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- PDB-4xaj: Crystal structure of human NR2E1/TLX -

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Basic information

Entry
Database: PDB / ID: 4xaj
TitleCrystal structure of human NR2E1/TLX
Components
  • Atrophin/grunge
  • Maltose-binding periplasmic protein,Nuclear receptor subfamily 2 group E member 1
KeywordsTRANSPORT PROTEIN/TRANSCRIPTION / helical sanwich / TRANSPORT PROTEIN-TRANSCRIPTION complex
Function / homology
Function and homology information


forebrain generation of neurons / inter-male aggressive behavior / regulation of timing of neuron differentiation / polytene chromosome interband / anterior commissure morphogenesis / imaginal disc-derived wing vein morphogenesis / imaginal disc-derived leg morphogenesis / regulation of cell migration involved in sprouting angiogenesis / aggressive behavior / segmentation ...forebrain generation of neurons / inter-male aggressive behavior / regulation of timing of neuron differentiation / polytene chromosome interband / anterior commissure morphogenesis / imaginal disc-derived wing vein morphogenesis / imaginal disc-derived leg morphogenesis / regulation of cell migration involved in sprouting angiogenesis / aggressive behavior / segmentation / larval somatic muscle development / amygdala development / negative regulation of neural precursor cell proliferation / cerebral cortex neuron differentiation / segment specification / astrocyte cell migration / layer formation in cerebral cortex / eye development / embryonic pattern specification / olfactory bulb development / dentate gyrus development / astrocyte differentiation / nuclear steroid receptor activity / histone deacetylase activity / regulation of dendrite morphogenesis / positive regulation of neuroblast proliferation / detection of maltose stimulus / negative regulation of epidermal growth factor receptor signaling pathway / maltose transport complex / positive regulation of stem cell proliferation / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / somatic stem cell population maintenance / social behavior / negative regulation of astrocyte differentiation / behavioral fear response / carbohydrate transmembrane transporter activity / negative regulation of neuron differentiation / cell fate commitment / neuroblast proliferation / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / positive regulation of cell cycle / negative regulation of smoothened signaling pathway / visual perception / extracellular matrix organization / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / Regulation of PTEN gene transcription / nuclear receptor binding / long-term synaptic potentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / Nuclear Receptor transcription pathway / positive regulation of angiogenesis / nuclear receptor activity / transcription corepressor activity / sequence-specific double-stranded DNA binding / retina development in camera-type eye / nervous system development / outer membrane-bounded periplasmic space / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / DNA-binding transcription factor binding / periplasmic space / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / DNA damage response / chromatin / negative regulation of apoptotic process / apoptotic process / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / membrane / nucleus
Similarity search - Function
Atrophin-like / Atrophin-1 family / ELM2 domain / ELM2 domain profile. / ELM2 / : / SANT domain profile. / SANT domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain ...Atrophin-like / Atrophin-1 family / ELM2 domain / ELM2 domain profile. / ELM2 / : / SANT domain profile. / SANT domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Homeobox-like domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type
Similarity search - Domain/homology
alpha-maltose / Grunge, isoform J / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein / Grunge, isoform A / Nuclear receptor subfamily 2 group E member 1
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Homo sapiens (human)
DROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.551 Å
AuthorsZhi, X. / Zhou, E. / Xu, E.
CitationJournal: Genes Dev. / Year: 2015
Title: Structural basis for corepressor assembly by the orphan nuclear receptor TLX.
Authors: Zhi, X. / Zhou, X.E. / He, Y. / Searose-Xu, K. / Zhang, C.L. / Tsai, C.C. / Melcher, K. / Xu, H.E.
History
DepositionDec 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references / Source and taxonomy
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / entity_src_gen / 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_entity_src_syn / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_conn / 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_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Nuclear receptor subfamily 2 group E member 1
C: Maltose-binding periplasmic protein,Nuclear receptor subfamily 2 group E member 1
Q: Atrophin/grunge
B: Maltose-binding periplasmic protein,Nuclear receptor subfamily 2 group E member 1
D: Maltose-binding periplasmic protein,Nuclear receptor subfamily 2 group E member 1
P: Atrophin/grunge
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,70710
Polymers258,3386
Non-polymers1,3694
Water00
1
A: Maltose-binding periplasmic protein,Nuclear receptor subfamily 2 group E member 1
C: Maltose-binding periplasmic protein,Nuclear receptor subfamily 2 group E member 1
Q: Atrophin/grunge
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,8545
Polymers129,1693
Non-polymers6852
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-24 kcal/mol
Surface area49660 Å2
MethodPISA
2
B: Maltose-binding periplasmic protein,Nuclear receptor subfamily 2 group E member 1
D: Maltose-binding periplasmic protein,Nuclear receptor subfamily 2 group E member 1
P: Atrophin/grunge
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,8545
Polymers129,1693
Non-polymers6852
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-25 kcal/mol
Surface area49890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.260, 130.743, 308.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Maltose-binding periplasmic protein,Nuclear receptor subfamily 2 group E member 1 / MBP / MMBP / Maltodextrin-binding protein / Nuclear receptor TLX / Protein tailless homolog / hTll


Mass: 63539.387 Da / Num. of mol.: 4
Fragment: maltose binding protein fused ligand binding domain
Mutation: K257R, N259T, K260L, C338V,K257R, N259T, K260L, C338V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, Z5632, ECs5017, NR2E1, TLX / Plasmid: pETduet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0AEY0, UniProt: Q9Y466, UniProt: P0AEX9*PLUS
#2: Protein/peptide Atrophin/grunge


Mass: 2090.319 Da / Num. of mol.: 2 / Fragment: atro box motif / Source method: obtained synthetically / Source: (synth.) DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q8IQA6, UniProt: M9PHT1*PLUS
#3: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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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: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 8, 2012
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.55→39.897 Å / Num. obs: 35657 / % possible obs: 98.2 % / Redundancy: 10.2 % / Net I/σ(I): 8.58

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
Omodel building
PHASERphasing
XDSdata reduction
SCALAdata scaling
RefinementResolution: 3.551→39.897 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3136 2528 7.13 %
Rwork0.2725 --
obs0.2754 35464 97.79 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.551→39.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18008 0 92 0 18100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618500
X-RAY DIFFRACTIONf_angle_d1.37325135
X-RAY DIFFRACTIONf_dihedral_angle_d10.2476795
X-RAY DIFFRACTIONf_chiral_restr0.0582857
X-RAY DIFFRACTIONf_plane_restr0.0073214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5507-3.61890.3631180.33591790X-RAY DIFFRACTION96
3.6189-3.69270.37711360.32321811X-RAY DIFFRACTION100
3.6927-3.7730.33991530.31921809X-RAY DIFFRACTION98
3.773-3.86070.35571310.31521771X-RAY DIFFRACTION97
3.8607-3.95710.36511390.29381841X-RAY DIFFRACTION99
3.9571-4.0640.31321410.29771783X-RAY DIFFRACTION97
4.064-4.18350.29891340.27871820X-RAY DIFFRACTION99
4.1835-4.31840.33211100.27851799X-RAY DIFFRACTION96
4.3184-4.47250.36331540.26731814X-RAY DIFFRACTION98
4.4725-4.65130.29411480.26541801X-RAY DIFFRACTION98
4.6513-4.86270.30791240.2721844X-RAY DIFFRACTION97
4.8627-5.11860.30371370.26351820X-RAY DIFFRACTION98
5.1186-5.43850.3551460.27111825X-RAY DIFFRACTION98
5.4385-5.85720.31281640.29551807X-RAY DIFFRACTION98
5.8572-6.44440.34961310.28481868X-RAY DIFFRACTION98
6.4444-7.37190.28131610.27511837X-RAY DIFFRACTION98
7.3719-9.26850.281380.22641919X-RAY DIFFRACTION98
9.2685-39.89950.2311630.20331977X-RAY DIFFRACTION98
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)
10.60190.38030.07561.1032-0.36480.96430.0902-0.2826-0.50070.58410.09550.4364-0.2260.0380.00130.4495-0.08310.0390.5187-0.00580.3287-0.657446.1550.6854
21.63160.52270.2050.5278-0.03910.82520.03450.0347-0.0105-0.0113-0.07030.05660.08850.1566-0.01470.28850.0351-0.06250.35470.09150.16288.358638.526532.7301
31.73130.0391-0.0381.07130.51321.4280.0931-0.1748-0.24040.42330.0106-0.16770.03960.1016-0.00150.2651-0.047-0.05290.16920.02490.22811.982133.584527.0275
41.21470.16370.46090.85510.58150.7633-0.0963-0.0882-0.04670.24770.0654-0.2016-0.0340.4122-0.01490.3055-0.12860.00090.2964-0.01360.227611.689243.892239.5403
51.4212-0.0713-0.27280.8902-0.08841.3593-0.1540.27150.72920.98020.06870.6409-0.8216-0.93330.06540.074-0.0883-0.07350.3086-0.05070.435-10.502540.565223.6776
61.57140.490.78941.4532-0.00011.13290.25430.01220.31190.2865-0.29590.89580.1218-0.2931-0.01210.2354-0.0320.13670.2973-0.04010.4097-9.458556.32952.2584
72.01841.3328-2.17121.63020.83391.2186-0.07520.330.365-0.09970.24770.2021-0.2234-0.38970.00330.2905-0.08770.04150.20930.05720.2881.69257.3736-1.6233
80.21450.0964-0.69121.4774-0.12411.220.13730.61540.5654-0.07220.15250.0536-0.2627-0.4236-0.01050.84210.0679-0.0911.09940.20580.68364.269853.1827-57.3725
91.0037-0.71670.18370.9002-0.1782.2296-0.33050.41020.0266-0.3430.17680.0642-0.2112-0.0163-0.00191.01840.00990.02681.2340.19750.61138.077146.6061-62.6847
101.3764-0.4790.31.75490.10952.73670.01140.24490.0863-0.2274-0.11320.3233-0.0036-0.1645-0.00870.1654-0.0369-0.03250.17940.02050.34368.655637.5357-18.865
111.64610.4279-0.20130.53390.49141.57290.9937-0.0963-1.2138-0.5807-0.1670.03360.5284-0.7014-0.01230.3911-0.05020.00830.3148-0.05460.3674-1.830229.3267-22.7409
120.4431-0.35030.21820.7979-0.05450.30080.70550.6809-1.3614-0.46630.77410.5220.37420.08810.07760.52290.04090.0527-0.4222-1.55880.0245-0.476122.3616-30.5812
130.73310.02760.28910.9225-0.27911.32990.40160.06270.7072-0.5648-0.14231.3923-0.1842-0.42570.00390.44240.1698-0.1740.50850.242-0.1196-29.981818.9727-205.0399
141.381-0.1232-0.81881.31760.99841.96960.10130.10460.2056-0.17340.0416-0.0769-0.06760.2837-0.01620.25010.0331-0.03440.23140.11910.1813-22.16427.048-187.4133
151.0978-0.1616-0.12610.75770.25420.3486-0.788-0.4247-0.2730.030.4695-0.3222-0.71510.01440.0024-0.12-0.06650.12820.27260.06790.4718-27.151123.4221-182.937
160.2215-0.80210.48571.552-0.96890.7780.3936-0.0879-0.4628-1.9306-0.40430.64292.0684-0.6303-0.1964-0.4885-0.1712-0.34640.557-0.08660.3902-37.30668.998-164.0191
173.0832-1.50150.5352.63570.8961.4267-0.0144-0.1403-0.28120.2225-0.0060.3862-0.0623-0.4277-0.01130.15530.0531-0.04560.2260.02120.2737-32.61410.1338-153.3198
180.04020.17360.27390.3991-0.20890.24390.3659-0.859-1.1014-0.0435-0.2257-0.18150.1996-0.09980.01781.1264-0.4228-0.28661.27410.59491.5193-31.16679.1768-102.8126
190.96410.4358-0.01110.25370.13851.33650.422-1.0314-0.24570.6021-0.5995-0.27520.2371-0.2119-0.01711.5491-0.5169-0.33041.62760.39210.8804-21.063121.2047-88.9297
201.73360.9293-0.07522.1087-0.40291.63660.0741-0.5136-0.03490.3535-0.16940.08740.1885-0.30470.01270.35770.03530.04610.273-0.07850.3987-22.595729.5507-127.4036
210.73661.4732-0.89951.75950.46022.2360.03420.38190.04340.10440.06650.1168-0.0696-0.06020.00010.2715-0.0453-0.01530.11980.01010.2924-17.00325.1326-148.0196
221.2078-0.81750.15460.93090.42741.6373-0.02860.08250.60250.13410.2874-0.3999-0.7434-0.56950.01320.44380.00350.09620.2897-0.07710.4822-30.910436.1114-131.682
231.29010.1701-0.0190.67150.130.13490.2458-0.63620.76840.4071-0.10530.7366-0.04660.1280.00910.47150.1560.35340.7936-0.55480.9532-29.699143.2464-123.5693
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 155 )
3X-RAY DIFFRACTION3chain 'A' and (resid 156 through 247 )
4X-RAY DIFFRACTION4chain 'A' and (resid 248 through 335 )
5X-RAY DIFFRACTION5chain 'A' and (resid 336 through 369 )
6X-RAY DIFFRACTION6chain 'A' and (resid 370 through 1277 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1278 through 1383 )
8X-RAY DIFFRACTION8chain 'C' and (resid 3 through 155 )
9X-RAY DIFFRACTION9chain 'C' and (resid 156 through 354 )
10X-RAY DIFFRACTION10chain 'C' and (resid 355 through 1352 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1353 through 1382 )
12X-RAY DIFFRACTION12chain 'Q' and (resid 1814 through 1831 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1 through 74 )
14X-RAY DIFFRACTION14chain 'B' and (resid 75 through 316 )
15X-RAY DIFFRACTION15chain 'B' and (resid 317 through 353 )
16X-RAY DIFFRACTION16chain 'B' and (resid 354 through 1210 )
17X-RAY DIFFRACTION17chain 'B' and (resid 1211 through 1382 )
18X-RAY DIFFRACTION18chain 'D' and (resid 3 through 98 )
19X-RAY DIFFRACTION19chain 'D' and (resid 99 through 354 )
20X-RAY DIFFRACTION20chain 'D' and (resid 355 through 1277 )
21X-RAY DIFFRACTION21chain 'D' and (resid 1278 through 1352 )
22X-RAY DIFFRACTION22chain 'D' and (resid 1353 through 1382 )
23X-RAY DIFFRACTION23chain 'P' and (resid 1814 through 1831 )

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  • 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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