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- PDB-4x10: JC Polyomavirus genotype 3 VP1 in complex with GM2 oligosaccharide -

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Basic information

Entry
Database: PDB / ID: 4x10
TitleJC Polyomavirus genotype 3 VP1 in complex with GM2 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 / host cell nucleus / 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: 1.9 Å
AuthorsStroh, L.J. / Stehle, T.
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 / 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.occupancy / _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 / _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.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_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)154,54536
Polymers150,1695
Non-polymers4,37631
Water21,2761181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33620 Å2
ΔGint-84 kcal/mol
Surface area44500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.410, 96.060, 128.750
Angle α, β, γ (deg.)90.00, 110.21, 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

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRASPASP1AA31 - 5114 - 34
21THRTHRASPASP1BB31 - 5114 - 34
31THRTHRASPASP1CC31 - 5114 - 34
41THRTHRASPASP1DD31 - 5114 - 34
51THRTHRASPASP1EE31 - 5114 - 34
12SERSERILEILE4AA71 - 8554 - 68
22SERSERILEILE4BB71 - 8554 - 68
32SERSERILEILE4CC71 - 8554 - 68
42SERSERILEILE4DD71 - 8554 - 68
52SERSERILEILE4EE71 - 8554 - 68
13METMETSERSER4AA101 - 12284 - 105
23METMETSERSER4BB101 - 12284 - 105
33METMETSERSER4CC101 - 12284 - 105
43METMETSERSER4DD101 - 12284 - 105
53METMETSERSER4EE101 - 12284 - 105
14GLYGLYTHRTHR4AA124 - 162107 - 145
24GLYGLYTHRTHR4BB124 - 162107 - 145
34GLYGLYTHRTHR4CC124 - 162107 - 145
44GLYGLYTHRTHR4DD124 - 162107 - 145
54GLYGLYTHRTHR4EE124 - 162107 - 145
15ASNASNGLNGLN4AA89 - 17772 - 160
25ASNASNGLNGLN4BB89 - 17772 - 160
35ASNASNGLNGLN4CC89 - 17772 - 160
45ASNASNGLNGLN4DD89 - 17772 - 160
55ASNASNGLNGLN4EE89 - 17772 - 160
16ALAALATHRTHR4AA194 - 205177 - 188
26ALAALATHRTHR4BB194 - 205177 - 188
36ALAALATHRTHR4CC194 - 205177 - 188
46ALAALATHRTHR4DD194 - 205177 - 188
56ALAALATHRTHR4EE194 - 205177 - 188
17LEULEUTHRTHR4AA251 - 263234 - 246
27LEULEUTHRTHR4BB251 - 263234 - 246
37LEULEUTHRTHR4CC251 - 263234 - 246
47LEULEUTHRTHR4DD251 - 263234 - 246
57LEULEUTHRTHR4EE251 - 263234 - 246
18PHEPHEASPASP4AA240 - 249223 - 232
28PHEPHEASPASP4BB240 - 249223 - 232
38PHEPHEASPASP4CC240 - 249223 - 232
48PHEPHEASPASP4DD240 - 249223 - 232
58PHEPHEASPASP4EE240 - 249223 - 232
19ASNASNASPASP4AA207 - 238190 - 221
29ASNASNASPASP4BB207 - 238190 - 221
39ASNASNASPASP4CC207 - 238190 - 221
49ASNASNASPASP4DD207 - 238190 - 221
59ASNASNASPASP4EE207 - 238190 - 221
110LEULEUTHRTHR4AA251 - 263234 - 246
210LEULEUTHRTHR4BB251 - 263234 - 246
310LEULEUTHRTHR4CC251 - 263234 - 246
410LEULEUTHRTHR4DD251 - 263234 - 246
510LEULEUTHRTHR4EE251 - 263234 - 246

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.44482, 0.849726, 0.28302), (-0.853157, 0.30587, 0.422571), (0.272502, -0.429429, 0.861007)11.23859, 20.01914, -5.66646
3given(-0.438712, 0.50929, 0.740375), (-0.524318, -0.814188, 0.249377), (0.72981, -0.278788, 0.624224)31.20605, 14.23905, -15.64456
4given(-0.435076, -0.533495, 0.725323), (0.520625, -0.8063, -0.280766), (0.734615, 0.255466, 0.628552)32.50682, -9.16286, -16.74257
5given(0.456825, -0.845938, 0.275136), (0.844931, 0.315898, -0.431625), (0.278214, 0.429648, 0.859069)12.98453, -17.84899, -6.5011

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


Type: oligosaccharide / Mass: 836.744 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3[DGalpNAcb1-4]DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[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/a4-b1_b3-c2_b4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}[(4+1)][b-D-GalpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-[2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)]beta-D-galactopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3[DGalpNAcb1-4]DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3/a3-b2_a4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}[(4+1)][b-D-GalpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 1209 molecules

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


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


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


Mass: 18.015 Da / Num. of mol.: 1181 / 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: 2.91 Å3/Da / Density % sol: 57.68 %
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: 1.9→30 Å / Num. obs: 131009 / % possible obs: 97.3 % / Redundancy: 4.3 % / Biso Wilson estimate: 24.8 Å2 / Rsym value: 0.138 / Net I/σ(I): 9.9
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2 / Rsym value: 0.855 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
Cootmodel building
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NXG

3nxg


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.763 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19571 6604 5 %RANDOM
Rwork0.16356 ---
obs0.16517 124405 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.026 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20.17 Å2
2--0.16 Å20 Å2
3---0.24 Å2
Refinement stepCycle: 1 / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9987 0 281 1181 11449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01910585
X-RAY DIFFRACTIONr_bond_other_d0.0010.029813
X-RAY DIFFRACTIONr_angle_refined_deg1.351.97714415
X-RAY DIFFRACTIONr_angle_other_deg0.761322661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35451318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80224.606469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.443151673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1731554
X-RAY DIFFRACTIONr_chiral_restr0.0820.21666
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111885
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022365
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_it1.3322.9215188
X-RAY DIFFRACTIONr_mcbond_other1.3272.925187
X-RAY DIFFRACTIONr_mcangle_it1.8934.0786480
X-RAY DIFFRACTIONr_mcangle_other1.8934.0796481
X-RAY DIFFRACTIONr_scbond_it2.5613.8625397
X-RAY DIFFRACTIONr_scbond_other2.5553.8625397
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6765.1267918
X-RAY DIFFRACTIONr_long_range_B_refined6.768.85212485
X-RAY DIFFRACTIONr_long_range_B_other6.768.85312486
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 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A3448medium positional0.240.5
B3448medium positional0.190.5
C3448medium positional0.270.5
D3448medium positional0.180.5
E3448medium positional0.210.5
A276tight thermal1.390.5
B276tight thermal1.410.5
C276tight thermal1.550.5
D276tight thermal1.470.5
E276tight thermal1.60.5
A3448medium thermal1.242
B3448medium thermal1.42
C3448medium thermal1.172
D3448medium thermal1.352
E3448medium thermal1.352
LS refinement shellResolution: 1.903→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 493 -
Rwork0.313 8820 -
obs--94.43 %
Refinement TLS params.

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

IDL11 (°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)
11.3362-0.17531.3080.5356-0.05663.2663-0.04220.12940.06140.0603-0.0147-0.1187-0.06540.23940.05690.025-0.0197-0.0160.11070.05410.143860.761811.815818.9892
20.6581-0.37820.16320.85240.07910.8404-0.02520.09540.0294-0.00370.008-0.0549-0.03720.11160.01720.0161-0.0276-0.03410.06460.04160.093158.1696.601619.4006
39.70690.45395.2290.60240.45834.97010.0366-0.6207-0.05050.1184-0.0006-0.112-0.1895-0.2041-0.0360.2174-0.0073-0.05760.1137-0.01040.218444.311330.181752.4005
40.8396-0.0363-0.02660.2299-0.10440.8787-0.0427-0.0110.11090.0216-0.0094-0.044-0.14250.00910.0520.0540.0005-0.06050.03540.03140.12837.961125.222327.6873
54.77373.53895.28623.08353.65828.55840.2362-0.2418-0.14840.4332-0.0715-0.05910.269-0.1789-0.16460.1760.0602-0.01580.1781-0.0250.162322.19085.193663.6458
60.47920.01320.21831.0103-0.18020.6351-0.018-0.01990.03110.08680.02050.0144-0.0719-0.1129-0.00250.02430.0216-0.02990.0832-0.00320.095116.54769.86938.5079
71.0589-0.10980.80032.10113.295511.2662-0.0942-0.23830.00850.16530.11990.00570.20790.2712-0.02560.1384-0.0178-0.02380.18990.03210.166535.8533-24.5158.4382
81.1085-0.30330.01830.4210.10180.5913-0.0009-0.0437-0.06250.01240.03520.05160.0885-0.0824-0.03430.031-0.0197-0.04230.0423-0.00040.12122.9605-17.66235.2267
91.6005-0.28672.77210.6463-1.40237.956-0.00940.1095-0.03970.0857-0.0262-0.07540.10340.45370.03560.09340.0558-0.01070.0798-0.02220.132561.0655-19.540629.177
100.8550.28710.21170.7104-0.14841.10550.02320.0531-0.0341-0.0393-0.02010.03180.11380.0548-0.0030.02170.017-0.02690.0291-0.02720.074347.9047-19.396423.0272
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 - 42
6X-RAY DIFFRACTION6C43 - 288
7X-RAY DIFFRACTION7D24 - 41
8X-RAY DIFFRACTION8D42 - 288
9X-RAY DIFFRACTION9E24 - 54
10X-RAY DIFFRACTION10E55 - 288

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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

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