNASNASNASNII32 - 3031 - 272
19ASNASNARGARGAA32 - 3021 - 271
29ASNASNARGARGJJ32 - 3021 - 271
110ASNASNASNASNBB32 - 3031 - 272
210ASNASNASNASNCC32 - 3031 - 272
111ASNASNASNASNBB32 - 3031 - 272
211ASNASNASNASNDD32 - 3031 - 272
112ILEILEASNASNBB33 - 3032 - 272
212ILEILEASNASNEE33 - 3032 - 272
113ILEILEASNASNBB33 - 3032 - 272
213ILEILEASNASNFF33 - 3032 - 272
114ILEILEASNASNBB33 - 3032 - 272
214ILEILEASNASNGG33 - 3032 - 272
115ASNASNASNASNBB32 - 3031 - 272
215ASNASNASNASNHH32 - 3031 - 272
116ASNASNASNASNBB32 - 3031 - 272
216ASNASNASNASNII32 - 3031 - 272
117ASNASNARGARGBB32 - 3021 - 271
217ASNASNARGARGJJ32 - 3021 - 271
118ASNASNASNASNCC32 - 3031 - 272
218ASNASNASNASNDD32 - 3031 - 272
119ILEILEARGARGCC33 - 3022 - 271
219ILEILEARGARGEE33 - 3022 - 271
120ILEILEARGARGCC33 - 3022 - 271
220ILEILEARGARGFF33 - 3022 - 271
121ILEILEARGARGCC33 - 3022 - 271
221ILEILEARGARGGG33 - 3022 - 271
122ASNASNASNASNCC32 - 3031 - 272
222ASNASNASNASNHH32 - 3031 - 272
123ASNASNASNASNCC32 - 3031 - 272
223ASNASNASNASNII32 - 3031 - 272
124ASNASNARGARGCC32 - 3021 - 271
224ASNASNARGARGJJ32 - 3021 - 271
125ILEILEASNASNDD33 - 3032 - 272
225ILEILEASNASNEE33 - 3032 - 272
126ILEILEASNASNDD33 - 3032 - 272
226ILEILEASNASNFF33 - 3032 - 272
127ILEILEASNASNDD33 - 3032 - 272
227ILEILEASNASNGG33 - 3032 - 272
128ASNASNASNASNDD32 - 3031 - 272
228ASNASNASNASNHH32 - 3031 - 272
129ASNASNASNASNDD32 - 3031 - 272
229ASNASNASNASNII32 - 3031 - 272
130ASNASNARGARGDD32 - 3021 - 271
230ASNASNARGARGJJ32 - 3021 - 271
131ILEILEASNASNEE33 - 3032 - 272
231ILEILEASNASNFF33 - 3032 - 272
132ILEILEASNASNEE33 - 3032 - 272
232ILEILEASNASNGG33 - 3032 - 272
133ILEILEASNASNEE33 - 3032 - 272
233ILEILEASNASNHH33 - 3032 - 272
134ILEILEARGARGEE33 - 3022 - 271
234ILEILEARGARGII33 - 3022 - 271
135ILEILEARGARGEE33 - 3022 - 271
235ILEILEARGARGJJ33 - 3022 - 271
136ILEILEASNASNFF33 - 3032 - 272
236ILEILEASNASNGG33 - 3032 - 272
137ILEILEASNASNFF33 - 3032 - 272
237ILEILEASNASNHH33 - 3032 - 272
138ILEILEARGARGFF33 - 3022 - 271
238ILEILEARGARGII33 - 3022 - 271
139ILEILEARGARGFF33 - 3022 - 271
239ILEILEARGARGJJ33 - 3022 - 271
140ILEILEASNASNGG33 - 3032 - 272
240ILEILEASNASNHH33 - 3032 - 272
141ILEILEARGARGGG33 - 3022 - 271
241ILEILEARGARGII33 - 3022 - 271
142ILEILEARGARGGG33 - 3022 - 271
242ILEILEARGARGJJ33 - 3022 - 271
143ASNASNASNASNHH32 - 3031 - 272
243ASNASNASNASNII32 - 3031 - 272
144ASNASNARGARGHH32 - 3021 - 271
244ASNASNARGARGJJ32 - 3021 - 271
145ASNASNARGARGII32 - 3021 - 271
245ASNASNARGARGJJ32 - 3021 - 271

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45

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Components

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
Capsid protein VP1


Mass: 30220.982 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichodysplasia spinulosa-associated polyomavirus
Gene: VP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E2ESL7

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Sugars , 3 types, 6 molecules

#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / 3'-sialyl-alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 633.552 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-alpha-lactose
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 2351 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2349 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium maolante

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→49.05 Å / Num. obs: 212141 / % possible obs: 99.8 % / Redundancy: 10.5 % / Biso Wilson estimate: 28.4 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.29 / Net I/σ(I): 8.52
Reflection shellResolution: 1.98→2.1 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 1.76 / Num. unique obs: 33610 / CC1/2: 0.65 / Rrim(I) all: 1.56 / % possible all: 98.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
PHASERphasing
PDB_EXTRACT3.24data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U60

4u60


Resolution: 1.98→49.05 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.302 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.152
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 2122 1 %RANDOM
Rwork0.1847 ---
obs0.1852 210019 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 127.18 Å2 / Biso mean: 26.585 Å2 / Biso min: 5.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å2-0 Å2-0 Å2
2---1.55 Å20 Å2
3---1.82 Å2
Refinement stepCycle: final / Resolution: 1.98→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20664 0 215 2360 23239
Biso mean--51.84 33.04 -
Num. residues----2696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01421364
X-RAY DIFFRACTIONr_bond_other_d0.0010.01718558
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.67929129
X-RAY DIFFRACTIONr_angle_other_deg0.8811.64643572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8552691
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89923.551017
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.847153367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4991594
X-RAY DIFFRACTIONr_chiral_restr0.0650.22859
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0224050
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023796
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A83070.05
12B83070.05
21A82930.08
22C82930.08
31A81550.05
32D81550.05
41A83130.06
42E83130.06
51A82920.06
52F82920.06
61A82650.07
62G82650.07
71A82170.05
72H82170.05
81A83690.06
82I83690.06
91A82210.06
92J82210.06
101B82850.07
102C82850.07
111B82170.06
112D82170.06
121B82650.06
122E82650.06
131B82900.05
132F82900.05
141B82420.06
142G82420.06
151B82840.05
152H82840.05
161B83120.06
162I83120.06
171B82130.06
172J82130.06
181C81610.07
182D81610.07
191C83230.08
192E83230.08
201C83710.07
202F83710.07
211C82900.08
212G82900.08
221C82980.06
222H82980.06
231C83630.07
232I83630.07
241C82630.07
242J82630.07
251D80740.07
252E80740.07
261D81100.06
262F81100.06
271D80780.06
272G80780.06
281D81500.06
282H81500.06
291D81170.06
292I81170.06
301D81040.06
302J81040.06
311E83130.07
312F83130.07
321E82960.08
322G82960.08
331E82270.06
332H82270.06
341E83150.07
342I83150.07
351E82040.07
352J82040.07
361F82520.08
362G82520.08
371F82340.05
372H82340.05
381F82620.07
382I82620.07
391F82100.06
392J82100.06
401G81750.06
402H81750.06
411G82490.07
412I82490.07
421G81200.07
422J81200.07
431H82370.05
432I82370.05
441H81860.05
442J81860.05
451I82140.06
452J82140.06
LS refinement shellResolution: 1.981→2.032 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 151 -
Rwork0.266 14977 -
all-15128 -
obs--97.14 %

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