[English] 日本語
Yorodumi
- PDB-5dig: Crystal Structure of the ER-alpha Ligand-binding Domain in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dig
TitleCrystal Structure of the ER-alpha Ligand-binding Domain in complex with a trifluoromethyl-substituted A-CD ring estrogen derivative (1S,3aR,5S,7aS)-5-[4-hydroxy-2-(trifluoromethyl)phenyl]-7a-methyloctahydro-1H-inden-1-ol
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
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 / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / androgen metabolic process / 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 / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / estrogen response element binding / 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 / Recycling of bile acids and salts / cellular response to hormone stimulus / 14-3-3 protein binding / protein localization to chromatin / estrogen receptor signaling pathway / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / steroid binding / nitric-oxide synthase regulator activity / Regulation of lipid metabolism by PPARalpha / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / regulation of cellular response to insulin stimulus / ESR-mediated signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / transcription corepressor binding / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / response to progesterone / nuclear receptor binding / stem cell differentiation / 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 / Transcriptional activation of mitochondrial biogenesis / euchromatin / 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 / nuclear receptor activity / male gonad development / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / HATs acetylate histones / ATPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / 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 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-5CE / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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
DepositionSep 1, 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 / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
C: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5626
Polymers61,9334
Non-polymers6292
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-28 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.261, 84.179, 58.905
Angle α, β, γ (deg.)90.000, 108.930, 90.000
Int Tables number4
Space group name H-MP1211

-
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 Nuclear receptor coactivator 2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1666.943 Da / Num. of mol.: 2 / Fragment: Nuclear receptor-interacting peptide / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-5CE / (1S,3aR,5S,7aS)-5-[4-hydroxy-2-(trifluoromethyl)phenyl]-7a-methyloctahydro-1H-inden-1-ol


Mass: 314.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21F3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.81 %
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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2010
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. obs: 24833 / % possible obs: 99.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.061 / Χ2: 1.564 / Net I/av σ(I): 28.294 / Net I/σ(I): 12.9 / Num. measured all: 90350
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.24-2.282.80.30211191.69888.7
2.28-2.323.20.27811861.11396.2
2.32-2.363.40.24712281.11698.6
2.36-2.413.50.25612471.14899.4
2.41-2.473.70.212591.1599.9
2.47-2.523.70.1912121.141100
2.52-2.593.80.16812671.147100
2.59-2.663.80.14612321.179100
2.66-2.733.70.13112471.227100
2.73-2.823.80.11512711.193100
2.82-2.923.80.09512391.329100
2.92-3.043.80.08412351.508100
3.04-3.183.80.07512561.712100
3.18-3.353.80.06512671.627100
3.35-3.563.80.04812311.561100
3.56-3.833.70.04612531.85999.7
3.83-4.223.70.04812692.299100
4.22-4.823.70.04712552.587100
4.82-6.083.70.04312692.028100
6.08-503.60.0412912.50199.5

-
Processing

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

2qa8


Resolution: 2.24→42.09 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2122 1918 8.05 %
Rwork0.1859 21921 -
obs0.1881 23839 94.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.26 Å2 / Biso mean: 44.2879 Å2 / Biso min: 18.08 Å2
Refinement stepCycle: final / Resolution: 2.24→42.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3950 0 44 208 4202
Biso mean--31.61 43.23 -
Num. residues----503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024077
X-RAY DIFFRACTIONf_angle_d0.645523
X-RAY DIFFRACTIONf_chiral_restr0.023654
X-RAY DIFFRACTIONf_plane_restr0.005682
X-RAY DIFFRACTIONf_dihedral_angle_d12.5481503
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2385-2.29450.3479980.29971173127171
2.2945-2.35650.23671350.23491446158189
2.3565-2.42580.24441320.21511496162892
2.4258-2.50410.25771280.20561561168994
2.5041-2.59360.23751330.21111572170596
2.5936-2.69740.24091520.20091578173096
2.6974-2.82020.27951460.20691600174698
2.8202-2.96880.25751410.20181602174398
2.9688-3.15480.22751400.19371623176399
3.1548-3.39830.20251380.19311619175799
3.3983-3.740.19791370.17641654179199
3.74-4.28080.19051470.155616471794100
4.2808-5.39160.18251420.155916661808100
5.3916-42.09690.18011490.181616841833100
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)
12.0691.2759-1.84413.8877-2.90152.6444-0.5779-0.12360.0647-0.56770.83610.9799-0.15430.4519-0.70560.8025-0.2482-0.16590.6366-0.11170.675419.864717.752529.367
22.56381.76220.98054.14564.47097.31310.0559-1.19430.65120.19410.1236-0.48950.57010.6199-0.20110.5395-0.0939-0.1230.5562-0.05580.386216.29256.302533.6402
35.36524.46840.63774.2165-0.19570.95030.0716-0.4953-0.15510.4335-0.28950.43530.53740.19250.07750.4946-0.0010.16420.4430.03090.5452-9.3454-8.82332.062
46.15622.8130.46285.35621.15922.74180.0702-0.25850.08990.408-0.02670.2757-0.1346-0.2256-0.13020.26040.04290.04730.25640.04070.2217-5.70771.264327.4342
52.34980.8574-0.45814.40580.37242.91940.2179-0.0920.4525-0.0877-0.0846-0.0176-0.65430.2323-0.13190.3508-0.01610.06380.2347-0.00130.3223.33718.268322.1628
63.94811.4956-2.09334.7036-0.143.5281-0.0762-0.3926-0.53170.2638-0.17730.10690.5852-0.17020.25350.38950.03640.06170.25160.00680.3246-3.2306-14.502924.0103
79.83773.21131.41692.50170.15232.2015-0.03450.3947-0.9142-0.1403-0.0389-0.17290.24450.28580.10230.34930.03820.01740.2693-0.02960.31014.8516-12.153817.856
85.8056-1.1037-0.84035.9479-1.59374.91690.1443-0.1486-0.19480.0116-0.1669-0.0450.17110.46810.05480.2215-0.01190.0080.3027-0.02540.247912.81780.576424.445
96.70483.6332-1.00754.11811.90257.00020.75950.20080.6398-2.7456-1.5150.0236-0.99610.5775-0.11750.9540.16350.18910.6689-0.00640.60988.230414.616912.5868
107.2724-2.4226-0.5573.8779-0.41034.3228-0.0938-0.25970.65630.7984-0.0444-0.2947-0.60680.36060.03290.2565-0.1208-0.00850.4516-0.04870.340820.96487.072122.5615
115.20010.7235-0.64080.945-0.6141.72720.0810.3437-0.2589-0.0486-0.01180.00810.07240.0444-0.06120.3070.0206-0.00810.2595-0.010.24136.4832-2.751914.2422
121.9171.12171.68611.05460.02833.58320.435-0.20620.70270.1363-0.32030.4284-0.5406-0.3655-0.15150.30060.08810.06280.32950.00780.5437-11.90795.416317.166
135.7998-0.20112.36061.76531.40082.53050.45240.6735-0.8231-0.3367-0.0404-0.64920.57151.3936-0.07840.37030.12230.04770.6131-0.02290.598829.9224-7.2512-1.2134
140.26940.06480.17160.334-0.1060.12080.02080.24860.275-0.5857-0.04140.0074-0.4310.16850.04180.77580.0378-0.02310.54920.07710.39717.83579.0093-17.8665
152.6967-0.72641.47883.1707-1.18255.11840.13270.1285-0.3239-0.3767-0.07210.01660.3231-0.0906-0.04880.3069-0.00430.01650.2708-0.01630.235610.4887-4.2208-6.3758
163.147-0.25440.28875.33960.09794.11020.00070.01740.3025-0.3823-0.0710.4289-0.7668-0.24030.17090.61690.0582-0.07140.31880.02390.3816.493614.8294-7.8269
176.1714-3.25655.77084.6873-2.68465.9323-0.1289-0.02081.53520.2713-0.211-0.0108-0.58750.03170.43270.41230.04090.04320.2624-0.02230.325910.582913.24792.3009
182.4101-0.08621.98876.48451.0394.0636-0.09910.18960.2267-0.23990.1077-0.1498-0.24150.37740.05570.26630.00290.05440.30220.0150.236520.62391.04911.8641
193.61793.5811-1.20273.9475-1.6010.8350.2699-0.66070.21920.8113-0.47230.06010.10310.50350.33920.560.11050.00510.8820.05420.4239.5141-14.74358.9365
203.45550.11230.16022.09190.13892.92290.07780.0134-0.26660.0717-0.0745-0.04110.17590.11730.01130.26760.00030.01930.25770.04480.276416.5417-0.98357.3284
217.85060.8655-5.06932.13690.63553.9918-0.01170.69620.1152-0.86070.00120.8722-0.0531-0.8770.0850.55190.001-0.07470.4764-0.03250.4574-3.1842-5.2173-8.0816
220.31720.103-0.12720.0546-0.0450.04420.5769-0.52950.499-0.1799-0.0059-0.2481-0.5098-0.21480.00120.51420.0180.17060.4242-0.01490.5862-6.540517.26826.8024
230.02940.1024-0.08141.1816-1.07641.0597-0.028-0.0975-0.4134-0.505-0.51620.01530.93020.1167-0.1220.79970.0025-0.0460.5819-0.04090.53138.2454-16.3004-11.2202
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 303 through 311 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 312 through 322 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 323 through 338 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 339 through 363 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 364 through 394 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 395 through 420 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 421 through 438 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 439 through 455 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 456 through 470 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 471 through 496 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 497 through 531 )A0
12X-RAY DIFFRACTION12chain 'A' and (resid 532 through 550 )A0
13X-RAY DIFFRACTION13chain 'B' and (resid 305 through 322 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 323 through 338 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 339 through 394 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 395 through 421 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 422 through 438 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 439 through 455 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 456 through 466 )B0
20X-RAY DIFFRACTION20chain 'B' and (resid 467 through 530 )B0
21X-RAY DIFFRACTION21chain 'B' and (resid 531 through 549 )B0
22X-RAY DIFFRACTION22chain 'C' and (resid 687 through 696 )C0
23X-RAY DIFFRACTION23chain 'D' and (resid 687 through 696 )D0

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more