[English] 日本語
Yorodumi
- PDB-2p15: Crystal structure of the ER alpha ligand binding domain with the ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2p15
TitleCrystal structure of the ER alpha ligand binding domain with the agonist ortho-trifluoromethylphenylvinyl estradiol
Components
  • Estrogen receptor
  • GRIP peptide
KeywordsHORMONE RECEPTOR / nulear receptor / ligand binding domain / helix 12
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 / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / uterus development / mammary gland branching involved in pregnancy / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / steroid hormone receptor signaling pathway / regulation of lipid metabolic process / androgen metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / cellular response to estrogen stimulus / mammary gland alveolus development / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Mitochondrial unfolded protein response (UPRmt) / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / transcription regulator inhibitor activity / Nuclear signaling by ERBB4 / cellular response to hormone stimulus / Recycling of bile acids and salts / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / estrogen receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / positive regulation of adipose tissue development / 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 / positive regulation of nitric-oxide synthase activity / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / ESR-mediated signaling / positive regulation of DNA-binding transcription factor activity / transcription coregulator binding / response to progesterone / transcription corepressor binding / nuclear receptor binding / nuclear estrogen receptor binding / negative regulation of smoothened signaling pathway / negative regulation of DNA-binding transcription factor activity / 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 / Transcriptional activation of mitochondrial biogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / transcription coactivator binding / euchromatin / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / response to estrogen / nuclear receptor activity / positive regulation of fibroblast proliferation / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / : / response to estradiol / PIP3 activates AKT signaling / HATs acetylate histones / ATPase binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
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 / 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-EZT / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsBruning, J.B. / Nettles, K.W. / Greene, G.L. / Kim, Y.
CitationJournal: Embo Rep. / Year: 2007
Title: Structural plasticity in the oestrogen receptor ligand-binding domain.
Authors: Nettles, K.W. / Bruning, J.B. / Gil, G. / O'Neill, E.E. / Nowak, J. / Guo, Y. / Kim, Y. / DeSombre, E.R. / Dilis, R. / Hanson, R.N. / Joachimiak, A. / Greene, G.L.
History
DepositionMar 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
C: GRIP peptide
D: GRIP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8186
Polymers61,9334
Non-polymers8852
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-23 kcal/mol
Surface area20770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.052, 84.220, 58.693
Angle α, β, γ (deg.)90.00, 109.59, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Estrogen receptor / ER / Estradiol receptor / ER-alpha


Mass: 29386.609 Da / Num. of mol.: 2 / Fragment: Ligand Binding Domain (residues 298-554) / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: P03372
#2: Protein/peptide GRIP peptide


Mass: 1579.866 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence can be naturally found in Homo sapiens (Human).
References: UniProt: Q15596
#3: Chemical ChemComp-EZT / (17BETA)-17-{(E)-2-[2-(TRIFLUOROMETHYL)PHENYL]VINYL}ESTRA-1(10),2,4-TRIENE-3,17-DIOL


Mass: 442.513 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H29F3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 4000, 0.2M Ammonium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921
DetectorType: SBC-2 / Detector: CCD / Date: Aug 23, 2004 / Details: SI 111 MONOCHROMATOR
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionRedundancy: 4.7 % / Av σ(I) over netI: 6.6 / Number: 186764 / Rmerge(I) obs: 0.08 / Χ2: 0.9 / D res high: 1.87 Å / D res low: 50 Å / Num. obs: 39661 / % possible obs: 92.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.035099.310.0491.8184.8
3.24.0399.910.0571.4555
2.793.299.810.0761.0415.1
2.542.7999.610.0990.7885.1
2.362.5499.510.1180.6315.1
2.222.3699.210.1530.6175.1
2.112.2299.210.1990.5335
2.012.1197.410.2640.5394.2
1.942.0174.410.3260.5213.7
1.871.9455.210.3950.4733
ReflectionResolution: 1.87→50 Å / Num. all: 39661 / Num. obs: 39661 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 20.061 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Χ2: 0.896 / Net I/σ(I): 6.6
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 3 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 1.738 / Num. unique all: 2369 / Rsym value: 0.395 / Χ2: 0.473 / % possible all: 55.2

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→27.71 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.303 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.167 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1871 5.1 %RANDOM
Rwork0.158 ---
all0.161 36913 --
obs0.161 36913 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.061 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.01 Å2
2--0.12 Å20 Å2
3----0.04 Å2
Refine analyzeLuzzati coordinate error obs: 0.215 Å / Luzzati d res low obs: 27.71 Å
Refinement stepCycle: LAST / Resolution: 1.94→27.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4007 0 64 461 4532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214247
X-RAY DIFFRACTIONr_angle_refined_deg1.35825779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0055536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21124.171175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97615802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5811523
X-RAY DIFFRACTIONr_chiral_restr0.0980.2685
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023063
X-RAY DIFFRACTIONr_nbd_refined0.2090.22153
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22944
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2331
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4090.228
X-RAY DIFFRACTIONr_mcbond_it1.0031.52686
X-RAY DIFFRACTIONr_mcangle_it1.19424151
X-RAY DIFFRACTIONr_scbond_it2.16431780
X-RAY DIFFRACTIONr_scangle_it3.144.51610
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 98 -
Rwork0.181 1917 -
obs-2015 72.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.966-3.27913.5743.4671-2.46294.89620.10840.2009-0.039-0.2578-0.1249-0.10270.12710.22860.0165-0.0091-0.01930.03710.0071-0.0411-0.0295-17.966-1.32518.541
25.9577-3.56483.05843.9804-2.00992.84420.03170.0603-0.0396-0.2544-0.0074-0.02120.2032-0.0627-0.02420.0590.00530.0221-0.00520.0007-0.034-27.816-3.82516.468
36.6296-5.34451.45812.3602-0.11542.22330.12420.081-0.45880.0144-0.09370.03070.502-0.0868-0.03060.1126-0.00060.0033-0.02430.00270.0296-26.574-16.09726.365
43.47640.59910.46254.8479-1.18081.44440.04150.03180.16140.0139-0.1107-0.1178-0.05870.1430.06920.02140.01290.00590.01250.0054-0.044-25.7383.76423.694
52.24980.96992.71877.09243.748311.625-0.13910.13690.3587-0.33560.04880.0328-0.616-0.02630.09030.08770.0187-0.0288-0.09270.0286-0.0229-28.08713.29717.164
60.61424.36-0.881230.9494-6.25491.26410.5616-0.71521.08231.169-0.09790.2907-0.8903-0.2144-0.46370.24960.10040.07350.1014-0.04140.2606-40.81714.76720.752
723.11520.52826.25934.2287-0.76861.9423-0.2791-0.20680.48290.15760.08260.074-0.3207-0.19010.19650.06940.01930.0193-0.05070.0014-0.0235-30.23211.45729.025
82.90262.27410.38996.1413-0.36821.554-0.0088-0.00320.1370.0896-0.02290.1106-0.07340.13130.03170.02850.007-0.00270.02020.0065-0.003-19.7450.26230.709
99.97946.3815-3.577413.228-2.41588.57860.44060.555-0.7388-0.0504-0.29110.12630.425-0.2081-0.14950.09140.0269-0.0204-0.0229-0.00070.0802-25.701-23.40336.421
1033.143227.64795.499825.76565.773318.33370.449-0.6327-1.21620.1703-0.333-0.83371.1966-0.1732-0.116-0.0070.0156-0.0127-0.11710.0639-0.0121-18.543-16.68536.267
114.54214.7041.435410.46421.98831.2829-0.06470.04410.0345-0.20010.0155-0.23960.02870.35350.0493-0.00960.02190.02560.07250.0420.057-8.991-1.45835.587
129.46021.43851.93473.2087-0.29043.2294-0.0087-0.12230.21840.077-0.0008-0.3091-0.13740.11340.00950.0287-0.01140.00670.0196-0.00790.0418-13.2315.22741.371
139.33570.31766.66370.840.83266.88520.0284-0.08080.01240.1006-0.0240.13070.1148-0.2007-0.00440.06080.02290.0345-0.00260.0156-0.003-34.6821.25630.861
1413.0204-11.2482-3.162112.34082.51994.89490.51490.7148-0.0763-0.5286-0.49280.788-0.1957-0.4293-0.0220.0397-0.0323-0.11190.056-0.01290.0475-43.784-2.65116.267
1510.78133.2026-2.67797.99729.084719.4172-0.188-0.2972-0.81660.1028-0.49770.39450.3273-0.87180.6857-0.0095-0.0155-0.0225-0.063-0.02440.0508-39.353-10.05423.495
1616.25486.9807-1.35123.5815-0.26012.2264-0.0915-0.53770.25790.15350.0547-0.0018-0.26680.47560.03680.0907-0.0004-0.03780.1214-0.0422-0.026-27.0283.9860.254
172.41552.86430.11695.4481-0.622.19430.1013-0.1002-0.15670.41260.05010.30360.2091-0.1744-0.15140.04170.01940.03860.0450.02780.071-52.105-10.23453.814
1811.26534.9717-3.12677.9628-1.50567.07420.4355-0.22890.46220.2339-0.0210.3001-0.5152-0.1626-0.41440.05060.01930.03070.0048-0.0034-0.0099-41.3834.16657.117
191.4070.4158-0.23094.7495-0.24631.82460.0697-0.06880.15270.15150.0054-0.042-0.27240.0737-0.07510.0577-0.00380.01940.0111-0.02280.012-34.6086.8150.495
202.91350.9627-0.00023.0970.75855.6454-0.0924-0.1403-0.41380.4857-0.05490.10220.48410.11870.14730.10360.0170.03140.00180.03220.085-39.533-15.98753.382
213.4511-3.8549-0.901913.2896-6.6956.83960.75680.3857-0.52350.1785-0.34830.87130.45030.1689-0.40850.0492-0.0497-0.030.0917-0.0490.0925-49.176-15.56443.341
2224.59621.89447.27185.02881.94974.87190.06780.2413-0.6003-0.3507-0.005-0.01990.1811-0.0356-0.06280.0705-0.02290.0236-0.0676-0.0130.0068-35.536-13.55343.372
235.4538-1.05470.444713.01761.16572.3859-0.0719-0.3908-0.5363-0.05040.1256-0.14130.19730.2341-0.05370.0320.0166-0.00510.04750.05520.0518-23.571-8.53852.706
243.5426-1.21120.28329.1538-3.5663.71250.0481-0.03130.2414-0.09960.0557-0.0049-0.1090.0791-0.10380.0326-0.02740.02250.0332-0.02510.0186-28.7835.45646.709
255.61272.057-0.061913.60042.40663.5492-0.0650.63930.8772-1.2995-0.12650.4033-0.4954-0.1350.19150.2717-0.0310.0713-0.01690.08230.0994-27.70419.44440.857
2611.0808-9.81783.154518.5769-6.40552.9087-0.0394-0.60050.24480.3738-0.0764-0.2016-0.22680.35040.1158-0.008-0.0657-0.03430.094-0.0347-0.0517-16.3184.05350.863
2714.9819-1.34823.96420.9287-1.28162.1602-0.01160.0382-0.17680.0231-0.0477-0.09810.05030.12280.05930.0366-0.00020.01690.02160.01610.0226-17.488-5.44243.722
2818.28-0.3502-2.12720.39940.15620.29460.05790.38520.1836-0.08490.04080.1526-0.0078-0.1386-0.09860.0560.0002-0.00490.03420.01670.027-46.61-2.89340.16
297.71045.0592-0.87959.56711.971712.3506-0.2688-0.2080.3232-0.195-0.00920.1643-0.288-0.42470.2779-0.06630.0086-0.0073-0.0683-0.03740.0413-49.4575.66547.663
3046.40854.650616.414817.23064.74224.6393-0.18491.19380.7934-1.23510.20450.1666-0.4167-0.3809-0.01960.0885-0.0043-0.02910.06260.014-0.0271-45.7196.95237.709
3147.4285-7.967827.189632.59993.789524.05061.47651.7677-1.6747-1.0332-0.68451.21851.45880.037-0.79210.08440.0287-0.0839-0.1252-0.1074-0.1177-29.725-17.90315.895
3233.908111.18265.790530.10539.176726.5868-0.1686-0.23172.4130.3283-0.30551.685-0.7634-1.57350.4741-0.12380.03410.0859-0.1168-0.07520.1235-44.88315.99253.376
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA306 - 33810 - 42
22AA339 - 36743 - 71
33AA368 - 38272 - 86
44AA383 - 39787 - 101
55AA398 - 411102 - 115
66AA412 - 421116 - 125
77AA422 - 435126 - 139
88AA436 - 460140 - 164
99AA461 - 471165 - 175
1010AA472 - 477176 - 181
1111AA478 - 496182 - 200
1212AA497 - 508201 - 212
1313AA509 - 526213 - 230
1414AA527 - 540231 - 244
1515AA541 - 549245 - 253
1616BB306 - 32910 - 33
1717BB330 - 35134 - 55
1818BB352 - 35956 - 63
1919BB360 - 39564 - 99
2020BB396 - 413100 - 117
2121BB414 - 421118 - 125
2222BB422 - 434126 - 138
2323BB435 - 447139 - 151
2424BB448 - 458152 - 162
2525BB459 - 474163 - 178
2626BB475 - 495179 - 199
2727BB496 - 513200 - 217
2828BB514 - 535218 - 239
2929BB536 - 544240 - 248
3030BB545 - 550249 - 254
3131CC687 - 6972 - 12
3232DD686 - 6961 - 11

+
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