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- PDB-4x0z: JC Polyomavirus genotype 3 VP1 in complex with GM1 oligosaccharide -

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Basic information

Entry
Database: PDB / ID: 4x0z
TitleJC Polyomavirus genotype 3 VP1 in complex with GM1 oligosaccharide
ComponentsMajor capsid protein
KeywordsVIRAL PROTEIN / beta-sandwich / jelly-roll / viral capsid protein / glycan
Function / homology
Function and homology information


T=7 icosahedral viral capsid / virion attachment to host cell / structural molecule activity
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
: / Capsid protein VP1
Similarity search - Component
Biological speciesJC polyomavirus type 3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsStroh, L.J. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
National Institutes of Health Germany
CitationJournal: J.Virol. / Year: 2015
Title: The Greater Affinity of JC Polyomavirus Capsid for alpha 2,6-Linked Lactoseries Tetrasaccharide c than for Other Sialylated Glycans Is a Major Determinant of Infectivity.
Authors: Stroh, L.J. / Maginnis, M.S. / Blaum, B.S. / Nelson, C.D. / Neu, U. / Gee, G.V. / O'Hara, B.A. / Motamedi, N. / DiMaio, D. / Atwood, W.J. / Stehle, T.
History
DepositionNov 24, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
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 / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / struct_asym / struct_conn / struct_conn_type / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 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: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,06553
Polymers150,1695
Non-polymers5,89648
Water23,1311284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39600 Å2
ΔGint-45 kcal/mol
Surface area42010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.300, 95.890, 128.980
Angle α, β, γ (deg.)90.00, 110.17, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRASPASPAA31 - 5114 - 34
21THRTHRASPASPBB31 - 5114 - 34
31THRTHRASPASPCC31 - 5114 - 34
41THRTHRASPASPDD31 - 5114 - 34
51THRTHRASPASPEE31 - 5114 - 34
12PROPROILEILEAA78 - 8561 - 68
22PROPROILEILEBB78 - 8561 - 68
32PROPROILEILECC78 - 8561 - 68
42PROPROILEILEDD78 - 8561 - 68
52PROPROILEILEEE78 - 8561 - 68
13METMETSERSERAA101 - 12284 - 105
23METMETSERSERBB101 - 12284 - 105
33METMETSERSERCC101 - 12284 - 105
43METMETSERSERDD101 - 12284 - 105
53METMETSERSEREE101 - 12284 - 105
14GLYGLYTHRTHRAA124 - 162107 - 145
24GLYGLYTHRTHRBB124 - 162107 - 145
34GLYGLYTHRTHRCC124 - 162107 - 145
44GLYGLYTHRTHRDD124 - 162107 - 145
54GLYGLYTHRTHREE124 - 162107 - 145
15GLNGLNLEULEUAA177 - 189160 - 172
25GLNGLNLEULEUBB177 - 189160 - 172
35GLNGLNLEULEUCC177 - 189160 - 172
45GLNGLNLEULEUDD177 - 189160 - 172
55GLNGLNLEULEUEE177 - 189160 - 172
16ALAALATHRTHRAA194 - 205177 - 188
26ALAALATHRTHRBB194 - 205177 - 188
36ALAALATHRTHRCC194 - 205177 - 188
46ALAALATHRTHRDD194 - 205177 - 188
56ALAALATHRTHREE194 - 205177 - 188
17LEULEUTHRTHRAA251 - 263234 - 246
27LEULEUTHRTHRBB251 - 263234 - 246
37LEULEUTHRTHRCC251 - 263234 - 246
47LEULEUTHRTHRDD251 - 263234 - 246
57LEULEUTHRTHREE251 - 263234 - 246
18SERSERVALVALAA266 - 280249 - 263
28SERSERVALVALBB266 - 280249 - 263
38SERSERVALVALCC266 - 280249 - 263
48SERSERVALVALDD266 - 280249 - 263
58SERSERVALVALEE266 - 280249 - 263
19ASNASNASPASPAA207 - 238190 - 221
29ASNASNASPASPBB207 - 238190 - 221
39ASNASNASPASPCC207 - 238190 - 221
49ASNASNASPASPDD207 - 238190 - 221
59ASNASNASPASPEE207 - 238190 - 221
110PHEPHEASPASPAA240 - 249223 - 232
210PHEPHEASPASPBB240 - 249223 - 232
310PHEPHEASPASPCC240 - 249223 - 232
410PHEPHEASPASPDD240 - 249223 - 232
510PHEPHEASPASPEE240 - 249223 - 232

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.444228, 0.850537, 0.281513), (-0.853662, 0.306481, 0.421107), (0.271889, -0.427384, 0.862218)11.27647, 20.02041, -5.65034
3given(-0.443791, 0.515357, 0.733114), (-0.526052, -0.81212, 0.252451), (0.725479, -0.273621, 0.631516)31.44086, 14.10171, -15.80406
4given(-0.437472, -0.532078, 0.724922), (0.518498, -0.807906, -0.280086), (0.734696, 0.253341, 0.629317)32.50664, -9.08416, -16.70771
5given(0.45311, -0.849452, 0.270411), (0.84471, 0.312185, -0.434747), (0.284879, 0.425407, 0.858995)13.17975, -17.76079, -6.88075

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Major capsid protein / VP1 / VP1 capsid protein


Mass: 30033.795 Da / Num. of mol.: 5 / Fragment: UNP residues 23-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) JC polyomavirus type 3 / Gene: VP1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P90498

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Sugars , 2 types, 3 molecules

#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose


Type: oligosaccharide / Mass: 836.744 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAcb1-4[DNeup5Aca2-3]DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-1/a3-b2_a4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 998.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAcb1-4[DNeup5Aca2-3]DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-4-2/a4-b1_b3-c2_b4-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 1329 molecules

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


Mass: 92.094 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1284 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.66 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 12, 2012
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 143308 / % possible obs: 98.3 % / Redundancy: 4.3 % / Biso Wilson estimate: 23.3 Å2 / Rsym value: 0.112 / Net I/σ(I): 11.5
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.737 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Cootmodel building
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NXG
Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.959 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19063 7166 5 %RANDOM
Rwork0.16316 ---
obs0.16454 136142 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.702 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0 Å2-0.37 Å2
2--0.74 Å2-0 Å2
3---0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9943 0 376 1284 11603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910612
X-RAY DIFFRACTIONr_bond_other_d0.0010.029824
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.98214433
X-RAY DIFFRACTIONr_angle_other_deg0.78322666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56151316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17824.536463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.006151650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6991554
X-RAY DIFFRACTIONr_chiral_restr0.0860.21679
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111829
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022357
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4413.5535174
X-RAY DIFFRACTIONr_mcbond_other0.443.5525173
X-RAY DIFFRACTIONr_mcangle_it0.7414.7856460
X-RAY DIFFRACTIONr_mcangle_other0.7414.7856461
X-RAY DIFFRACTIONr_scbond_it0.6694.1575438
X-RAY DIFFRACTIONr_scbond_other0.6694.1575438
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0385.4547954
X-RAY DIFFRACTIONr_long_range_B_refined4.76111.76512717
X-RAY DIFFRACTIONr_long_range_B_other4.76111.76612718
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2682 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.130.5
Bmedium positional0.140.5
Cmedium positional0.250.5
Dmedium positional0.170.5
Emedium positional0.150.5
Amedium thermal0.622
Bmedium thermal0.682
Cmedium thermal0.532
Dmedium thermal0.532
Emedium thermal0.652
LS refinement shellResolution: 1.853→1.901 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 481 -
Rwork0.281 9771 -
obs--95.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.4878-0.19461.34180.55740.03013.0898-0.04610.12580.02540.0396-0.0282-0.1168-0.06890.16890.07430.0327-0.0277-0.00630.12720.05540.056260.304411.726418.4794
20.4779-0.27880.06850.85640.05440.7477-0.02550.1280.0174-0.02070.0016-0.0458-0.04480.12160.02390.0105-0.0321-0.00830.10530.0280.014658.12946.614419.6098
38.25480.32794.99140.64750.71374.29060.0033-0.44860.02930.084-0.0048-0.0747-0.1806-0.11770.00140.1908-0.0047-0.05370.112-0.00140.135944.322330.05352.4059
40.86920.0084-0.02290.2316-0.12591.0301-0.04940.01640.09610.0059-0.0117-0.0236-0.1824-0.00380.0610.06540.0005-0.03830.04320.0270.04837.916725.191427.819
51.33220.30492.21150.76410.54174.90090.0391-0.20250.03780.1745-0.00840.05670.022-0.2958-0.03070.04980.02420.0030.1388-0.01680.072213.5994.808246.5644
60.49110.03520.25230.9823-0.14460.6174-0.023-0.01630.04180.07240.01230.0044-0.0942-0.12230.01070.02120.029-0.00720.1001-0.00840.018317.590910.327839.0877
70.5232-0.05910.7731.96012.35610.5152-0.1158-0.1654-0.07870.25170.04110.01280.19770.22650.07470.114-0.0191-0.00530.16770.02680.119235.6611-24.879856.7591
80.9335-0.29450.01230.45030.0570.60250.0077-0.0415-0.0706-0.00270.02510.06890.092-0.1096-0.03290.0248-0.0269-0.0150.0611-0.00040.033922.9527-17.494435.2414
91.1988-0.12391.26361.5889-2.65889.4861-0.0233-0.0318-0.04230.2305-0.1423-0.0932-0.07650.31760.16570.10160.0477-0.01140.1039-0.01530.091464.8679-20.206740.4877
100.81410.27110.26620.6207-0.06151.01110.02780.0827-0.0547-0.0631-0.01180.01110.13050.077-0.0160.02510.0233-0.00910.0544-0.02450.012548.0751-19.297322.4861
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 68
2X-RAY DIFFRACTION2A69 - 288
3X-RAY DIFFRACTION3B24 - 42
4X-RAY DIFFRACTION4B43 - 288
5X-RAY DIFFRACTION5C25 - 61
6X-RAY DIFFRACTION6C62 - 288
7X-RAY DIFFRACTION7D24 - 42
8X-RAY DIFFRACTION8D43 - 288
9X-RAY DIFFRACTION9E24 - 43
10X-RAY DIFFRACTION10E44 - 288

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