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- PDB-7ujf: Estrogen Receptor Alpha Ligand Binding Domain in Complex with a M... -

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Basic information

Entry
Database: PDB / ID: 7ujf
TitleEstrogen Receptor Alpha Ligand Binding Domain in Complex with a Methylated Lasofoxifene Derivative with Selective Estrogen Receptor Degrader Properties
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / Alpha helical bundle / estrogen receptor / hormone / breast cancer
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 / prostate epithelial cord elongation / epithelial cell development / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / androgen metabolic process / TFIIB-class transcription factor binding / steroid hormone mediated signaling pathway / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / positive regulation of phospholipase C activity / intracellular steroid hormone receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / steroid binding / nitric-oxide synthase regulator activity / ESR-mediated signaling / 14-3-3 protein binding / transcription corepressor binding / negative regulation of miRNA transcription / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of nitric-oxide synthase activity / euchromatin / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / nuclear receptor activity / positive regulation of nitric oxide biosynthetic process / positive regulation of DNA-binding transcription factor activity / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / sequence-specific double-stranded DNA binding / response to estradiol / PIP3 activates AKT signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / positive regulation of cytosolic calcium ion concentration / fibroblast proliferation / regulation of inflammatory response / 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 / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
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-R3V / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHosfield, D.J. / Greene, G.L. / Fanning, S.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Elife / Year: 2022
Title: Stereospecific lasofoxifene derivatives reveal the interplay between estrogen receptor alpha stability and antagonistic activity in ESR1 mutant breast cancer cells.
Authors: Hosfield, D.J. / Weber, S. / Li, N.S. / Suavage, M. / Joiner, C.F. / Hancock, G.R. / Sullivan, E.A. / Ndukwe, E. / Han, R. / Cush, S. / Laine, M. / Mader, S.C. / Greene, G.L. / Fanning, S.W.
History
DepositionMar 30, 2022Deposition site: RCSB / Processing site: RCSB
SupersessionJun 15, 2022ID: 6VMU
Revision 1.0Jun 15, 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
B: Estrogen receptor
A: Estrogen receptor
C: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,3958
Polymers120,6844
Non-polymers1,7104
Water14,934829
1
B: Estrogen receptor
A: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1974
Polymers60,3422
Non-polymers8552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-14 kcal/mol
Surface area20500 Å2
MethodPISA
2
C: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1974
Polymers60,3422
Non-polymers8552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-12 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.655, 58.655, 276.370
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: 30171.119 Da / Num. of mol.: 4
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-R3V / (5R,6S)-5-(4-{2-[(3S)-3-methylpyrrolidin-1-yl]ethoxy}phenyl)-6-phenyl-5,6,7,8-tetrahydronaphthalen-2-ol


Mass: 427.578 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H33NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 829 / 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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 8,000, Tris pH 7.7, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 117080 / % possible obs: 100 % / Redundancy: 4.9 % / Rpim(I) all: 0.083 / Net I/σ(I): 10.1
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 1393 / CC1/2: 0.669

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UFX

5ufx


Resolution: 1.7→47.677 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 26.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 4759 4.98 %
Rwork0.1947 90754 -
obs0.1969 95513 81.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.81 Å2 / Biso mean: 24.0899 Å2 / Biso min: 3.84 Å2
Refinement stepCycle: final / Resolution: 1.7→47.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7393 0 128 829 8350
Biso mean--18.32 31.15 -
Num. residues----938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097893
X-RAY DIFFRACTIONf_angle_d1.21810723
X-RAY DIFFRACTIONf_chiral_restr0.0541270
X-RAY DIFFRACTIONf_plane_restr0.0051328
X-RAY DIFFRACTIONf_dihedral_angle_d14.3952895
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7001-1.71950.3097130.30392868
1.7195-1.73970.3964280.323561817
1.7397-1.76090.2698420.282491425
1.7609-1.78320.3073620.2911111030
1.7832-1.80670.3289690.2924126435
1.8067-1.83140.3139890.2678154441
1.8314-1.85760.31411070.2529189053
1.8576-1.88530.26781430.2337246566
1.8853-1.91480.31081520.2423311985
1.9148-1.94620.29491910.2393358395
1.9462-1.97970.2581820.2385364099
1.9797-2.01570.24962110.22193723100
2.0157-2.05450.27151910.2233601100
2.0545-2.09640.25642190.20823809100
2.0964-2.1420.23351880.19453633100
2.142-2.19180.25011850.20413731100
2.1918-2.24670.2432160.19573709100
2.2467-2.30740.25191880.19393657100
2.3074-2.37530.24221980.19513709100
2.3753-2.4520.27151960.1963748100
2.452-2.53960.24111630.18983750100
2.5396-2.64130.22941950.19223634100
2.6413-2.76150.2682010.18693704100
2.7615-2.9070.25172070.20013718100
2.907-3.08910.22892010.18423725100
3.0891-3.32760.22621900.19663634100
3.3276-3.66240.21971980.17053770100
3.6624-4.1920.21631800.15853715100
4.192-5.28040.18691760.16333685100
5.2804-47.6770.20821780.1954366699
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)
13.90910.93840.72172.62781.68693.7733-0.0130.4941-0.7533-0.6038-0.0396-0.21350.58730.37420.03770.3970.14090.05570.2576-0.0680.407318.033-16.216-25.778
21.92380.05990.10181.6392-0.18060.927-0.0712-0.10270.07670.1417-0.0259-0.2323-0.07390.1878-0.00930.0334-0.0399-0.00910.2051-0.01340.084922.2685.221-19.937
31.870.26910.71490.6590.02541.6979-0.0915-0.29520.1170.0768-0.0168-0.0166-0.1359-0.06130.05340.0139-0.0087-0.02830.1527-0.01840.058614.6275.163-13.95
42.4270.12560.29432.23510.68972.9903-0.0515-0.12270.00160.00520.01220.0498-0.0048-0.14340.0082-0.02580.0201-0.00940.10480.00820.07098.277-1.873-16.209
52.13110.13540.57693.5186-2.50156.6272-0.10250.317-0.3123-0.23590.1297-0.10810.30730.2801-0.04560.149-0.0010.05570.1235-0.08510.17456.739-13.287-27.867
62.89950.47420.17433.9598-0.63541.4265-0.1243-0.0860.0970.05750.028-0.06380.0235-0.00770.0312-0.00450.0294-0.01550.0986-0.00390.02023.419-1.678-15.184
71.6762-0.2442-0.76855.87415.40995.15990.0950.66161.2216-1.25360.19420.205-1.1238-0.2565-0.28080.6106-0.0442-0.09520.34280.13610.574213.28819.32-24.147
87.6252-2.959-5.82452.51982.07086.97910.11040.30470.1352-0.2713-0.0081-0.1909-0.46590.4534-0.10.4324-0.28320.00810.5606-0.01770.18522.1586.245-36.403
91.6829-0.25660.9077.1657-2.32662.39730.1177-0.456-0.610.6253-0.08340.13170.2255-0.3104-0.0320.371-0.1610.10620.28680.04470.3738-18.005-16.229-10.73
101.80720.1603-0.24991.65320.21040.8919-0.06840.12720.1387-0.1893-0.02940.2573-0.0864-0.2166-0.02340.05070.0519-0.02230.21010.00030.0971-22.3786.125-17.984
111.4903-0.26260.55270.6021-0.02721.188-0.06950.27050.0852-0.0858-0.0260.0259-0.08360.06730.02720.01180.0002-0.03740.16290.02260.0537-12.9183.727-24.445
122.9347-0.12460.18933.14560.31754.33730.0126-0.1389-0.09820.20580.0618-0.2132-0.00990.2124-0.06040.0157-0.02330.01690.0920.02760.0903-8.256-5.204-13.874
131.7647-0.6341-0.25972.98892.01944.7979-0.0778-0.2452-0.31710.20330.19120.1040.3798-0.2247-0.12190.1672-0.00850.05420.1130.09610.1997-6.857-13.649-9.362
142.9352-1.4999-0.11694.15741.39061.8457-0.10320.06850.12310.03340.01160.0346-0.01470.01580.0599-0.0017-0.0358-0.00950.09410.00150.0339-3.709-0.964-21.525
151.96382.6573-2.02515.9824-3.54014.17640.1541-0.0680.24140.18610.02040.2454-1.0768-0.1802-0.15760.67320.26790.02010.52440.02750.2161-16.2412.845-6.499
167.0921-4.5345-3.27236.21112.57593.9560.0121-0.09590.05170.06720.0069-0.363-0.34220.2632-0.03750.1567-0.125-0.03710.18630.06830.16513.792-15.205-63.975
172.2301-0.6881-0.45413.57521.05131.5689-0.1023-0.05430.19150.0621-0.04050.1214-0.1112-0.0420.01040.174-0.0613-0.00870.0495-0.02540.07484.141-11.899-66.183
180.46590.0954-0.20691.4029-0.07211.2620.01330.0391-0.003-0.2452-0.062-0.07270.00970.0166-0.00660.1157-0.02490.03150.0151-0.01860.04825.72-22.103-72.311
190.88140.31590.71252.06620.62741.56630.0663-0.0672-0.00110.245-0.0454-0.1032-0.01340.0648-0.04240.2563-0.1126-0.03620.1387-0.01830.09496.279-15.398-50.301
207.99521.58075.09224.18560.73055.6587-0.1242-0.92760.94280.8123-0.18130.535-0.5829-0.80460.30110.4286-0.04850.1150.4037-0.15510.367-7.519-15.68-48.418
215.4687-1.5128-0.6886.99721.88664.45440.0077-0.35110.00320.4264-0.11210.23140.1445-0.1440.09260.1843-0.11730.00330.1364-0.00120.06311.648-25.181-51.801
222.1955-0.1764-0.27632.4679-0.12973.30360.05460.0156-0.1605-0.09810.0061-0.11980.04840.0469-0.07130.0545-0.0380.02140.01460.0030.08249.608-28.921-67.617
232.753-0.80341.41762.6057-1.09995.21960.09090.1197-0.0642-0.3645-0.0541-0.32120.0850.392-0.03360.12470.01330.08870.11910.00120.156815.221-34.69-73.54
244.1871-1.38140.50093.865-0.09241.3689-0.0354-0.11620.07330.049-0.06440.1005-0.00260.0080.05370.0465-0.0667-0.00810.0366-0.01150.01922.621-31.125-61.33
255.9286-5.7187-6.96015.53226.74428.22940.41980.2550.8399-0.47970.06070.454-0.6448-0.7718-0.47270.55420.2343-0.07490.5602-0.04260.4816-9.11-12.789-70.99
265.86742.5689-3.64564.2234-3.73546.5718-0.05260.45770.2608-0.27560.0738-0.0982-0.6138-0.2606-0.01550.79570.09040.02260.26160.01030.19635.572-11.587-82.426
276.6643-2.41122.4664.7723-0.53753.4779-0.1676-0.5142-0.32680.77470.1792-0.57660.30680.0875-0.01620.42290.12690.02640.20450.08950.34644.94-57.701-57.194
280.65230.2445-0.13581.15620.09631.0111-0.06620.0153-0.054-0.1435-0.07010.16250.1328-0.1962-0.06050.1094-0.1192-0.03060.0831-0.02610.0717-13.758-47.475-66.102
292.41840.11840.81452.2401-0.30153.1922-0.06590.01710.0339-0.1561-0.0257-0.0269-0.08280.06220.03630.0895-0.05160.002-0.00640.00160.0684-2.402-42.116-66.935
303.2316-0.315-1.77572.0111.13384.77040.1101-0.3734-0.2660.1584-0.0484-0.21910.43670.224-0.07790.15070.0257-0.05160.15850.08980.17698.317-46.645-55.431
316.0632-1.6877-0.76393.19660.52431.4019-0.02060.02090.0879-0.1171-0.07930.08920.0052-0.0060.06510.1005-0.0329-0.0140.0031-0.02010.028-1.039-37.559-67.572
320.8451-0.69941.7865.4894-5.19047.4375-0.0377-0.2724-0.05710.61780.31050.5786-0.7104-1.1607-0.28590.3172-0.01080.03730.79580.01760.2289-19.387-41.563-52.29
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 307:321 )A307 - 321
2X-RAY DIFFRACTION2( CHAIN A AND RESID 322:371 )A322 - 371
3X-RAY DIFFRACTION3( CHAIN A AND RESID 372:414 )A372 - 414
4X-RAY DIFFRACTION4( CHAIN A AND RESID 421:465 )A421 - 465
5X-RAY DIFFRACTION5( CHAIN A AND RESID 466:496 )A466 - 496
6X-RAY DIFFRACTION6( CHAIN A AND RESID 497:527 )A497 - 527
7X-RAY DIFFRACTION7( CHAIN A AND RESID 528:536 )A528 - 536
8X-RAY DIFFRACTION8( CHAIN A AND RESID 537:545 )A537 - 545
9X-RAY DIFFRACTION9( CHAIN B AND RESID 307:321 )B307 - 321
10X-RAY DIFFRACTION10( CHAIN B AND RESID 322:371 )B322 - 371
11X-RAY DIFFRACTION11( CHAIN B AND RESID 372:437 )B372 - 437
12X-RAY DIFFRACTION12( CHAIN B AND RESID 438:465 )B438 - 465
13X-RAY DIFFRACTION13( CHAIN B AND RESID 466:496 )B466 - 496
14X-RAY DIFFRACTION14( CHAIN B AND RESID 497:528 )B497 - 528
15X-RAY DIFFRACTION15( CHAIN B AND RESID 529:545 )B529 - 545
16X-RAY DIFFRACTION16( CHAIN C AND RESID 309:340 )C309 - 340
17X-RAY DIFFRACTION17( CHAIN C AND RESID 341:363 )C341 - 363
18X-RAY DIFFRACTION18( CHAIN C AND RESID 364:394 )C364 - 394
19X-RAY DIFFRACTION19( CHAIN C AND RESID 395:411 )C395 - 411
20X-RAY DIFFRACTION20( CHAIN C AND RESID 412:420 )C412 - 420
21X-RAY DIFFRACTION21( CHAIN C AND RESID 421:437 )C421 - 437
22X-RAY DIFFRACTION22( CHAIN C AND RESID 438:465 )C438 - 465
23X-RAY DIFFRACTION23( CHAIN C AND RESID 466:496 )C466 - 496
24X-RAY DIFFRACTION24( CHAIN C AND RESID 497:528 )C497 - 528
25X-RAY DIFFRACTION25( CHAIN C AND RESID 529:536 )C529 - 536
26X-RAY DIFFRACTION26( CHAIN C AND RESID 537:550 )C537 - 550
27X-RAY DIFFRACTION27( CHAIN D AND RESID 307:321 )D307 - 321
28X-RAY DIFFRACTION28( CHAIN D AND RESID 322:420 )D322 - 420
29X-RAY DIFFRACTION29( CHAIN D AND RESID 421:465 )D421 - 465
30X-RAY DIFFRACTION30( CHAIN D AND RESID 466:496 )D466 - 496
31X-RAY DIFFRACTION31( CHAIN D AND RESID 497:528 )D497 - 528
32X-RAY DIFFRACTION32( CHAIN D AND RESID 529:546 )D529 - 546

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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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