[English] 日本語
Yorodumi
- PDB-2q59: Crystal Structure of PPARgamma LBD bound to full agonist MRL20 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q59
TitleCrystal Structure of PPARgamma LBD bound to full agonist MRL20
Components(Peroxisome Proliferator-Activated Receptor gamma) x 2
KeywordsLigand binding protein / Protein-ligand complex
Function / homology
Function and homology information


prostaglandin receptor activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / positive regulation of cholesterol transport / negative regulation of cardiac muscle hypertrophy in response to stress / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of low-density lipoprotein receptor activity ...prostaglandin receptor activity / negative regulation of connective tissue replacement involved in inflammatory response wound healing / negative regulation of receptor signaling pathway via STAT / MECP2 regulates transcription factors / negative regulation of extracellular matrix assembly / negative regulation of vascular endothelial cell proliferation / positive regulation of cholesterol transport / negative regulation of cardiac muscle hypertrophy in response to stress / negative regulation of cellular response to transforming growth factor beta stimulus / positive regulation of low-density lipoprotein receptor activity / arachidonate binding / positive regulation of adiponectin secretion / lipoprotein transport / negative regulation of sequestering of triglyceride / DNA binding domain binding / macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / STAT family protein binding / WW domain binding / positive regulation of fatty acid metabolic process / response to lipid / negative regulation of SMAD protein signal transduction / LBD domain binding / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / E-box binding / alpha-actinin binding / lipid homeostasis / negative regulation of vascular associated smooth muscle cell proliferation / R-SMAD binding / monocyte differentiation / negative regulation of blood vessel endothelial cell migration / negative regulation of macrophage derived foam cell differentiation / cellular response to low-density lipoprotein particle stimulus / negative regulation of lipid storage / white fat cell differentiation / negative regulation of BMP signaling pathway / positive regulation of cholesterol efflux / negative regulation of mitochondrial fission / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / cell fate commitment / negative regulation of MAPK cascade / BMP signaling pathway / retinoic acid receptor signaling pathway / long-chain fatty acid transport / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cell maturation / negative regulation of signaling receptor activity / epithelial cell differentiation / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / hormone-mediated signaling pathway / regulation of cellular response to insulin stimulus / negative regulation of angiogenesis / response to nutrient / negative regulation of miRNA transcription / Regulation of PTEN gene transcription / transcription coregulator binding / fatty acid metabolic process / positive regulation of apoptotic signaling pathway / negative regulation of smooth muscle cell proliferation / negative regulation of transforming growth factor beta receptor signaling pathway / peptide binding / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / placenta development / regulation of circadian rhythm / PPARA activates gene expression / lipid metabolic process / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / negative regulation of inflammatory response / regulation of blood pressure / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / nuclear receptor activity / rhythmic process / glucose homeostasis / cellular response to hypoxia / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / sequence-specific DNA binding / nucleic acid binding / cell differentiation / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / intracellular membrane-bounded organelle / innate immune response / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression
Similarity search - Function
Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type ...Peroxisome proliferator-activated receptor gamma / Peroxisome proliferator-activated receptor gamma, N-terminal / PPAR gamma N-terminal region / Peroxisome proliferator-activated receptor / : / Retinoid X Receptor / Retinoid X 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-240 / Peroxisome proliferator-activated receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBruning, J.B. / Nettles, K.W.
CitationJournal: Structure / Year: 2007
Title: Partial Agonists Activate PPARgamma Using a Helix 12 Independent Mechanism
Authors: Bruning, J.B. / Chalmers, M.J. / Prasad, S. / Busby, S.A. / Kamenecka, T.M. / He, Y. / Nettles, K.W. / Griffin, P.R.
History
DepositionMay 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peroxisome Proliferator-Activated Receptor gamma
B: Peroxisome Proliferator-Activated Receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7224
Polymers62,6672
Non-polymers1,0552
Water4,396244
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.161, 63.939, 119.187
Angle α, β, γ (deg.)90.000, 103.430, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-7087-

HOH

-
Components

#1: Protein Peroxisome Proliferator-Activated Receptor gamma / PPAR-gamma


Mass: 31371.428 Da / Num. of mol.: 1 / Fragment: Ligand binding domain
Source method: isolated from a genetically manipulated source
Details: CYS A 285 IS 2-HYDROXYETHYLATED / Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: P37231
#2: Protein Peroxisome Proliferator-Activated Receptor gamma / PPAR-gamma


Mass: 31295.314 Da / Num. of mol.: 1 / Fragment: Ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARG, NR1C3 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: P37231
#3: Chemical ChemComp-240 / (2S)-2-(2-{[1-(4-METHOXYBENZOYL)-2-METHYL-5-(TRIFLUOROMETHOXY)-1H-INDOL-3-YL]METHYL}PHENOXY)PROPANOIC ACID / MRL20


Mass: 527.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H24F3NO6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.4 M sodium citrate, 0.125 M Tris 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Details: Mirrors
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 32936 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 57.4 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Χ2: 1.008 / Net I/σ(I): 23.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3140 / Rsym value: 0.42 / Χ2: 1.02 / % possible all: 95.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KNU

1knu


Resolution: 2.2→15 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.961 / SU ML: 0.132 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.233 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1667 5.1 %RANDOM
Rwork0.183 ---
obs0.185 32930 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.892 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-0.33 Å2
2--1.25 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4025 0 76 244 4345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224236
X-RAY DIFFRACTIONr_angle_refined_deg1.3022.0115738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23925.165182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00515783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4021517
X-RAY DIFFRACTIONr_chiral_restr0.0720.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023108
X-RAY DIFFRACTIONr_nbd_refined0.2010.22047
X-RAY DIFFRACTIONr_nbtor_refined0.30.22998
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2247
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.210
X-RAY DIFFRACTIONr_mcbond_it0.3841.52655
X-RAY DIFFRACTIONr_mcangle_it0.64424147
X-RAY DIFFRACTIONr_scbond_it1.0431841
X-RAY DIFFRACTIONr_scangle_it1.6084.51581
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 107 -
Rwork0.236 2142 -
obs-2249 94.77 %
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)
112.9267-10.7688-1.528836.94563.52571.98470.10270.6165-0.3785-0.1651-0.3520.19780.00680.2480.2492-0.03280.06210.00720.11060.00840.10074.907-1.52-22.752
26.2849-1.82390.88378.5328-0.91930.9160.0343-0.36210.18230.54970.0044-0.1089-0.10530.0731-0.03870.0584-0.0127-0.03180.0910.00810.09330.42411.853-15.616
36.017-3.1358-2.71082.88573.09753.4893-0.0652-0.3844-0.11630.07330.2279-0.10320.01130.0927-0.16260.05790.0162-0.0010.09940.01950.0616-9.16914.3160.484
435.39787.3166-2.90727.459913.870710.59010.003-0.89841.9466-1.2872-0.0834-0.4455-1.4358-0.28560.08040.20550.17770.02960.0264-0.09540.2075-21.16329.1992.172
520.06543.85036.29628.3564-13.259229.45240.2278-0.7011.17541.0191-0.32810.5935-2.7003-0.67080.10040.22940.0649-0.00920.0691-0.06660.0601-22.8130.701-9.575
616.9323-12.5885-7.577910.87266.22616.2995-0.1721-0.09230.41340.15120.2116-0.2336-0.29720.0577-0.03950.11370.0138-0.0613-0.00130.00270.0857-8.6321.209-19.268
72.4512-0.2814-0.39362.1147-0.15023.060.08660.22070.128-0.1844-0.05690.155-0.24320.0736-0.02970.06460.0323-0.05050.0561-0.01340.0708-7.72613.855-30.934
81.7893-1.6524-1.24495.68933.51697.5467-0.07060.0322-0.01710.02880.0821-0.0656-0.1735-0.0849-0.01150.010.0283-0.01960.08980.01470.0662-14.64715.46-6.706
93.5313-4.19852.65958.46111.37977.94830.14950.235-0.1492-0.2693-0.34410.4641-0.3098-1.00050.1946-0.06090.0596-0.01260.25030.0020.1131-27.19319.279-9.31
108.4501-4.5488-4.74157.20590.63213.6535-0.0724-0.1536-0.64450.1363-0.13220.53940.284-0.3030.20460.0181-0.035-0.02260.0656-0.02550.0783-15.6934.506-10.804
112.7509-0.44212.271.4622-1.57525.7412-0.00350.1969-0.2178-0.1755-0.03820.05160.1016-0.05970.04170.05830.0225-0.03320.063-0.0540.1019-8.2965.812-30.048
121.9678-0.84612.56864.917-3.060513.7236-0.01980.0624-0.5318-0.16230.1406-0.33580.13240.0509-0.12080.00190.0271-0.02190.0424-0.03410.1867-3.254-4.301-22.381
135.98680.14422.37057.8106-2.44977.4465-0.1463-0.1482-0.390.2922-0.28970.05510.4036-0.44140.436-0.0105-0.02060.01080.0835-0.09430.1318-12.039-5.423-16.618
1410.5873-13.92610.464837.64741.87321.18120.37740.2332-0.4276-0.1427-0.3670.4690.1161-0.0995-0.0103-0.03160.0251-0.05450.0672-0.0250.0802-25.80618.582-22.572
159.1615-4.7048-1.273317.28281.140.95030.11890.57110.2594-0.15180.10750.4947-0.1704-0.2886-0.22640.11820.09730.02940.03340.07690.0858-17.66925.984-26.176
1628.3423-1.208810.240745.347-23.298133.66950.2476-1.1957-0.25492.1673-0.9691-1.3680.79051.07280.72150.10060.0907-0.1530.0026-0.10420.3646-9.766-25.778-21.539
171.7244-1.07390.32433.1758-2.7375.55690.12960.3421-0.4606-0.31280.12620.12410.5081-0.0669-0.25590.0832-0.0158-0.00610.0365-0.07330.1056-23.1-22.79-35.317
1823.8448-6.3567.38517.3759-4.450717.65930.60231.4572-1.2002-0.6304-0.45140.470.7958-0.1593-0.15090.0754-0.00820.02230.2034-0.0543-0.2538-32.318-11.779-55.117
1912.67661.09620.07040.6109-3.123118.9734-0.17391.1096-0.3046-0.77140.260.33150.6762-1.6339-0.08610.12890.07480.00370.5251-0.0299-0.0952-43.926-10.384-48.538
203.78150.831.324513.6694-11.111621.17180.16940.06230.0303-0.24140.15310.2278-0.3077-1.0246-0.32250.00140.080.02680.2034-0.0133-0.0025-40.65-9.071-38.904
212.0185-0.49820.28491.92730.04065.05770.04910.0832-0.21270.0884-0.13430.01490.2987-0.28120.08520.0344-0.03110.00740.05990.01750.1033-31.232-18.945-20.71
221.88460.6942-6.47571.6307-0.122625.97390.2410.25140.1696-0.09630.090.0711-0.5614-0.7757-0.33090.01130.02570.00350.07950.01810.1025-29.076-9.549-29.481
236.12942.30284.74736.44641.344311.8170.14410.0096-0.3045-0.1655-0.175-0.12230.0348-0.09710.03090.0830.04270.06040.0516-0.0228-0.0152-28.819-11.303-47.695
2413.1455-4.14110.03524.95963.95384.30110.14770.54221.3118-0.0826-0.46570.0504-1.0332-0.640.31810.4380.11890.06540.11990.11480.1025-33.4961.461-46.004
259.1015-5.73526.95228.9415-3.85857.8882-0.61180.22180.25940.0290.4416-0.5414-0.85340.31360.17020.1925-0.08560.09490.0443-0.0246-0.0206-19.213-6.358-39.118
261.2661-0.8736-2.08251.60641.45075.25150.1417-0.0721-0.0794-0.0351-0.0049-0.1254-0.12760.0189-0.13680.0304-0.0317-0.00290.0785-0.00940.0991-22.804-13.105-19.904
274.9627-0.7263-1.58523.74792.87975.4874-0.05270.0903-0.1706-0.09110.1636-0.503-0.13420.5374-0.1109-0.0077-0.0212-0.00180.0626-0.06620.1272-10.077-14.201-27.637
2845.6832-19.3252-1.3689.01143.29378.85471.2987-0.26491.5504-0.644-0.4899-0.8003-0.43690.2714-0.80880.1521-0.02860.0081-0.0511-0.00150.1283-24.417-1.023-29.329
29136.22035.987246.685923.152316.073268.56440.0147-2.14444.5196-1.8644-1.34990.3095-3.3144-5.38791.33520.27740.2995-0.03430.3761-0.10340.1059-37.4594.477-32.236
3042.9373-5.82515.679714.66784.783739.12420.15210.85482.89990.0355-0.2192-0.2026-1.80781.30190.06720.07960.00240.0509-0.03940.12710.0913-48.833-6.852-30.913
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA207 - 2174 - 14
2X-RAY DIFFRACTION2AA218 - 22815 - 25
3X-RAY DIFFRACTION3AA229 - 25026 - 47
4X-RAY DIFFRACTION4AA251 - 25948 - 56
5X-RAY DIFFRACTION5AA260 - 28257 - 79
6X-RAY DIFFRACTION6AA283 - 30280 - 99
7X-RAY DIFFRACTION7AA303 - 326100 - 123
8X-RAY DIFFRACTION8AA327 - 348124 - 145
9X-RAY DIFFRACTION9AA349 - 367146 - 164
10X-RAY DIFFRACTION10AA368 - 381165 - 178
11X-RAY DIFFRACTION11AA382 - 410179 - 207
12X-RAY DIFFRACTION12AA411 - 423208 - 220
13X-RAY DIFFRACTION13AA424 - 438221 - 235
14X-RAY DIFFRACTION14AA439 - 462236 - 259
15X-RAY DIFFRACTION15AA463 - 475260 - 272
16X-RAY DIFFRACTION16BB207 - 2124 - 9
17X-RAY DIFFRACTION17BB213 - 23610 - 33
18X-RAY DIFFRACTION18BB237 - 25634 - 53
19X-RAY DIFFRACTION19BB257 - 27954 - 76
20X-RAY DIFFRACTION20BB280 - 29177 - 88
21X-RAY DIFFRACTION21BB292 - 31589 - 112
22X-RAY DIFFRACTION22BB316 - 333113 - 130
23X-RAY DIFFRACTION23BB334 - 347131 - 144
24X-RAY DIFFRACTION24BB348 - 365145 - 162
25X-RAY DIFFRACTION25BB366 - 380163 - 177
26X-RAY DIFFRACTION26BB381 - 409178 - 206
27X-RAY DIFFRACTION27BB410 - 437207 - 234
28X-RAY DIFFRACTION28BB438 - 449235 - 246
29X-RAY DIFFRACTION29BB450 - 456247 - 253
30X-RAY DIFFRACTION30BB466 - 475263 - 272

+
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