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- PDB-5kcf: Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) i... -

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Basic information

Entry
Database: PDB / ID: 5kcf
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with an N-ethyl, 4-methoxybenzyl OBHS-N derivative
Components
  • Estrogen receptor
  • NCOA2
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 / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis ...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 / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / epithelial cell development / mammary gland branching involved in pregnancy / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / uterus development / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / steroid hormone receptor signaling pathway / androgen metabolic process / 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 / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Mitochondrial unfolded protein response (UPRmt) / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / cellular response to hormone stimulus / Recycling of bile acids and salts / negative regulation of canonical NF-kappaB signal transduction / estrogen receptor signaling pathway / positive regulation of adipose tissue development / protein localization to chromatin / : / steroid binding / 14-3-3 protein binding / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / peroxisome proliferator activated receptor signaling pathway / TBP-class protein binding / regulation of cellular response to insulin stimulus / nitric-oxide synthase regulator activity / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / positive regulation of nitric-oxide synthase activity / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / ESR-mediated signaling / : / transcription coregulator binding / response to progesterone / nuclear receptor binding / transcription corepressor binding / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / stem cell differentiation / cellular response to estradiol stimulus / SUMOylation of intracellular receptors / circadian regulation of gene expression / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / euchromatin / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / response to estrogen / nuclear receptor activity / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of fibroblast proliferation / male gonad development / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / : / PIP3 activates AKT signaling / response to estradiol / HATs acetylate histones / ATPase binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of inflammatory response
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 domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / 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 / Double treble clef zinc finger, C4 type / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-OB4 / Chem-OB5 / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.07 Å
AuthorsNwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Dharmarajan, V. / Goswami, D. / Kastrati, I. / Novick, S. / Nowak, J. / Zhou, H.B. / Boonmuen, N. ...Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Dharmarajan, V. / Goswami, D. / Kastrati, I. / Novick, S. / Nowak, J. / Zhou, H.B. / Boonmuen, N. / Zhao, Y. / Min, J. / Frasor, J. / Katzenellenbogen, B.S. / Griffin, P.R. / Katzenellenbogen, J.A. / Nettles, K.W.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Full antagonism of the estrogen receptor without a prototypical ligand side chain.
Authors: Srinivasan, S. / Nwachukwu, J.C. / Bruno, N.E. / Dharmarajan, V. / Goswami, D. / Kastrati, I. / Novick, S. / Nowak, J. / Cavett, V. / Zhou, H.B. / Boonmuen, N. / Zhao, Y. / Min, J. / Frasor, ...Authors: Srinivasan, S. / Nwachukwu, J.C. / Bruno, N.E. / Dharmarajan, V. / Goswami, D. / Kastrati, I. / Novick, S. / Nowak, J. / Cavett, V. / Zhou, H.B. / Boonmuen, N. / Zhao, Y. / Min, J. / Frasor, J. / Katzenellenbogen, B.S. / Griffin, P.R. / Katzenellenbogen, J.A. / Nettles, K.W.
History
DepositionJun 6, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionNov 16, 2016ID: 4ZWK
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Dec 28, 2016Group: Database references
Revision 1.3Feb 26, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: Estrogen receptor
B: Estrogen receptor
C: NCOA2
D: NCOA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9206
Polymers61,9334
Non-polymers9872
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-33 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.880, 81.574, 58.898
Angle α, β, γ (deg.)90.000, 110.190, 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: 29299.535 Da / Num. of mol.: 2 / Fragment: ligand-binding domain / 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 NCOA2


Mass: 1666.943 Da / Num. of mol.: 2 / Fragment: Nuclear receptor-interacting peptide / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596*PLUS
#3: Chemical ChemComp-OB5 / (1R,2S,4R)-N-ethyl-5,6-bis(4-hydroxyphenyl)-N-(4-methoxyphenyl)-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonamide


Mass: 493.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H27NO6S
#4: Chemical ChemComp-OB4 / (1S,2R,4S)-N-ethyl-5,6-bis(4-hydroxyphenyl)-N-(4-methoxyphenyl)-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonamide


Mass: 493.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H27NO6S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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 Å3/Da / Density % sol: 38.61 % / Mosaicity: 0.872 °
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: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2012
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: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 29369 / % possible obs: 98.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 29.35 Å2 / Rmerge(I) obs: 0.088 / Χ2: 0.542 / Net I/av σ(I): 16 / Net I/σ(I): 4.4 / Num. measured all: 199461
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.07-2.116.50.8415110.48898.3
2.11-2.146.40.70714380.45498.6
2.14-2.195.90.55614370.44495.2
2.19-2.236.70.59714190.45297.9
2.23-2.286.90.55114880.95998.3
2.28-2.337.10.41414670.47198.7
2.33-2.3970.36114720.4599.4
2.39-2.456.90.3214470.4798.2
2.45-2.5370.26814720.46998.9
2.53-2.616.90.24814900.47399.7
2.61-2.76.80.19814560.50499.1
2.7-2.816.20.16114350.595.5
2.81-2.946.90.13514530.52797.9
2.94-3.097.20.10914920.54499.1
3.09-3.297.10.08814830.57699.4
3.29-3.5470.06914810.60899.8
3.54-3.96.80.06115000.76598.9
3.9-4.466.60.04614110.62395.3
4.46-5.627.10.04315040.5199.7
5.62-506.80.03515130.5297.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1690refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 2.07→46.537 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.57
RfactorNum. reflection% reflection
Rfree0.2361 1863 6.8 %
Rwork0.1897 --
obs0.1929 27407 91.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 129.28 Å2 / Biso mean: 41.2044 Å2 / Biso min: 10.12 Å2
Refinement stepCycle: final / Resolution: 2.07→46.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3770 0 65 185 4020
Biso mean--30.05 39.16 -
Num. residues----482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034006
X-RAY DIFFRACTIONf_angle_d0.6495431
X-RAY DIFFRACTIONf_chiral_restr0.025637
X-RAY DIFFRACTIONf_plane_restr0.002670
X-RAY DIFFRACTIONf_dihedral_angle_d13.7021496
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.068-2.12390.34151380.28391779191784
2.1239-2.18640.28011180.24121774189282
2.1864-2.2570.40681250.31961694181981
2.257-2.33770.28071220.22181810193283
2.3377-2.43130.26571510.20451947209893
2.4313-2.54190.22551370.19932007214494
2.5419-2.67590.22551550.20492038219395
2.6759-2.84360.24571410.20721994213593
2.8436-3.06310.24261400.20182078221897
3.0631-3.37120.2461680.20162091225998
3.3712-3.85890.22441520.17182120227298
3.8589-4.86090.19971550.14552071222696
4.8609-46.54880.20171610.16622141230298
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)
10.30070.0148-0.08420.2853-0.31770.32070.20260.16540.5756-0.2581-0.4474-0.2555-0.3509-0.238500.32530.0726-0.04270.36190.01330.422-14.801234.5649-31.8426
20.24650.51810.4920.5340.2270.24940.13470.2757-0.286-0.2657-0.174-0.34250.3407-0.05780.00020.36960.02760.07470.29130.01270.35814.05667.4165-34.0207
30.79130.2145-0.88810.47840.37740.63150.10610.24850.0328-0.288-0.1309-0.0217-0.110.48580.03350.17720.0441-0.03820.2462-0.00150.20434.42117.7063-28.5808
40.7091-0.1512-0.80540.250.240.63580.0051-0.03980.01660.064-0.0553-0.1267-0.03150.072500.2045-0.0147-0.01630.1981-0.00040.2361-2.867225.8864-22.9426
50.4019-0.6665-0.1490.9795-0.39451.2177-0.50330.0868-0.51480.0498-0.1975-0.50080.59880.2085-0.24620.44590.0030.09210.1898-0.02790.3261-2.67452.8803-26.7341
62.1086-0.3431-0.96780.35210.36430.686-0.0475-0.0113-0.07430.1443-0.10710.17810.1869-0.0337-0.00020.3052-0.03330.00320.2226-0.02710.2168-11.379616.3616-21.8496
70.9179-0.4899-0.47960.7228-0.27960.99750.13880.12410.3376-0.0531-0.17180.136-0.2252-0.27020.13170.18040.0343-0.04070.2293-0.01860.2386-20.54529.8108-23.8031
80.049-0.0352-0.17650.8583-0.36150.6331-0.1634-0.0177-0.29070.2011-0.0481-0.05720.07740.0808-0.00060.3132-0.03020.01110.238-0.00910.2362-9.949216.3272-15.9817
90.2239-0.16620.25980.0868-0.27540.1406-0.4174-0.4672-0.25250.30170.2681-0.3186-0.00550.40180.00060.35710.04930.04120.4850.06850.466911.85918.5273-17.7282
100.02030.11860.10620.14890.0183-0.0030.3619-0.50510.04240.43030.07340.23070.2028-1.13470.00280.2411-0.0454-0.01070.59250.03010.4086-33.330416.3583-1.4481
110.19680.0009-0.24870.50870.02080.1422-0.22720.1564-0.4803-0.17660.3063-0.2869-0.64630.3380.00030.4085-0.0151-0.03180.5196-0.01810.3493-7.724724.856717.9335
120.8337-0.2383-0.51021.03710.20931.1921-0.2572-0.5432-0.20090.14460.11030.06050.2291-0.0331-0.08820.2008-0.02710.04280.14380.01220.1362-14.669713.55617.7558
130.7357-0.41910.33520.1529-0.04210.72020.05260.0903-0.11460.215-0.22970.01280.1895-0.1350.00040.2878-0.00890.03110.238-0.01060.2315-13.817413.97090.4056
140.6391-0.1787-0.15870.1505-0.03960.068-0.1751-0.2127-0.06890.08340.06650.0507-0.7620.5724-0.01890.5325-0.0683-0.02090.3744-0.03840.2832-7.32131.64188.3424
150.3597-0.1205-0.08320.04580.16120.0479-0.1021-0.32360.2781-0.14650.1528-0.3204-0.7520.4053-0.00290.3942-0.13310.00220.2694-0.01630.2964-8.304931.167-2.2115
160.23470.11080.20120.0732-0.02160.42960.19190.08540.0328-0.1825-0.2497-0.0534-0.118-0.334200.29590.01680.0140.3227-0.03120.244-21.734323.1406-3.5277
170.2379-0.20920.1790.0414-0.0231-0.0098-0.16220.1710.3281-0.19670.78390.20710.23260.0606-0.00030.65360.0242-0.00580.45020.01990.402-16.283.9361-12.105
180.6567-0.1453-0.45860.2529-0.44751.4641-0.05310.1864-0.0853-0.3095-0.1397-0.01250.3228-0.54-0.01720.2514-0.00230.00960.3739-0.01080.2916-28.380918.1683-10.8684
19-0.0366-0.7799-0.34340.271-0.51470.7124-0.1299-0.02160.09460.0501-0.0311-0.0006-0.28490.0608-0.00080.244-0.00820.0010.2524-0.0330.2477-13.089124.2746-9.7271
200.65480.43320.15450.37370.23640.55430.22430.0216-0.3866-0.4513-0.3874-0.50880.14180.1569-0.06170.39330.15650.04010.39870.06650.5065-2.68598.44544.6771
210.0152-0.08020.07060.4317-0.10710.0813-0.69810.177-1.4587-0.04870.1575-0.7480.5364-0.10280.01940.42370.0460.08020.20520.12460.7318-15.44490.52338.1066
220.26940.4529-0.08070.8692-0.34270.0332-0.0639-0.24450.7244-0.64240.0153-0.89110.2835-0.1932-0.01840.1783-0.0566-0.00080.3344-0.01260.5779.481533.0584-25.6662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 303 through 322 )A303 - 322
2X-RAY DIFFRACTION2chain 'A' and (resid 323 through 338 )A323 - 338
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 363 )A339 - 363
4X-RAY DIFFRACTION4chain 'A' and (resid 364 through 395 )A364 - 395
5X-RAY DIFFRACTION5chain 'A' and (resid 396 through 420 )A396 - 420
6X-RAY DIFFRACTION6chain 'A' and (resid 421 through 472 )A421 - 472
7X-RAY DIFFRACTION7chain 'A' and (resid 473 through 496 )A473 - 496
8X-RAY DIFFRACTION8chain 'A' and (resid 497 through 529 )A497 - 529
9X-RAY DIFFRACTION9chain 'A' and (resid 530 through 549 )A530 - 549
10X-RAY DIFFRACTION10chain 'B' and (resid 305 through 322 )B305 - 322
11X-RAY DIFFRACTION11chain 'B' and (resid 323 through 338 )B323 - 338
12X-RAY DIFFRACTION12chain 'B' and (resid 339 through 371 )B339 - 371
13X-RAY DIFFRACTION13chain 'B' and (resid 372 through 394 )B372 - 394
14X-RAY DIFFRACTION14chain 'B' and (resid 395 through 421 )B395 - 421
15X-RAY DIFFRACTION15chain 'B' and (resid 422 through 437 )B422 - 437
16X-RAY DIFFRACTION16chain 'B' and (resid 438 through 455 )B438 - 455
17X-RAY DIFFRACTION17chain 'B' and (resid 456 through 469 )B456 - 469
18X-RAY DIFFRACTION18chain 'B' and (resid 470 through 496 )B470 - 496
19X-RAY DIFFRACTION19chain 'B' and (resid 497 through 525 )B497 - 525
20X-RAY DIFFRACTION20chain 'B' and (resid 526 through 548 )B526 - 548
21X-RAY DIFFRACTION21chain 'C' and (resid 688 through 696 )C688 - 696
22X-RAY DIFFRACTION22chain 'D' and (resid 687 through 696 )D687 - 696

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Yorodumi

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  • 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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