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- PDB-1al2: P1/MAHONEY POLIOVIRUS, SINGLE SITE MUTANT V1160I -

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Basic information

Entry
Database: PDB / ID: 1al2
TitleP1/MAHONEY POLIOVIRUS, SINGLE SITE MUTANT V1160I
Components(P1/MAHONEY POLIOVIRUS) x 5
KeywordsVIRUS / PICORNAVIRUS / POLIOVIRUS / COAT PROTEIN / Icosahedral virus
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A ...Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Few Secondary Structures / Irregular / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
MYRISTIC ACID / SPHINGOSINE / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWien, M.W. / Curry, S. / Filman, D.J. / Hogle, J.M.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Structural studies of poliovirus mutants that overcome receptor defects.
Authors: Wien, M.W. / Curry, S. / Filman, D.J. / Hogle, J.M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: A Pseudo-Cell Based Approach to Efficient Crystallographic Refinement of Viruses
Authors: Jacobson, D.H. / Hogle, J.M. / Filman, D.J.
#2: Journal: Science / Year: 1985
Title: Three-Dimensional Structure of Poliovirus at 2.9 A Resolution
Authors: Hogle, J.M. / Chow, M. / Filman, D.J.
History
DepositionJun 9, 1997Processing site: BNL
Revision 1.0Nov 19, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_PDB_matrix / pdbx_database_remark / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn / struct_ncs_oper
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _cell.Z_PDB / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx_vector[3] / _pdbx_struct_oper_list.id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3] / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: P1/MAHONEY POLIOVIRUS
1: P1/MAHONEY POLIOVIRUS
2: P1/MAHONEY POLIOVIRUS
3: P1/MAHONEY POLIOVIRUS
4: P1/MAHONEY POLIOVIRUS
1: SPHINGOSINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4847
Polymers97,9565
Non-polymers5282
Water9,620534
1
0: P1/MAHONEY POLIOVIRUS
1: P1/MAHONEY POLIOVIRUS
2: P1/MAHONEY POLIOVIRUS
3: P1/MAHONEY POLIOVIRUS
4: P1/MAHONEY POLIOVIRUS
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,909,053420
Polymers5,877,382300
Non-polymers31,672120
Water5,405300
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
0: P1/MAHONEY POLIOVIRUS
1: P1/MAHONEY POLIOVIRUS
2: P1/MAHONEY POLIOVIRUS
3: P1/MAHONEY POLIOVIRUS
4: P1/MAHONEY POLIOVIRUS
hetero molecules
x 5


  • icosahedral pentamer
  • 492 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)492,42135
Polymers489,78225
Non-polymers2,63910
Water45025
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
0: P1/MAHONEY POLIOVIRUS
1: P1/MAHONEY POLIOVIRUS
2: P1/MAHONEY POLIOVIRUS
3: P1/MAHONEY POLIOVIRUS
4: P1/MAHONEY POLIOVIRUS
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 591 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)590,90542
Polymers587,73830
Non-polymers3,16712
Water54030
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
0: P1/MAHONEY POLIOVIRUS
1: P1/MAHONEY POLIOVIRUS
2: P1/MAHONEY POLIOVIRUS
3: P1/MAHONEY POLIOVIRUS
4: P1/MAHONEY POLIOVIRUS
hetero molecules
x 30


  • crystal asymmetric unit, crystal frame
  • 2.95 MDa, 150 polymers
Theoretical massNumber of molelcules
Total (without water)2,954,527210
Polymers2,938,691150
Non-polymers15,83660
Water2,702150
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)320.150, 355.300, 377.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.30980982, -0.8217736, 0.47794699), (0.79627491, 0.49920717, 0.34181871), (-0.51977854, 0.27475994, 0.80901699)44.96416, 32.15752, -17.96724
3generate(-0.80680217, -0.53350813, 0.2538423), (0.4665299, -0.31123181, 0.8277527), (-0.36275772, 0.78658788, 0.5)23.8809, 77.87308, -47.03885
4generate(-0.80671615, 0.46642334, -0.36260899), (-0.53353864, -0.31131783, 0.7862577), (0.25406502, 0.828155, 0.5)-34.11342, 73.96932, -47.03885
5generate(0.30994899, 0.79614949, -0.51949216), (-0.82186997, 0.499068, 0.27467839), (0.47826163, 0.34201696, 0.80901699)-48.87263, 25.84111, -17.96724
6generate(-0.99096868, -0.13416957), (-0.13401747, 0.99096868), (-1)-188.15542
7generate(-0.41384768, 0.74737349, -0.51949216), (0.74756357, 0.6048307, 0.27467839), (0.51977854, -0.27475994, -0.80901699)-48.87263, 25.84111, -170.18818
8generate(0.73692157, 0.57044768, -0.36260899), (0.57044211, -0.23692157, 0.7862577), (0.36275772, -0.78658788, -0.5)-34.11342, 73.96932, -141.11656
9generate(0.87101509, -0.42044155, 0.2538423), (-0.42060602, -0.37101509, 0.8277527), (-0.25406502, -0.828155, -0.5)23.8809, 77.87308, -141.11656
10generate(-0.19687981, -0.85591895, 0.47794699), (-0.85598598, 0.38786281, 0.34181871), (-0.47826163, -0.34201696, -0.80901699)44.96416, 32.15752, -170.18818
11generate(-0.06708977, -0.00452112, 0.99743915), (0.99555833, 0.06708977, 0.06714032), (-0.06717578, 0.99796599)93.83679, 6.31641, -94.07771
12generate(-0.54283259, 0.32693194, 0.77333446), (0.32695755, -0.76618439, 0.5530743), (0.77384356, 0.55339507, 0.30901699)72.75354, 52.03196, -65.0061
13generate(-0.30980982, 0.8217736, 0.47794699), (-0.79627491, -0.49920717, 0.34181871), (0.51977854, -0.27475994, 0.80901699)44.96416, 32.15752, -17.96724
14generate(0.30994899, 0.79614949, 0.51949216), (-0.82186997, 0.499068, -0.27467839), (-0.47826163, -0.34201696, 0.80901699)48.87263, -25.84111, -17.96724
15generate(0.45995824, 0.28547127, 0.84055597), (0.28554387, 0.84905875, -0.44443899), (-0.84101934, 0.44457092, 0.30901699)79.07758, -41.8118, -65.0061
16generate(0.06708977, 0.00452112, 0.99743915), (-0.99555833, -0.06708977, 0.06714032), (0.06717578, -0.99796599)93.83679, 6.31641, -94.07771
17generate(-0.49406235, 0.22118069, 0.84055597), (-0.39675374, 0.80307933, -0.44443899), (-0.77384356, -0.55339507, -0.30901699)79.07758, -41.8118, -123.14932
18generate(-0.41384768, 0.74737349, 0.51949216), (0.74756357, 0.6048307, -0.27467839), (-0.51977854, 0.27475994, -0.80901699)48.87263, -25.84111, -170.18818
19generate(0.19687981, 0.85591895, 0.47794699), (0.85598598, -0.38786281, 0.34181871), (0.47826163, 0.34201696, -0.80901699)44.96416, 32.15752, -170.18818
20generate(0.49411551, 0.39681093, 0.77333446), (-0.2213226, -0.80313249, 0.5530743), (0.84101934, -0.44457092, -0.30901699)72.75354, 52.03196, -123.14932
21generate(-0.06700375, 0.99541035, -0.06722151), (-0.0045102, 0.06700376, 0.99751329), (0.99804017, 0.06725702)-6.32405, 93.84377, -94.07771
22generate(0.80680217, 0.53350813, 0.2538423), (-0.4665299, 0.31123181, 0.8277527), (0.36275772, -0.78658788, 0.5)23.8809, 77.87308, -47.03885
23generate(0.54283259, -0.32693194, 0.77333446), (-0.32695755, 0.76618439, 0.5530743), (-0.77384356, -0.55339507, 0.30901699)72.75354, 52.03196, -65.0061
24generate(-0.49411551, -0.39681093, 0.77333446), (0.2213226, 0.80313249, 0.5530743), (-0.84101934, 0.44457092, -0.30901699)72.75354, 52.03196, -123.14932
25generate(-0.87101509, 0.42044155, 0.2538423), (0.42060602, 0.37101509, 0.8277527), (0.25406502, 0.828155, -0.5)23.8809, 77.87308, -141.11656
26generate(0.06700375, -0.99541035, -0.06722151), (0.0045102, -0.06700376, 0.99751329), (-0.99804017, -0.06725702)-6.32405, 93.84377, -94.07771
27generate(-0.73692157, -0.57044768, -0.36260899), (-0.57044211, 0.23692157, 0.7862577), (-0.36275772, 0.78658788, -0.5)-34.11342, 73.96932, -141.11656
28generate(-0.49406235, 0.22118069, -0.84055597), (-0.39675374, 0.80307933, 0.44443899), (0.77384356, 0.55339507, -0.30901699)-79.07758, 41.8118, -123.14932
29generate(0.45995824, 0.28547127, -0.84055597), (0.28554387, 0.84905875, 0.44443899), (0.84101934, -0.44457092, 0.30901699)-79.07758, 41.8118, -65.0061
30generate(0.80671615, -0.46642334, -0.36260899), (0.53353864, 0.31131783, 0.7862577), (-0.25406502, -0.828155, 0.5)-34.11342, 73.96932, -47.03885

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Components

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Protein/peptide , 1 types, 1 molecules 0

#1: Protein/peptide P1/MAHONEY POLIOVIRUS


Mass: 437.404 Da / Num. of mol.: 1 / Fragment: VIRUS PROTOMER / Mutation: CHAIN 1, V160I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney

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Protein , 4 types, 4 molecules 1234

#2: Protein P1/MAHONEY POLIOVIRUS


Mass: 33502.641 Da / Num. of mol.: 1 / Fragment: VIRUS PROTOMER / Mutation: CHAIN 1, V160I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300
#3: Protein P1/MAHONEY POLIOVIRUS


Mass: 30075.783 Da / Num. of mol.: 1 / Fragment: VIRUS PROTOMER / Mutation: CHAIN 1, V160I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300
#4: Protein P1/MAHONEY POLIOVIRUS


Mass: 26547.482 Da / Num. of mol.: 1 / Fragment: VIRUS PROTOMER / Mutation: CHAIN 1, V160I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03300
#5: Protein P1/MAHONEY POLIOVIRUS


Mass: 7393.050 Da / Num. of mol.: 1 / Fragment: VIRUS PROTOMER / Mutation: CHAIN 1, V160I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03299, UniProt: P03300*PLUS

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Non-polymers , 3 types, 536 molecules 1

#6: Chemical ChemComp-SPH / SPHINGOSINE / Sphingosine


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2
#7: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.59 Å3/Da / Density % sol: 30 %
Crystal growMethod: microdiaylsis / pH: 7.5
Details: VIRUS WAS CRYSTALLIZED BY MICRODIALYSIS AGAINST 10MM PIPES, 0-70 MM NACL, PH 7.5, 2% PEG 400, microdiaylsis
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
170 mM11NaCl
22 %PEG40011

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Dec 1, 1995 / Details: SUPPER LONG MIRRORS
RadiationMonochromator: SUPPER LONG MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 615179 / % possible obs: 66 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.113
Reflection
*PLUS
Num. measured all: 2649615

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PLV

2plv


Resolution: 2.9→11 Å
Details: XX12 PROTOMER BOX BASED REFINEMENT, SEE JACOBSON ET AL. PROGRAM : PROTOMER-BOX-BASED PSEUDO-REAL-SPACE AUTHORS : FILMAN
RfactorNum. reflection% reflection
Rwork0.241 --
obs0.241 615066 66 %
Refinement stepCycle: LAST / Resolution: 2.9→11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6633 0 36 534 7203
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.55
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.27
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.9→2.99 Å / Total num. of bins used: 16 /
RfactorNum. reflection
Rwork0.294 54758
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.27

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
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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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