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- PDB-32nj: Cryo-EM structure of SKM-M.smegmatis 70S ribosomal complex -

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Basic information

Entry
Database: PDB / ID: 32nj
TitleCryo-EM structure of SKM-M.smegmatis 70S ribosomal complex
Components
  • (Small ribosomal subunit protein ...) x 17
  • 16S rRNA
KeywordsRIBOSOME / Antibiotics / 70S complex
Function / homology
Function and homology information


ribosomal small subunit biogenesis / ribosome biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation ...ribosomal small subunit biogenesis / ribosome biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Ribosomal protein S14, type Z / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S7, bacterial/organellar-type ...Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / Ribosomal protein S14, type Z / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S14/S29 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / : / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S10 / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / K homology domain superfamily, prokaryotic type / : / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S8 signature. / K homology domain-like, alpha/beta / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S15 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal protein S10p/S20e / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / RNA-binding S4 domain superfamily / Ribosomal protein S11 / Ribosomal protein S12 signature. / Ribosomal protein S11 / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S9 / Ribosomal protein S9/S16
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS22 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS22 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS14B / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein bS18B
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsCook, M.A. / Xu, M. / Morici, M. / Travin, D.T. / Wang, W. / Klepacki, D. / Nandini, N. / Rao, V.N. / Sahile, H. / Hackenberger, D. ...Cook, M.A. / Xu, M. / Morici, M. / Travin, D.T. / Wang, W. / Klepacki, D. / Nandini, N. / Rao, V.N. / Sahile, H. / Hackenberger, D. / Golas, A.J. / Nietupski, R.M. / Fitzgerald, M. / Safdari, H.A. / Berger, M. / Corazza, M. / Bond, A. / Ben-Zion, I. / Guitor, A.K. / Tertigas, D. / Wang, L. / Schaenzer, A.J. / Ejim, L. / Yarlagadda, V. / Gomez, J. / Surette, M.G. / Av-Gay, Y. / Dhar, N. / Hung, D.T. / Vazquez Laslop, N. / Mankin, A. / Wilson, D.N. / Wright, G.D.
Funding support United States, Canada, Germany, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 GM127134 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)NIH R01 AI162961 United States
Canadian Institutes of Health Research (CIHR)FDN148463 Canada
German Research Foundation (DFG)WI3285/12-1 Germany
CitationJournal: To Be Published
Title: Cryo-EM structure of SKM-M.smegmatis 70S ribosomal complex
Authors: Morici, M. / Wilson, D.N.
History
DepositionJul 16, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S rRNA
x: Small ribosomal subunit protein bS22
C: Small ribosomal subunit protein uS3
D: Small ribosomal subunit protein uS4
E: Small ribosomal subunit protein uS5
F: Small ribosomal subunit protein bS6
G: Small ribosomal subunit protein uS7
H: Small ribosomal subunit protein uS8
I: Small ribosomal subunit protein uS9
J: Small ribosomal subunit protein uS10
K: Small ribosomal subunit protein uS11
L: Small ribosomal subunit protein uS12
N: Small ribosomal subunit protein uS14B
O: Small ribosomal subunit protein uS15
P: Small ribosomal subunit protein bS16
Q: Small ribosomal subunit protein uS17
R: Small ribosomal subunit protein bS18B
T: Small ribosomal subunit protein bS20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)742,33598
Polymers739,40018
Non-polymers2,93580
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain 16S rRNA


Mass: 495373.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / References: GenBank: 2093960070

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Small ribosomal subunit protein ... , 17 types, 17 molecules xCDEFGHIJKLNOPQRT

#2: Protein/peptide Small ribosomal subunit protein bS22


Mass: 4164.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0QR10
#3: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 30191.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0QSD7
#4: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23415.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0QSL7
#5: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 21946.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0QSG6
#6: Protein Small ribosomal subunit protein bS6


Mass: 10991.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0A2U9Q0X2
#7: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 17660.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0QS97
#8: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14492.638 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0QSG3
#9: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 16794.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0QSP9
#10: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10


Mass: 11454.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0QSD0
#11: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 14671.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0QSL6
#12: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 13896.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0QS96
#13: Protein Small ribosomal subunit protein uS14B / 30S ribosomal protein S14 type Z


Mass: 6976.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0QSG2
#14: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10368.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0QVQ3
#15: Protein Small ribosomal subunit protein bS16 / 30S ribosomal protein S16


Mass: 16795.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0QV37
#16: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 11127.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0QSE0
#17: Protein Small ribosomal subunit protein bS18B / 30S ribosomal protein S18 2


Mass: 9524.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0R7F7
#18: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 9556.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycolicibacterium smegmatis (bacteria) / References: UniProt: A0R102

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Non-polymers , 4 types, 83 molecules

#19: Chemical ChemComp-A1JAI / [(2~{S},3~{S},4~{R},5~{R},6~{S})-4-[(2~{S},3~{R},4~{S},5~{R},6~{S})-5-acetamido-6-(hydroxymethyl)-4-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-4-[(2~{S},3~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-5-methoxy-3,4-bis(oxidanyl)oxan-2-yl]oxy-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-oxan-2-yl]oxy-2-(hydroxymethyl)-6-[[~{N}-[4-[(~{N}-methylcarbamimidoyl)amino]butyl]carbamimidoyl]amino]-5-oxidanyl-oxan-3-yl] carbamate


Mass: 932.924 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H64N8O21 / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 77 / Source method: obtained synthetically / Formula: Mg
#21: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#22: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SKM-M.smegmatis 70S complex / Type: RIBOSOME / Entity ID: #1-#18 / Source: NATURAL
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1400 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 43 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLO1.7.5particle selection
2REFMAC5.8.0430model refinement
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68217 / Symmetry type: POINT
RefinementResolution: 3→227.97 Å / Cor.coef. Fo:Fc: 0.957 / SU B: 14.248 / SU ML: 0.258 / ESU R: 0.327
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.29697 --
obs0.29697 513401 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 90.622 Å2
Refinement stepCycle: 1 / Total: 44891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.01148553
ELECTRON MICROSCOPYr_bond_other_d0.0010.01729279
ELECTRON MICROSCOPYr_angle_refined_deg0.6851.84772373
ELECTRON MICROSCOPYr_angle_other_deg0.2511.73868910
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.3751932
ELECTRON MICROSCOPYr_dihedral_angle_2_deg2.212.16225
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.699102954
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0310.29190
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.0235309
ELECTRON MICROSCOPYr_gen_planes_other0.0030.028946
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it7.19210.097779
ELECTRON MICROSCOPYr_mcbond_other7.18810.097779
ELECTRON MICROSCOPYr_mcangle_it11.65218.2029694
ELECTRON MICROSCOPYr_mcangle_other11.65118.2029695
ELECTRON MICROSCOPYr_scbond_it6.8758.75740774
ELECTRON MICROSCOPYr_scbond_other6.8758.75740775
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other10.90815.85962680
ELECTRON MICROSCOPYr_long_range_B_refined14.66296.6358903
ELECTRON MICROSCOPYr_long_range_B_other14.66296.6358904
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.473 38060 -
obs--100 %

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