[English] 日本語
Yorodumi
- PDB-3hax: Crystal structure of a substrate-bound Gar1-minus H/ACA RNP from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hax
TitleCrystal structure of a substrate-bound Gar1-minus H/ACA RNP from Pyrococcus furiosus
Components
  • 5'-R(*AP*UP*AP*AP*UP*UP*(FHU)P*GP*AP*CP*UP*CP*AP*A)-3'
  • 50S ribosomal protein L7AeRibosome
  • H/ACA RNA
  • Probable tRNA pseudouridine synthase B
  • Ribosome biogenesis protein Nop10
KeywordsISOMERASE/BIOSYNTHETIC PROTEIN/RNA / H/ACA / guide RNA / RNA-protein complex / pseudouridine synthase / Isomerase / tRNA processing / Ribonucleoprotein / Ribosome biogenesis / rRNA processing / Ribosomal protein / RNA-binding / ISOMERASE-BIOSYNTHETIC PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


tRNA pseudouridine55 synthase / tRNA pseudouridine synthase activity / pseudouridine synthesis / tRNA pseudouridine synthesis / ribonuclease P activity / tRNA 5'-leader removal / snoRNA binding / rRNA processing / rRNA binding / ribosome ...tRNA pseudouridine55 synthase / tRNA pseudouridine synthase activity / pseudouridine synthesis / tRNA pseudouridine synthesis / ribonuclease P activity / tRNA 5'-leader removal / snoRNA binding / rRNA processing / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding / cytoplasm
Similarity search - Function
H/ACA ribonucleoprotein complex, subunit Nop10 / Probable tRNA pseudouridine synthase B, archaeal / H/ACA ribonucleoprotein complex subunit Nop10 , archaeal-type / tRNA pseudouridine synthase B family / Dyskerin-like / DKCLD (NUC011) domain / DKCLD (NUC011) domain / H/ACA ribonucleoprotein complex, subunit Nop10 / H/ACA ribonucleoprotein complex, subunit Nop10 superfamily / Nucleolar RNA-binding protein, Nop10p family ...H/ACA ribonucleoprotein complex, subunit Nop10 / Probable tRNA pseudouridine synthase B, archaeal / H/ACA ribonucleoprotein complex subunit Nop10 , archaeal-type / tRNA pseudouridine synthase B family / Dyskerin-like / DKCLD (NUC011) domain / DKCLD (NUC011) domain / H/ACA ribonucleoprotein complex, subunit Nop10 / H/ACA ribonucleoprotein complex, subunit Nop10 superfamily / Nucleolar RNA-binding protein, Nop10p family / Pseudouridine synthase / Pseudouridine synthase II, N-terminal / tRNA pseudouridylate synthase B, C-terminal / TruB family pseudouridylate synthase (N terminal domain) / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase / Uncharacterised domain CHP00451 / PUA domain / PUA domain / Pseudouridine synthase, catalytic domain superfamily / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. / PUA domain superfamily / Ribosomal protein L7Ae, archaea / Ribosomal protein L30/S12 / Rubrerythrin, domain 2 / PUA-like superfamily / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Single Sheet / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / RNA / RNA (> 10) / Probable tRNA pseudouridine synthase B / Large ribosomal subunit protein eL8 / Ribosome biogenesis protein Nop10
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsYe, K.
CitationJournal: Mol.Cell / Year: 2009
Title: Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase.
Authors: Duan, J. / Li, L. / Lu, J. / Wang, W. / Ye, K.
History
DepositionMay 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 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 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable tRNA pseudouridine synthase B
C: Ribosome biogenesis protein Nop10
D: 50S ribosomal protein L7Ae
E: H/ACA RNA
F: 5'-R(*AP*UP*AP*AP*UP*UP*(FHU)P*GP*AP*CP*UP*CP*AP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,62816
Polymers85,8225
Non-polymers80611
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14510 Å2
ΔGint-95 kcal/mol
Surface area30770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.809, 63.696, 83.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 3 types, 3 molecules ACD

#1: Protein Probable tRNA pseudouridine synthase B / Cbf5 / tRNA pseudouridine 55 synthase / Psi55 synthase / tRNA-uridine isomerase / tRNA ...Cbf5 / tRNA pseudouridine 55 synthase / Psi55 synthase / tRNA-uridine isomerase / tRNA pseudouridylate synthase


Mass: 39453.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: truB, PF1785 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7LWY0, Isomerases; Intramolecular transferases; Transferring other groups
#2: Protein Ribosome biogenesis protein Nop10 /


Mass: 7214.603 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF1141 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1R4
#3: Protein 50S ribosomal protein L7Ae / Ribosome


Mass: 14314.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: rpl7ae, PF1367 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U160

-
RNA chain , 2 types, 2 molecules EF

#4: RNA chain H/ACA RNA


Mass: 20386.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION
#5: RNA chain 5'-R(*AP*UP*AP*AP*UP*UP*(FHU)P*GP*AP*CP*UP*CP*AP*A)-3'


Mass: 4452.682 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Non-polymers , 6 types, 394 molecules

#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#10: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M ammonium acetate, 0.15M magnesium acetate, 4% PEG 8000, 50mM cacodylate sodium, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorDate: May 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 57734 / % possible obs: 99.6 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 13.7
Reflection shellResolution: 2.09→2.16 Å / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 2.7 / % possible all: 99

-
Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HVY

2hvy


Resolution: 2.11→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.968 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.157 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22034 2944 5.1 %RANDOM
Rwork0.203 ---
obs0.20389 54667 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.912 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2---0.33 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.11→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3990 1540 47 383 5960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225856
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9592.3248245
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7735500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89623.473167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54115768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3471531
X-RAY DIFFRACTIONr_chiral_restr0.0550.2976
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023742
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1560.22386
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2850.23823
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.2464
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1871.52614
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.31824074
X-RAY DIFFRACTIONr_scbond_it0.45234169
X-RAY DIFFRACTIONr_scangle_it0.7534.54165
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.164 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 173 -
Rwork0.233 3155 -
obs--79.26 %
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)
12.2057-0.38330.68882.33190.5195.8080.21160.40070.0877-0.5978-0.1628-0.38110.29960.3752-0.04880.24060.08930.03870.10450.09880.21730.48631.3366.364
21.3886-0.2553-0.11331.67150.03460.9276-0.0577-0.04740.05260.0851-0.02380.08870.0015-0.05820.0816-0.07350.02830.0061-0.10650.003-0.163634.71610.65821.031
34.4741-1.7463-2.39112.07911.93564.2041-0.07430.482-0.4328-0.3249-0.11140.14370.1041-0.27260.18580.1425-0.047-0.0403-0.035-0.07930.003633.3-7.4041.754
40.69970.29610.24641.7391.47732.057-0.04930.0935-0.109-0.20080.00850.01150.0012-0.03790.0407-0.01130.00620.0104-0.0810.0057-0.129938.6642.2210.396
52.2905-1.00030.99281.2266-0.60611.84390.11320.3620.1841-0.1525-0.12250.00510.04660.05940.0093-0.00470.0440.0159-0.04860.0348-0.06327.74427.71313.179
63.0754-0.53080.27362.882-0.52834.13640.00510.39010.3195-0.3229-0.06850.3198-0.1629-0.26280.06340.02460.0517-0.02830.02050.05140.067616.97231.40210.434
712.841710.7483-7.419924.2567-13.447115.25780.1207-0.36170.1936-0.0411-0.2518-0.0552-0.0780.62630.1311-0.01840.04490.0401-0.0461-0.046-0.175252.583.5999.617
812.54430.6552-6.24989.0091-2.034110.04330.0543-0.2798-0.1502-0.2388-0.1372-0.7449-0.06560.78270.0829-0.04740.00020.0261-0.0352-0.0279-0.080156.6093.1537.625
93.98030.80421.872.58630.86923.3341-0.082-0.3687-0.16720.17990.11090.05080.2058-0.0861-0.0288-0.02270.06260.0092-0.12340.0313-0.121449.3046.5731.78
106.0855-2.2024-2.462216.1266-5.34648.5323-0.00070.07850.5308-0.4218-0.1357-0.7664-0.48230.39230.1364-0.06770.00550.0023-0.0411-0.0202-0.111657.56117.66630.001
113.6321-2.74840.95689.3044-5.4615.27470.28620.34790.0568-0.5534-0.4926-0.70160.30060.5770.2064-0.04640.06030.03640.0892-0.0095-0.016573.305-1.28628.394
123.3992-0.5273-0.11592.19680.73163.56870.0263-0.0101-0.1280.074-0.08830.10990.01380.00310.062-0.08930.0310.0267-0.0770.0091-0.119461.671-1.25633.882
133.7324-0.40230.56583.1172-0.37652.64120.03660.0058-0.0930.01280.0009-0.2250.01610.2472-0.0375-0.09890.03190.0352-0.03930.0216-0.130166.358-1.51132.43
144.7064-9.13785.498643.9204-15.806511.4826-0.35120.29650.86850.8387-0.1907-1.5106-0.75610.77030.5419-0.004-0.0433-0.02110.17330.01980.119778.9653.46136.833
155.9599-2.82361.63115.65951.42834.8275-0.003-0.1579-0.37460.37770.06270.86550.0452-0.1471-0.0597-0.05910.07190.0319-0.07610.02080.07958.84225.6822.952
1622.776627.0170.255843.8595-8.93597.22950.7805-1.3117-2.47921.1392-1.2657-1.89470.6348-0.05780.48520.4820.15250.07720.10720.00780.330313.51310.86833.414
1727.2526-18.7786-7.741823.97167.004615.5075-1.4226-1.7171.22411.89280.9015-0.0162-0.35330.37840.5210.1430.04880.01080.39440.19090.398523.249-6.03338.12
182.06410.17790.53062.464-0.42241.9941-0.05350.1173-0.3413-0.2050.08880.02820.2232-0.0636-0.0352-0.06340.01260.0124-0.05440.0364-0.105745.575-7.76835.122
1919.46133.4881-5.566422.9466-5.649125.6115-0.67542.0955-2.4401-2.52440.65290.99721.9614-2.03110.02250.2765-0.105-0.04030.3056-0.20830.288353.697-14.57823.447
200.031-0.09830.19660.5555-0.7671.3313-0.0246-0.125-0.116-0.01410.08740.08720.0148-0.0767-0.0628-0.0610.0189-0.0089-0.0223-0.0014-0.062838.734-4.06533.107
211.8176-0.2309-0.91295.6550.33171.66010.06980.142-0.07620.4959-0.13710.7020.0206-0.23310.0673-0.05990.069900.0286-0.04080.10169.33824.72323.31
227.76980.8704-5.18558.30774.325211.6322-0.32090.0745-0.12941.1674-0.10961.39941.1608-0.70320.43050.08880.02530.11430.0485-0.07180.276313.13.93820.548
237.9862-2.51213.95165.7541-7.44039.69230.0511-0.0574-0.2905-0.5282-0.2837-0.390.76730.07070.23260.0080.0212-0.0005-0.0936-0.0355-0.032928.723-1.22618.806
248.78451.599-9.178920.0954-5.976323.1043-0.763-0.38-0.13090.92820.26821.75611.556-1.48050.49480.1005-0.11040.06140.39990.1480.489617.238-9.37134.253
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 40
2X-RAY DIFFRACTION2A41 - 120
3X-RAY DIFFRACTION3A121 - 150
4X-RAY DIFFRACTION4A151 - 230
5X-RAY DIFFRACTION5A231 - 304
6X-RAY DIFFRACTION6A305 - 339
7X-RAY DIFFRACTION7C3 - 13
8X-RAY DIFFRACTION8C14 - 30
9X-RAY DIFFRACTION9C31 - 45
10X-RAY DIFFRACTION10C46 - 55
11X-RAY DIFFRACTION11D4 - 31
12X-RAY DIFFRACTION12D32 - 63
13X-RAY DIFFRACTION13D64 - 108
14X-RAY DIFFRACTION14D109 - 124
15X-RAY DIFFRACTION15E1 - 6
16X-RAY DIFFRACTION16E7 - 10
17X-RAY DIFFRACTION17E11 - 15
18X-RAY DIFFRACTION18E16 - 26
19X-RAY DIFFRACTION19E28 - 31
20X-RAY DIFFRACTION20E32 - 45
21X-RAY DIFFRACTION21E46 - 61
22X-RAY DIFFRACTION22F1 - 5
23X-RAY DIFFRACTION23F6 - 9
24X-RAY DIFFRACTION24F10 - 14

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more