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- PDB-4znv: Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) i... -

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Basic information

Entry
Database: PDB / ID: 4znv
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in complex with a 2-Methoxy-substituted OBHS derivative
Components
  • Estrogen receptor
  • Nuclear receptor-interacting peptide
KeywordsTRANSCRIPTION / Nuclear receptor / transcription factor / ligand binding / protein-ligand complex
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / prostate epithelial cord elongation / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / aryl hydrocarbon receptor binding / androgen metabolic process / TFIIB-class transcription factor binding / regulation of lipid metabolic process / steroid hormone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / cellular response to hormone stimulus / Recycling of bile acids and salts / protein localization to chromatin / 14-3-3 protein binding / estrogen receptor signaling pathway / positive regulation of adipose tissue development / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / steroid binding / TBP-class protein binding / nitric-oxide synthase regulator activity / Regulation of lipid metabolism by PPARalpha / regulation of cellular response to insulin stimulus / ESR-mediated signaling / transcription corepressor binding / SUMOylation of transcription cofactors / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / nuclear receptor coactivator activity / positive regulation of nitric-oxide synthase activity / stem cell differentiation / transcription coregulator binding / cellular response to estradiol stimulus / response to progesterone / nuclear receptor binding / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / circadian regulation of gene expression / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / euchromatin / Transcriptional activation of mitochondrial biogenesis / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / transcription coactivator binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / beta-catenin binding / response to estrogen / RNA polymerase II transcription regulator complex / Constitutive Signaling by Aberrant PI3K in Cancer / male gonad development / nuclear receptor activity / Regulation of RUNX2 expression and activity / positive regulation of nitric oxide biosynthetic process / positive regulation of fibroblast proliferation / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / HATs acetylate histones / positive regulation of cytosolic calcium ion concentration / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / fibroblast proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific
Similarity search - Function
Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 ...Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / : / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS 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 / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Ligand-binding domain of nuclear hormone receptor / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-4Q7 / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.771 Å
AuthorsNwachukwu, J.C. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Cavett, V. / Nowak, J. / Houtman, R. ...Nwachukwu, J.C. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Cavett, V. / Nowak, J. / Houtman, R. / Carlson, K.E. / Josan, J.S. / Elemento, O. / Katzenellenbogen, J.A. / Zhou, H.B. / Nettles, K.W.
CitationJournal: Mol.Syst.Biol. / Year: 2016
Title: Predictive features of ligand-specific signaling through the estrogen receptor.
Authors: Nwachukwu, J.C. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Nowak, J. / Wright, N.J. / Houtman, R. / Carlson, K.E. / Josan, J.S. / Elemento, O. / ...Authors: Nwachukwu, J.C. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Nowak, J. / Wright, N.J. / Houtman, R. / Carlson, K.E. / Josan, J.S. / Elemento, O. / Katzenellenbogen, J.A. / Zhou, H.B. / Nettles, K.W.
History
DepositionMay 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
C: Nuclear receptor-interacting peptide
D: Nuclear receptor-interacting peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7526
Polymers61,8194
Non-polymers9332
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-32 kcal/mol
Surface area20420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.817, 81.224, 58.594
Angle α, β, γ (deg.)90.000, 111.210, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 29329.457 Da / Num. of mol.: 2 / Fragment: ligand-binding domain, UNP residues 301-559 / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03372
#2: Protein/peptide Nuclear receptor-interacting peptide / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1579.866 Da / Num. of mol.: 2 / Fragment: UNP residues 686-698 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-4Q7 / 2-methoxyphenyl (1S,2R,4S)-5,6-bis(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonate


Mass: 466.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H22O7S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.06 Å3/Da / Density % sol: 40.28 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 15% PEG 3350, 0.05M MgCl2, 0.067M NaCl, 0.1M Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2011
RadiationMonochromator: Side scattering bent cube i-beam single crystal asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 46159 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.058 / Χ2: 2.84 / Net I/av σ(I): 44.577 / Net I/σ(I): 23.5 / Num. measured all: 170014
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.77-1.83.70.28122731.291100
1.8-1.833.70.23723241.26100
1.83-1.873.80.20723091.342100
1.87-1.913.70.19223211.561100
1.91-1.953.70.15823502.03599.8
1.95-1.993.80.12623041.62100
1.99-2.043.80.10322861.726100
2.04-2.13.70.10323342.31699.9
2.1-2.163.80.0823042.098100
2.16-2.233.70.07723292.392100
2.23-2.313.70.07322962.95399.7
2.31-2.43.70.06623372.963100
2.4-2.513.70.06223153.16499.8
2.51-2.643.70.05823203.40599.8
2.64-2.813.70.05523223.6699.8
2.81-3.033.70.05223253.99599.4
3.03-3.333.60.05223074.60499.1
3.33-3.813.50.05422735.14797.6
3.81-4.83.40.05522875.48896.9
4.8-503.40.05122434.79693.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QA8

2qa8


Resolution: 1.771→32.591 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1969 1936 4.31 %
Rwork0.1778 42948 -
obs0.1786 44884 96.28 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.955 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso max: 128.73 Å2 / Biso mean: 39.4462 Å2 / Biso min: 16.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.3926 Å20 Å25.517 Å2
2---0.4083 Å2-0 Å2
3----0.9843 Å2
Refinement stepCycle: final / Resolution: 1.771→32.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3974 0 66 327 4367
Biso mean--27.25 44 -
Num. residues----499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064185
X-RAY DIFFRACTIONf_angle_d0.9875675
X-RAY DIFFRACTIONf_chiral_restr0.07661
X-RAY DIFFRACTIONf_plane_restr0.004704
X-RAY DIFFRACTIONf_dihedral_angle_d14.4551588
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.771-1.81490.22521250.1955278788
1.8149-1.8640.24971400.2001291193
1.864-1.91880.23781310.2126297893
1.9188-1.98080.26691210.2012300195
1.9808-2.05160.20761430.1909306997
2.0516-2.13370.25171490.1891311698
2.1337-2.23080.23731310.1841310698
2.2308-2.34830.21921510.1719311298
2.3483-2.49540.19351380.1745316399
2.4954-2.6880.18821520.1815316599
2.688-2.95840.21741310.1837317399
2.9584-3.38610.19571490.1807315799
3.3861-4.26460.16351380.1606312897
4.26460.18051370.1751308295
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)
12.05141.1591-2.55030.9258-1.61673.4364-0.77350.765-0.1409-0.02190.41630.36560.112-0.49070.09230.5683-0.0806-0.04640.5737-0.04010.5001-34.76569.7818-5.5433
24.65040.48752.62891.81090.58145.75770.1039-0.5623-0.19760.2538-0.0166-0.0762-0.1664-0.55770.03030.26130.06440.01960.24890.01380.237-23.181921.39017.9787
30.3391-0.8346-0.32942.17040.49151.54140.0616-0.51590.24750.0120.2076-0.6691-0.58031.3666-0.02880.4099-0.1656-0.0641.174-0.22030.55891.47127.303218.7793
42.3023-0.4506-0.22331.89140.28444.1051-0.1163-0.2088-0.18060.07640.01990.04260.10970.06580.02870.20460.0210.01280.17990.02510.1659-14.73117.53945.1016
54.0991.0773-4.31415.9538-1.29094.9463-0.4334-0.2935-0.1382-0.43460.4147-1.3521-0.57231.0913-0.6610.5132-0.17980.01050.6415-0.15480.53161.913830.96996.7134
64.4922-0.01920.39811.11170.06884.1304-0.00560.09170.3263-0.1719-0.0313-0.1126-0.4566-0.0265-0.02260.2490.01990.00930.18130.00710.1755-14.930625.3952-3.5457
71.62572.3406-0.28794.1691-0.54611.97030.41520.3256-0.4045-0.79630.0465-1.1227-0.7960.5295-0.32481.03340.09270.09990.47550.08610.6959-19.76920.6025-11.7479
83.9471-0.0512-0.53985.1184-1.76845.3104-0.08460.0457-0.4399-0.2960.18180.91410.1081-0.78530.19050.1720.0247-0.00740.39730.01320.2435-28.879819.7255-11.2771
93.7938-0.8610.72041.9723-0.58123.41260.09060.21370.1478-0.048-0.1821-0.0194-0.10170.16090.02240.2025-0.0010.01330.1519-0.00330.1544-13.083624.4077-9.2343
101.32121.18830.19391.6721.17051.69030.198-0.17260.02320.069-0.2866-1.10820.82621.0317-0.20690.4090.1772-0.14510.60450.08080.46015.271413.55854.2855
111.1145-0.34-1.18952.34030.29874.1171-0.091-0.7459-0.29280.51410.2951-0.35470.64491.65950.17690.46120.13010.00830.59570.09880.3455-2.40679.52137.7597
124.05-1.29194.9641.329-0.6327.10220.26390.5503-0.1281-0.35591.1856-0.24481.2368-0.50080.03460.5586-0.0080.10680.55290.09250.5381.93256.7171-4.7171
134.289-2.0038-0.45326.64244.1953.44770.42940.59180.008-0.29070.0085-0.8563-0.6430.4333-0.4360.52220.13550.07180.32690.14340.7985-13.779642.0349-27.2564
146.9389-4.5867-0.87884.76891.02980.50350.53460.76570.6422-0.3513-0.5511-0.3431-0.3583-0.25650.10340.38090.1307-0.01770.51420.06540.2445-12.267528.375-34.2191
155.9125-6.0852-3.02897.10413.95875.4601-0.64830.233-0.497-0.1457-0.3587-1.07390.45980.6626-0.75570.36120.05650.14320.38790.04860.44296.336310.3998-36.3933
168.12050.79380.66696.04614.08892.76840.2531.23460.01030.57170.39970.02570.4102-0.13860.47971.08960.0083-0.03350.50050.05930.7777.4742-0.9365-29.813
172.9628-0.7277-0.77262.43630.48292.2846-0.05050.10010.1276-0.07280.0057-0.1367-0.05460.07910.05070.16880.0007-0.03620.1810.01060.17340.251122.194-24.9497
182.27220.694-1.11321.17520.60733.1642-0.38620.0723-0.79190.06760.0265-0.10170.88830.01280.22540.3824-0.01170.07840.2005-0.0190.3721-3.60184.754-22.8683
194.1601-0.8428-1.55373.7938-0.2913.1086-0.02250.1832-0.17390.0146-0.05340.1043-0-0.3330.12210.16410.0235-0.00390.23170.00050.1904-13.699120.8883-24.4632
203.53562.51732.44932.89763.1285.19140.2788-1.37750.50060.27910.00830.1367-0.3544-0.0305-0.39910.5853-0.08970.11160.54350.05020.4996-10.098136.1828-14.5174
214.46170.1939-0.41562.59160.57273.7842-0.03490.2760.9338-0.2773-0.32220.4837-0.9083-0.94220.0270.33620.1329-0.04240.39830.02110.2896-20.592530.1457-24.2204
223.211-0.5679-0.42291.82230.29162.1522-0.138-0.0117-0.11590.0487-0.00450.12730.0432-0.24650.12880.1633-0.0120.00320.1631-0.01660.1367-13.212817.6542-17.0037
232.4608-0.5394-0.98172.29050.17352.1124-0.2584-0.7190.06370.46370.2345-0.39390.03170.84350.14330.2760.04710.01260.41720.04980.336612.672117.9011-18.2031
241.4015-1.80360.11672.49680.52482.8462-0.5415-0.7899-0.35851.3511-0.4019-0.42830.14180.7270.12540.54830.0181-0.03440.59880.12170.51387.297622.6705-7.7646
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 305:310)A305 - 310
2X-RAY DIFFRACTION2(chain A and resid 311:332)A311 - 332
3X-RAY DIFFRACTION3(chain A and resid 333:342)A333 - 342
4X-RAY DIFFRACTION4(chain A and resid 343:409)A343 - 409
5X-RAY DIFFRACTION5(chain A and resid 410:420)A410 - 420
6X-RAY DIFFRACTION6(chain A and resid 421:460)A421 - 460
7X-RAY DIFFRACTION7(chain A and resid 461:471)A461 - 471
8X-RAY DIFFRACTION8(chain A and resid 472:497)A472 - 497
9X-RAY DIFFRACTION9(chain A and resid 498:525)A498 - 525
10X-RAY DIFFRACTION10(chain A and resid 526:531)A526 - 531
11X-RAY DIFFRACTION11(chain A and resid 532:547)A532 - 547
12X-RAY DIFFRACTION12(chain A and resid 548:552)A548 - 552
13X-RAY DIFFRACTION13(chain B and resid 304:309)B304 - 309
14X-RAY DIFFRACTION14(chain B and resid 310:326)B310 - 326
15X-RAY DIFFRACTION15(chain B and resid 327:331)B327 - 331
16X-RAY DIFFRACTION16(chain B and resid 333:337)B333 - 337
17X-RAY DIFFRACTION17(chain B and resid 338:397)B338 - 397
18X-RAY DIFFRACTION18(chain B and resid 398:435)B398 - 435
19X-RAY DIFFRACTION19(chain B and resid 436:458)B436 - 458
20X-RAY DIFFRACTION20(chain B and resid 459:476)B459 - 476
21X-RAY DIFFRACTION21(chain B and resid 477:491)B477 - 491
22X-RAY DIFFRACTION22(chain B and resid 492:528)B492 - 528
23X-RAY DIFFRACTION23(chain B and resid 529:546)B529 - 546
24X-RAY DIFFRACTION24(chain B and resid 547:552)B547 - 552

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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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