[English] 日本語
Yorodumi
- PDB-5kcf: Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) i... -

+
Open data


ID or keywords:

Loading...

-
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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / antral ovarian follicle growth / 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 / nuclear estrogen receptor activity / epithelial cell development / steroid hormone receptor signaling pathway ...regulation of epithelial cell apoptotic process / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / antral ovarian follicle growth / 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 / nuclear estrogen receptor activity / epithelial cell development / steroid hormone receptor signaling pathway / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / locomotor rhythm / mammary gland branching involved in pregnancy / uterus development / negative regulation of smooth muscle cell apoptotic process / aryl hydrocarbon receptor binding / vagina development / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / 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 / positive regulation of DNA-binding transcription factor activity / negative regulation of DNA-binding transcription factor activity / Nuclear signaling by ERBB4 / cellular response to hormone stimulus / Recycling of bile acids and salts / RNA polymerase II preinitiation complex assembly / transcription regulator inhibitor activity / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / protein localization to chromatin / : / steroid binding / positive regulation of adipose tissue development / 14-3-3 protein binding / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / negative regulation of canonical NF-kappaB signal transduction / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / ESR-mediated signaling / negative regulation of miRNA transcription / TBP-class protein binding / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / nuclear receptor binding / transcription corepressor binding / transcription coregulator binding / negative regulation of smoothened signaling pathway / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / euchromatin / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Cytoprotection by HMOX1 / beta-catenin binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / response to estrogen / RNA polymerase II transcription regulator complex / transcription coactivator binding / male gonad development / nuclear receptor activity / positive regulation of fibroblast proliferation / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / : / response to estradiol / PIP3 activates AKT signaling / HATs acetylate histones / positive regulation of cytosolic calcium ion concentration / 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 / regulation of inflammatory response / 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) / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 ...Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / 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 / Nuclear receptor coactivators bHLH domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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