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- PDB-3vr8: Mitochondrial rhodoquinol-fumarate reductase from the parasitic n... -

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Basic information

Entry
Database: PDB / ID: 3vr8
TitleMitochondrial rhodoquinol-fumarate reductase from the parasitic nematode Ascaris suum
Components
  • Cytochrome b-large subunit
  • Flavoprotein subunit of complex II
  • Iron-sulfur subunit of succinate dehydrogenaseIron-sulfur protein
  • Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
KeywordsOXIDOREDUCTASE / Ascaris suum / membrane protein / reductase / mitochondria membrane
Function / homology
Function and homology information


TIM22 mitochondrial import inner membrane insertion complex / mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone) / mitochondrial electron transport, succinate to ubiquinone / : / succinate dehydrogenase / protein insertion into mitochondrial inner membrane / succinate dehydrogenase (quinone) activity / oxidoreductase activity, acting on the CH-CH group of donors / 3 iron, 4 sulfur cluster binding / ubiquinone binding ...TIM22 mitochondrial import inner membrane insertion complex / mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone) / mitochondrial electron transport, succinate to ubiquinone / : / succinate dehydrogenase / protein insertion into mitochondrial inner membrane / succinate dehydrogenase (quinone) activity / oxidoreductase activity, acting on the CH-CH group of donors / 3 iron, 4 sulfur cluster binding / ubiquinone binding / protein transmembrane transporter activity / tricarboxylic acid cycle / respiratory electron transport chain / electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / heme binding / mitochondrion / metal ion binding / plasma membrane
Similarity search - Function
CybS, succinate dehydrogenase cytochrome B small subunit / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / succinate dehydrogenase protein domain / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit ...CybS, succinate dehydrogenase cytochrome B small subunit / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / succinate dehydrogenase protein domain / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / FAD-dependent oxidoreductase SdhA/FrdA/AprA / Fumarate reductase / succinate dehydrogenase FAD-binding site. / 3 helical TM bundles of succinate and fumarate reductases / 4Fe-4S dicluster domain / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / Alpha-helical ferredoxin / FAD binding domain / Rhinovirus 14, subunit 4 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Ubiquitin-like (UB roll) / Few Secondary Structures / Irregular / Roll / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-EPH / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / MALONATE ION / Chem-RQX / IRON/SULFUR CLUSTER / Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] cytochrome b large subunit, mitochondrial ...Chem-EPH / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / MALONATE ION / Chem-RQX / IRON/SULFUR CLUSTER / Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] cytochrome b large subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit 1, mitochondrial / Succinate dehydrogenase [rhodoquinone] flavoprotein subunit 1, mitochondrial
Similarity search - Component
Biological speciesAscaris suum (pig roundworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsShimizu, H. / Shiba, T. / Inaoka, D.K. / Osanai, A. / Kita, K. / Sakamoto, K. / Harada, S.
CitationJournal: J.Biochem. / Year: 2012
Title: Crystal structure of mitochondrial quinol-fumarate reductase from the parasitic nematode Ascaris suum
Authors: Shimizu, H. / Osanai, A. / Sakamoto, K. / Inaoka, D.K. / Shiba, T. / Harada, S. / Kita, K.
History
DepositionApr 7, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Atomic model
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flavoprotein subunit of complex II
B: Iron-sulfur subunit of succinate dehydrogenase
C: Cytochrome b-large subunit
D: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
E: Flavoprotein subunit of complex II
F: Iron-sulfur subunit of succinate dehydrogenase
G: Cytochrome b-large subunit
H: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)288,92324
Polymers282,3228
Non-polymers6,60116
Water0
1
A: Flavoprotein subunit of complex II
B: Iron-sulfur subunit of succinate dehydrogenase
C: Cytochrome b-large subunit
D: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,46212
Polymers141,1614
Non-polymers3,3018
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21720 Å2
ΔGint-175 kcal/mol
Surface area42120 Å2
MethodPISA
2
E: Flavoprotein subunit of complex II
F: Iron-sulfur subunit of succinate dehydrogenase
G: Cytochrome b-large subunit
H: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,46212
Polymers141,1614
Non-polymers3,3018
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21530 Å2
ΔGint-175 kcal/mol
Surface area42400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.707, 129.090, 221.167
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Flavoprotein subunit of complex II / / Rhodoquinol-fumarate reductase Fp subunit


Mass: 71304.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ascaris suum (pig roundworm) / Organelle: mitochondriaMitochondrion / References: UniProt: Q33862
#2: Protein Iron-sulfur subunit of succinate dehydrogenase / Iron-sulfur protein / Rhodoquinol-fumarate reductase Ip subunit


Mass: 31673.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ascaris suum (pig roundworm) / Organelle: mitochondriaMitochondrion / References: UniProt: O44074
#3: Protein Cytochrome b-large subunit / Rhodoquinol-fumarate reductase CybL subunit


Mass: 21168.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ascaris suum (pig roundworm) / Organelle: mitochondriaMitochondrion / References: UniProt: P92506
#4: Protein Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / CybS / Cytochrome b558 small subunit / Succinate-ubiquinone reductase membrane anchor subunit / ...CybS / Cytochrome b558 small subunit / Succinate-ubiquinone reductase membrane anchor subunit / Rhodoquinol-fumarate reductase CybS subunit


Mass: 17014.932 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ascaris suum (pig roundworm) / Organelle: mitochondriaMitochondrion / References: UniProt: P92507

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Non-polymers , 8 types, 16 molecules

#5: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#6: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#8: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#9: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#10: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#11: Chemical ChemComp-RQX / 2-amino-3-methoxy-6-methyl-5-[(2E)-3-methylhex-2-en-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 263.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H21NO3
#12: Chemical ChemComp-EPH / L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 709.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H68NO8P / Comment: phospholipid*YM

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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: 3.13 Å3/Da / Density % sol: 60.67 %
Crystal growTemperature: 293 K / Method: microdialysis / pH: 8.4
Details: 15% (w/v) PEG 3350, 100mM Tris-HCl pH 8.4, 200mM NaCl, 1mM sodium malonate, 0.06% (w/v) C12E8, 0.04% (w/v) C12M, MICRODIALYSIS, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Oct 5, 2004 / Details: monochromator
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 80093 / Num. obs: 79622 / % possible obs: 92.5 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 7.9
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 1.26 / % possible all: 67.5

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZOY

1zoy


Resolution: 2.81→48.56 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.839 / SU B: 20.231 / SU ML: 0.365 / Cross valid method: THROUGHOUT / ESU R: 1.606 / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29717 4025 5 %RANDOM
Rwork0.23116 ---
obs0.23446 76011 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2--0.35 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.81→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17862 0 370 0 18232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02218697
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.99125399
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.15252277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76423.24784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.059153111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.69715124
X-RAY DIFFRACTIONr_chiral_restr0.1140.22743
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114042
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5981.511346
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.138218246
X-RAY DIFFRACTIONr_scbond_it1.42637351
X-RAY DIFFRACTIONr_scangle_it2.4444.57071
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.808→2.881 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.504 218 -
Rwork0.466 3732 -
obs--100 %

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