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- PDB-7n9o: Estrogen Receptor Alpha Ligand Binding Domain in Complex with Ali... -

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Basic information

Entry
Database: PDB / ID: 7n9o
TitleEstrogen Receptor Alpha Ligand Binding Domain in Complex with Aliphatic SERD S-C10(15)
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / Breast Cancer / Selective Estrogen Receptor Degrader / Aliphatic SERD / Antagonist / Alpha Helical Bundle
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 / 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 ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / 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 / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / steroid hormone receptor signaling pathway / mammary gland alveolus development / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / : / 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 / protein localization to chromatin / 14-3-3 protein binding / TBP-class protein binding / nitric-oxide synthase regulator activity / steroid binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / negative regulation of miRNA transcription / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / SUMOylation of intracellular receptors / euchromatin / negative regulation of DNA-binding transcription factor activity / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / response to estrogen / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / ATPase binding / regulation of inflammatory response / fibroblast proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / Extra-nuclear estrogen signaling / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) ...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 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
Chem-5YR / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDiennet, M. / El Ezzy, M. / Thiombane, K. / Cotnoir-White, D. / Poupart, J. / Gao, Z. / Mendoza, S.R. / Marinier, A. / Gleason, J. / Mader, S.C. / Fanning, S.W.
CitationJournal: To Be Published
Title: Estrogen Receptor Alpha Ligand Binding Domain in Complex with Aliphatic SERD S-C10(15)
Authors: Fanning, S.W. / Mader, S.C.
History
DepositionJun 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,5408
Polymers113,4214
Non-polymers2,1194
Water9,782543
1
A: Estrogen receptor
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7704
Polymers56,7102
Non-polymers1,0602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-17 kcal/mol
Surface area20570 Å2
MethodPISA
2
C: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7704
Polymers56,7102
Non-polymers1,0602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-14 kcal/mol
Surface area20390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.158, 58.158, 274.394
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 28355.207 Da / Num. of mol.: 4 / Mutation: C381S, C417S, C530S, L536S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03372
#2: Chemical
ChemComp-5YR / 10-{[3,17beta-dihydroxyestra-1,3,5(10)-trien-7beta-yl]sulfanyl}-N-methyl-N-propyldecanamide


Mass: 529.817 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H51NO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 66111 / % possible obs: 94.48 % / Redundancy: 5.5 % / CC1/2: 0.99 / Rpim(I) all: 0.011 / Net I/σ(I): 23.83
Reflection shellResolution: 2→2.073 Å / Num. unique obs: 3634 / CC1/2: 0.635

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UFX

5ufx


Resolution: 2→49.54 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 23.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 3346 5.06 %
Rwork0.182 62748 -
obs0.1842 66094 94.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.55 Å2 / Biso mean: 31.3202 Å2 / Biso min: 10.51 Å2
Refinement stepCycle: final / Resolution: 2→49.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7539 0 148 543 8230
Biso mean--38.24 34.72 -
Num. residues----951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077855
X-RAY DIFFRACTIONf_angle_d1.03210630
X-RAY DIFFRACTIONf_dihedral_angle_d11.8651062
X-RAY DIFFRACTIONf_chiral_restr0.0581255
X-RAY DIFFRACTIONf_plane_restr0.0051300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.030.2545630.22451143120642
2.03-2.060.2987800.23471538161856
2.06-2.090.2743980.22632080217874
2.09-2.130.2881170.21932679279697
2.13-2.160.30211570.217628132970100
2.16-2.20.2891360.205827182854100
2.2-2.240.24341370.203128502987100
2.25-2.290.26911290.190127482877100
2.29-2.340.22591630.192427512914100
2.34-2.40.23291450.191227502895100
2.4-2.450.2631610.182527862947100
2.46-2.520.2361640.186528072971100
2.52-2.60.22661480.183226672815100
2.6-2.680.23031550.182527742929100
2.68-2.780.27221530.187328102963100
2.78-2.890.25461660.188927332899100
2.89-3.020.22641400.183727602900100
3.02-3.180.22441380.186227812919100
3.18-3.380.20281510.181127562907100
3.38-3.640.20551660.170227842950100
3.64-40.19861530.15627162869100
4-4.580.21221450.15192775292099
4.58-5.770.18631290.182627942923100
5.77-49.540.19751520.18072735288799
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)
15.4298-3.00931.39985.17-1.384.3614-0.086-0.0845-0.3234-0.01060.07510.5290.8739-0.4762-0.04050.2453-0.18250.02750.2558-0.07790.276216.0134-36.5175-16.4265
20.6123-0.1754-0.76932.606-0.80743.71790.0008-0.0134-0.1007-0.3739-0.10720.05770.494-0.14270.10810.2285-0.0601-0.02390.107-0.00630.170323.7337-32.5059-23.507
31.342-0.06761.66976.31750.51882.087-0.0685-0.4533-0.2470.6466-0.14990.65380.4404-0.64220.20760.3651-0.15970.06330.28890.00330.200621.4071-34.0832-4.5259
42.6599-0.35880.47415.3863-1.03734.74960.0863-0.46740.09890.6945-0.1179-0.55820.10360.28540.05140.3082-0.1055-0.0470.26970.00990.190430.1245-29.4403-4.3547
51.9666-1.21171.03693.25530.556.78470.01090.07510.0364-0.1989-0.05770.166-0.02370.10790.01180.1359-0.0368-0.04410.1026-0.01680.191520.3952-21.2127-22.987
62.8557-1.1014-1.18353.88791.33653.20420.01660.09060.2302-0.7845-0.20990.7609-0.3601-0.925-0.10260.0830.0417-0.10350.3107-0.06270.324313.7065-15.7876-27.3935
79.0209-4.5502-0.58386.72540.20163.34690.0257-0.15460.15730.1003-0.1251-0.2235-0.011-0.12470.08780.1226-0.0672-0.00240.09990.00630.117925.7097-18.6722-14.7708
88.89280.19877.58432.5359-0.10576.49320.5238-0.3405-1.1473-0.14230.1128-0.17161.05571.0114-0.54940.52560.14320.02350.5042-0.0050.415138.6031-36.7426-21.7437
98.31194.39352.21395.99571.69757.0082-0.728-0.2308-0.3755-0.40020.1257-0.06170.7737-0.37530.54420.74720.05540.01450.2735-0.05260.281123.4982-38.9243-36.0108
104.4179-0.1077-0.67891.6805-0.64223.53290.2271-0.09720.47640.0923-0.18970.042-0.90470.38610.02240.3903-0.0553-0.06670.1014-0.01830.294839.53993.9328-19.6709
117.6329-1.9105-3.91793.53711.81577.11280.069-0.08740.2090.3608-0.3047-0.3429-0.20410.53280.16380.2384-0.1141-0.05430.21180.05460.217445.2995-1.9267-16.2255
122.88070.839-0.68541.332-0.3554.6879-0.12740.1405-0.0024-0.27770.0373-0.0422-0.17250.16710.07270.1893-0.0526-0.00350.07120.00340.163838.4424-7.4922-23.3992
134.30650.2304-1.27021.96430.88876.184-0.028-0.32390.04580.24120.00970.17470.01240.02070.04980.1537-0.03550.00280.1046-0.03880.196928.7769-7.2323-13.0482
143.6477-0.0670.7711.9683-0.11253.69230.0014-0.47920.4320.0637-0.14620.2947-0.5517-0.61210.02740.23040.05660.03030.2183-0.10580.285420.6491-4.0668-9.398
155.4815-1.9503-0.58914.4081-0.40522.64780.02890.1078-0.2-0.239-0.10540.0762-0.1463-0.12690.07080.1501-0.0168-0.01530.0615-0.00770.102528.4996-12.6425-21.9322
161.829-2.1405-1.42995.66992.95854.6299-0.3805-0.763-0.13040.35750.4863-1.104-0.06411.6425-0.43510.2106-0.07490.05090.6541-0.11840.454347.4557-9.0297-7.2644
174.21811.23352.05682.40640.93174.83360.2250.1841-0.325-0.1395-0.22570.2390.84250.580.03050.41250.05090.02220.0279-0.03220.35610.0524-20.8374-62.8345
182.8146-0.69460.83750.8705-1.20154.37940.23290.1195-0.2156-0.0761-0.3615-0.14290.67920.26320.13650.24850.1186-0.010.1718-0.01240.19112.8862-14.9964-69.5517
192.4275-0.65180.70260.8686-0.43425.8745-0.0340.2363-0.0535-0.0393-0.2382-0.02260.32920.56570.21030.14870.0547-0.00230.1193-0.01690.14778.5107-9.3185-68.7909
204.0954-2.24531.52883.73141.31152.3997-0.2781-0.7543-0.62960.69290.04450.27221.16820.06190.05450.54020.15670.0780.15710.07870.208811.1925-15.2714-50.2328
215.462-1.27411.1043.20350.31634.2908-0.2581-0.55470.44320.47240.2179-0.1578-0.10790.14390.03830.30310.0774-0.02210.1905-0.01750.15910.8309-5.6251-50.1987
223.83330.7967-0.23273.8069-0.87413.75820.03320.1053-0.1082-0.17350.07540.34910.2556-0.0954-0.0880.15880.014-0.01240.092-0.03920.189-0.5178-10.3865-68.4061
234.61.0595-3.04242.5258-1.72095.3570.08720.7088-0.4406-0.101-0.09870.46360.5458-0.8676-0.13990.233-0.07-0.0220.2169-0.120.3428-8.5074-12.792-73.1065
248.47172.49510.00764.8103-0.54632.62940.0443-0.01550.13740.2326-0.0938-0.05570.0933-0.13020.08280.1690.03340.01120.0706-0.00610.1121-0.0287-3.7938-60.5394
256.90686.57416.50379.06976.18146.1310.70860.1458-0.36370.4584-0.1006-0.6822-0.69631.3324-0.52930.4223-0.13440.06780.6825-0.03440.437122.071-1.4864-67.5124
265.71072.56821.38177.39253.11427.4270.2477-0.7263-0.5537-0.6101-0.6585-0.28680.73820.90880.23490.42050.20640.03750.6320.00330.289916.5177-15.8847-81.7607
272.0320.73780.40073.3631-0.49863.2927-0.17260.27190.29340.14540.31940.4441-0.5995-0.5375-0.09390.22120.1687-0.02010.2582-0.05180.3043-12.927519.1968-65.4929
281.30921.01180.23243.7571-1.88693.9095-0.08290.03860.31160.42140.05690.2159-0.6159-0.27730.0660.31050.0775-0.0090.1335-0.01820.1801-6.545418.7071-58.6566
291.05460.3763-0.44773.1846-0.59093.239-0.00260.21180.05-0.3607-0.1234-0.0449-0.26150.0150.10710.19750.0840.00470.1406-00.1628-2.570313.0357-71.3481
302.83760.977-0.73473.7226-0.71876.55240.1156-0.284-0.40780.23680.0010.21620.0111-0.0038-0.07130.150.02790.03420.1066-0.03080.218-8.41244.5195-58.7808
312.51011.18041.2493.46470.86323.1570.1379-0.1702-0.25230.6974-0.16760.69750.4482-0.8754-0.15230.127-0.04040.1150.3124-0.06510.3463-15.3458-0.9501-55.2048
328.1094.13180.09425.8931-0.43682.44620.03290.1979-0.207-0.0508-0.0898-0.19130.0737-0.15070.0460.12220.0650.00820.1112-0.01210.114-3.42181.9077-67.6624
333.2868-1.81711.32444.88211.32537.23630.4606-0.20070.61310.1449-0.3138-0.9491-0.99181.0888-0.36910.6116-0.12760.17610.2947-0.03830.46053.032719.9709-53.4562
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 309 through 341 )A309 - 341
2X-RAY DIFFRACTION2chain 'A' and (resid 342 through 394 )A342 - 394
3X-RAY DIFFRACTION3chain 'A' and (resid 395 through 407 )A395 - 407
4X-RAY DIFFRACTION4chain 'A' and (resid 408 through 437 )A408 - 437
5X-RAY DIFFRACTION5chain 'A' and (resid 438 through 465 )A438 - 465
6X-RAY DIFFRACTION6chain 'A' and (resid 466 through 496 )A466 - 496
7X-RAY DIFFRACTION7chain 'A' and (resid 497 through 527 )A497 - 527
8X-RAY DIFFRACTION8chain 'A' and (resid 528 through 536 )A528 - 536
9X-RAY DIFFRACTION9chain 'A' and (resid 537 through 550 )A537 - 550
10X-RAY DIFFRACTION10chain 'B' and (resid 306 through 341 )B306 - 341
11X-RAY DIFFRACTION11chain 'B' and (resid 342 through 363 )B342 - 363
12X-RAY DIFFRACTION12chain 'B' and (resid 364 through 438 )B364 - 438
13X-RAY DIFFRACTION13chain 'B' and (resid 439 through 465 )B439 - 465
14X-RAY DIFFRACTION14chain 'B' and (resid 466 through 496 )B466 - 496
15X-RAY DIFFRACTION15chain 'B' and (resid 497 through 526 )B497 - 526
16X-RAY DIFFRACTION16chain 'B' and (resid 527 through 545 )B527 - 545
17X-RAY DIFFRACTION17chain 'C' and (resid 307 through 341 )C307 - 341
18X-RAY DIFFRACTION18chain 'C' and (resid 342 through 371 )C342 - 371
19X-RAY DIFFRACTION19chain 'C' and (resid 372 through 394 )C372 - 394
20X-RAY DIFFRACTION20chain 'C' and (resid 395 through 407 )C395 - 407
21X-RAY DIFFRACTION21chain 'C' and (resid 408 through 438 )C408 - 438
22X-RAY DIFFRACTION22chain 'C' and (resid 439 through 465 )C439 - 465
23X-RAY DIFFRACTION23chain 'C' and (resid 466 through 496 )C466 - 496
24X-RAY DIFFRACTION24chain 'C' and (resid 497 through 527 )C497 - 527
25X-RAY DIFFRACTION25chain 'C' and (resid 528 through 536 )C528 - 536
26X-RAY DIFFRACTION26chain 'C' and (resid 537 through 550 )C537 - 550
27X-RAY DIFFRACTION27chain 'D' and (resid 307 through 341 )D307 - 341
28X-RAY DIFFRACTION28chain 'D' and (resid 342 through 371 )D342 - 371
29X-RAY DIFFRACTION29chain 'D' and (resid 372 through 438 )D372 - 438
30X-RAY DIFFRACTION30chain 'D' and (resid 439 through 465 )D439 - 465
31X-RAY DIFFRACTION31chain 'D' and (resid 466 through 496 )D466 - 496
32X-RAY DIFFRACTION32chain 'D' and (resid 497 through 527 )D497 - 527
33X-RAY DIFFRACTION33chain 'D' and (resid 528 through 545 )D528 - 545

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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

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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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