[English] 日本語
Yorodumi
- PDB-7apo: Crystal structure of RARalpha ligand binding domain in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7apo
TitleCrystal structure of RARalpha ligand binding domain in complex with a fragment of the TIF2 coactivator
Components
  • Nuclear receptor coactivator 2
  • Retinoic acid receptor alpha
KeywordsDNA BINDING PROTEIN / Nuclear hormone receptor / coactivator / transcription factor / retinoic acid
Function / homology
Function and homology information


Sertoli cell fate commitment / positive regulation of binding / trachea cartilage development / glandular epithelial cell development / ventricular cardiac muscle cell differentiation / chondroblast differentiation / embryonic camera-type eye development / protein kinase B binding / growth plate cartilage development / negative regulation of granulocyte differentiation ...Sertoli cell fate commitment / positive regulation of binding / trachea cartilage development / glandular epithelial cell development / ventricular cardiac muscle cell differentiation / chondroblast differentiation / embryonic camera-type eye development / protein kinase B binding / growth plate cartilage development / negative regulation of granulocyte differentiation / prostate gland development / positive regulation of T-helper 2 cell differentiation / retinoic acid-responsive element binding / negative regulation of cartilage development / regulation of hematopoietic progenitor cell differentiation / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / retinoic acid binding / outflow tract septum morphogenesis / TGFBR3 expression / response to vitamin A / heterocyclic compound binding / limb development / apoptotic cell clearance / ureteric bud development / Signaling by Retinoic Acid / regulation of myelination / DNA-binding transcription repressor activity / protein kinase A binding / positive regulation of interleukin-4 production / face development / germ cell development / alpha-actinin binding / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / cellular response to estrogen stimulus / response to retinoic acid / retinoic acid receptor signaling pathway / positive regulation of cell cycle / cellular response to retinoic acid / response to cytokine / positive regulation of neuron differentiation / negative regulation of miRNA transcription / mRNA regulatory element binding translation repressor activity / nuclear receptor binding / neural tube closure / RNA polymerase II transcription regulatory region sequence-specific DNA binding / hippocampus development / SUMOylation of intracellular receptors / liver development / mRNA transcription by RNA polymerase II / female pregnancy / regulation of synaptic plasticity / chromatin DNA binding / mRNA 5'-UTR binding / Nuclear Receptor transcription pathway / transcription coactivator binding / RNA polymerase II transcription regulator complex / histone deacetylase binding / multicellular organism growth / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear receptor activity / Transcriptional regulation of granulopoiesis / sequence-specific double-stranded DNA binding / rhythmic process / response to estradiol / actin cytoskeleton / cellular response to lipopolysaccharide / response to ethanol / spermatogenesis / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription coactivator activity / protein phosphorylation / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / signaling receptor binding / protein domain specific binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / dendrite / chromatin binding / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / nucleolus / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / : / Retinoic acid receptor / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator ...: / : / Retinoic acid receptor / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 / 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 / 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
Similarity search - Domain/homology
Chem-EQN / Nuclear receptor coactivator 2 / Retinoic acid receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
Authorsle Maire, A. / Guee, L. / Bourguet, W.
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Structural Insights into the Interaction of the Intrinsically Disordered Co-activator TIF2 with Retinoic Acid Receptor Heterodimer (RXR/RAR).
Authors: Senicourt, L. / le Maire, A. / Allemand, F. / Carvalho, J.E. / Guee, L. / Germain, P. / Schubert, M. / Bernado, P. / Bourguet, W. / Sibille, N.
History
DepositionOct 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Retinoic acid receptor alpha
B: Retinoic acid receptor alpha
C: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1738
Polymers62,2864
Non-polymers8874
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-41 kcal/mol
Surface area21470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.694, 47.573, 120.999
Angle α, β, γ (deg.)90.000, 96.169, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Retinoic acid receptor alpha / RAR-alpha / Nuclear receptor subfamily 1 group B member 1


Mass: 28078.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RARA, NR1B1 / Production host: Escherichia coli (E. coli) / References: UniProt: P10276
#2: Protein/peptide Nuclear receptor coactivator 2


Mass: 3064.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOA2 / Production host: Escherichia coli (E. coli) / References: UniProt: E7EWM1
#3: Chemical ChemComp-EQN / 4-{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino}benzoic acid


Mass: 351.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25NO3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Lithium Chloride, 0.1M MES pH6.0, 20% PEG6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→46.96 Å / Num. obs: 22707 / % possible obs: 93.85 % / Redundancy: 2.4 % / Biso Wilson estimate: 39.55 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.05802 / Net I/σ(I): 9.35
Reflection shellResolution: 2.4→2.486 Å / Rmerge(I) obs: 0.2506 / Num. unique obs: 2250 / CC1/2: 0.923

-
Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
MOLREPphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KMR

3kmr


Resolution: 2.4→46.96 Å / SU ML: 0.2611 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6338
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2407 1080 4.76 %
Rwork0.1852 21606 -
obs0.1877 22686 93.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.17 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4005 0 64 129 4198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00924167
X-RAY DIFFRACTIONf_angle_d0.85415654
X-RAY DIFFRACTIONf_chiral_restr0.0547673
X-RAY DIFFRACTIONf_plane_restr0.0049716
X-RAY DIFFRACTIONf_dihedral_angle_d20.91361585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.510.29071410.25332670X-RAY DIFFRACTION93.95
2.51-2.640.27611390.23582617X-RAY DIFFRACTION91.81
2.64-2.810.26641320.21242796X-RAY DIFFRACTION97.34
2.81-3.020.29761670.21392728X-RAY DIFFRACTION97.34
3.02-3.330.23561250.20862750X-RAY DIFFRACTION95.93
3.33-3.810.2141230.1692649X-RAY DIFFRACTION91.45
3.81-4.80.20651200.15122773X-RAY DIFFRACTION95.1
4.8-46.960.23511330.1732623X-RAY DIFFRACTION88.39
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)
13.39053074764-2.05913006124-5.434514702372.378015121773.561724651598.819718115490.2955866241580.5520243304710.238140576213-1.0563037130.2561281615120.71208991523-0.0833174030574-1.2346926982-0.5376187503670.6549497184190.127825469694-0.08836712410270.785254800510.05128716149450.553913530252-39.64956950458.64555199254-42.0437565288
29.864715949960.4100684493184.055202456197.018011854792.538153532945.210280686930.2686473488440.585897548341-0.842269265181-0.8369886813-0.215403232910.1656451325570.5856720256690.253624242651-0.1391867772160.7903455976940.04047833597660.04788212848420.3743813419460.08054038527810.341109846938-18.3598848066-9.3007148103-49.986263642
38.12248800488-5.68312203941-3.568015253817.194825644532.057252031013.953635577850.1001550168540.373309995838-0.0312852747396-0.49818432467-0.203263531095-0.117031903309-0.132442446013-0.2478462307860.07798274890380.542651845022-0.0234293124597-0.02193918323490.3982875473560.02155739277070.193999022465-20.45789374545.73583584809-49.6321244312
41.262673944730.6710343139630.2336880659734.219930945282.174335357321.03986569250.08490978028990.1151824512640.0880070192288-0.430851987026-0.00639250675861-0.180726619511-0.321707626786-0.103523786038-0.08868031668060.5759178537870.0367519289373-0.004088432672940.3271840883170.03086609497710.173283508391-24.684456439813.0165400288-39.6760777225
54.39227808512-6.305431023981.577581491459.12095802184-2.595335335932.20544929078-0.0190405564969-0.0565780346641-0.379837112801-0.2446408057930.1528695649490.2750026107960.4763018721720.390738788821-0.1116732069050.704817721567-0.06651340912830.02973315796650.366740707312-0.04050869721710.312842611432-24.9141277216-11.9606792764-43.3637567968
62.700094593850.535954992629-1.485867133421.811018642441.428055202225.96895158158-0.0332636219321-0.287595948625-0.289421423599-0.125217920491-0.004353149696-0.1061633045180.3330463288030.111705163338-0.007111856458270.4100906008140.0497625387734-0.06956123043070.2290317475330.03828381209150.260598806775-18.7168142505-7.24698908937-40.6667274195
73.993554714524.184047959992.1157036617.367576139292.936168612528.60071880870.2657514560820.106650377962-0.3587951033990.246972995763-0.204058970451-0.62697854398-0.219160435105-0.0273369650896-0.2039972179660.4510281925090.0761343187735-0.05343601700290.3343785150470.0115280925220.313943321409-28.487776472910.5614110536-34.1019180398
87.540764286654.857085418340.8108366144354.260618848931.06899326373.352307566750.831277661933-0.768240844435-0.4442468363481.11187032447-0.860340353615-0.282530970425-0.182712793018-0.363381605636-0.02580751505030.4403424104230.02619833832730.03133549339830.4653417952810.00495915636750.314446656849-37.43853421318.39508708109-28.5942370243
94.224881086751.81430801966-5.966750191392.80431634755-2.563802564678.27133458637-0.332375523745-1.23404953631-0.780563897176-0.0562515714172-0.162641126007-0.5304958809020.1684998467450.8289684080780.4355748262250.5795766476720.0368354729143-0.1440791581140.410165479767-0.03244209424020.407348150986-17.81409858992.50523456026-32.8307315852
104.99130051666-5.73003053582-2.586793961766.544985991113.323423696176.78653982094-0.2694579080620.3686289482790.7985534922530.1362154665470.618540621348-1.423730050310.4327692483590.236804175029-0.5018170368970.639114335937-0.100226018589-0.009901356078630.41590793531-0.03189505779750.375771057018-9.7217496068510.1731037234-46.9688065034
115.596853131965.471631893192.66407560799.379842041281.155961699496.880222993170.60434902491-3.07736659719-0.424575526481.61387789515-0.6930365055680.3175936582590.0524394313297-1.287792752680.06557202758630.574279861958-0.08787267928110.09717305319420.7137366712310.01769459208270.471790526748-27.70972962661.13873756932-3.27414250317
125.409047666732.026346619-4.095651204389.58823124985-0.7734097892357.659167161410.6811528940780.08107029916790.678660854410.899885652365-0.388290231917-0.027491846758-1.53054624883-0.023512373708-0.3827409392710.5842812161030.0556003158614-0.1921328427230.3167258801240.06242846009740.49170678991-4.4144607698719.743080457-9.80537410533
131.229242742391.659452934920.6686097193036.5865007151-0.3970165659251.365115693190.103161719866-0.0996096237961-0.1847767416370.3480087101790.0363541195718-0.170026603980.213585185252-0.0135105597792-0.1576729662080.2902293867760.0269617484982-0.0705334008380.2993415052030.02081663551070.198611440717-11.36695883891.18239980236-11.3560282602
144.98860450109-6.414707831215.412901808078.4273743585-7.087595291375.97896275309-0.562769627493-0.1112852658460.8920609888750.802993862503-0.0717082204416-0.538180140775-0.8717573605180.1434285165070.6637750723480.524876626995-0.0179886210044-0.1243059729680.403096110831-0.01508764818260.415168863587-11.488629864120.2835598781-9.36933365188
158.45222922578-2.5681580422.986891102882.511469898780.4241476198143.24107615855-0.1752561784230.5502067298050.377140090759-0.244051910755-0.142142363537-0.122387333531-0.3686353745230.156161246370.2539032305290.350517915549-0.0390973283099-0.05679895941830.2878210569830.07637195746810.277532250708-11.165339070718.1752052431-18.502249899
169.52663917462-5.93459272472-3.616827611379.568636459875.485419513377.216915282570.5839133165040.2913822466520.0616855034141-0.402605535147-0.273719639176-0.5893575390610.213930424565-0.603873378597-0.3619818877460.467175081579-0.0651839184336-0.1212247344240.3716095117110.09965475180830.241991846997-22.2477381449-0.156121845571-16.141306446
178.56487622711-3.28471960927-0.2514745133614.054373479971.443247328316.969039283810.368258066087-0.106440101695-0.727863683351-0.65906540591-0.3130815139891.583316431530.0372451199286-0.92479539952-0.07437910847610.25996290833-0.0628819105303-0.1029962246450.4781697802070.06483232434240.421036599077-32.5899353551.15205995603-14.9760994441
188.092023492020.6593742909511.758955160191.30938359844-0.3281471033842.543117524660.129829848560.1185350931010.042442680689-0.254059534729-0.0886572749386-0.101273203982-0.2255151036540.0448607760515-0.1414663242730.5575340332730.0187093332489-0.03377971076180.295309154831-0.0211304044640.242170488512-14.70496371997.84597257125-23.4786351284
193.139730138740.857492992621-4.00445270773.66362836016-4.915082702219.39866356753-0.3683861496530.0956678491262-0.855356202517-0.982815792881-0.130931575496-0.6332555727770.3072942565110.1365323561620.5915980489960.4852029092830.01031014773050.05076737814560.372683058887-0.00736892620670.4604966091910.3615137692140.0575793060918-17.1791546286
205.3834359875-2.86707956263-4.209303427943.44272800625-1.055402550178.99739461391.51202813059-0.3108060997971.78934609224-0.384377870881-0.405098651576-0.766138825091-1.710165451421.22285789899-0.8314994496821.22357543962-0.1352562568430.2008945007250.466630309295-0.1280129846480.583986536337-19.048474881420.6056728158-49.0065403212
218.335931624995.920828956884.200967821274.487936623884.334885239078.20772161332-2.07573612398-1.275431853831.013060833851.4593582753-0.1615301115320.793933921961-3.14196866248-0.7336306857292.293347526311.08766079680.0971452990668-0.2311485171060.486656520502-0.06767611658080.723997338627-28.228320645720.0724637867-55.5182031757
224.27112683976-3.716601152765.469845290218.9902357394-5.491282150657.1297651011-0.1057340588220.7557041021240.614601934966-0.0707219936925-0.251623321597-0.441176641873-0.04698943717071.153370773230.3266216378440.568770561441-0.05669358386440.05090015565480.571646660037-0.01600564074560.222756896799-19.661280120514.648385356-57.9385106369
236.822000208585.355283926451.035102089524.664550150272.780445181088.552716428031.12027899676-1.19544500646-2.098023752560.7001139430510.251107577175-1.09789478069-0.2126875702310.43289997292-0.7363551618590.557877511545-0.0182184142064-0.2658844274140.3982572249060.01665269567420.816585482256-5.80507116713-10.3781983849-9.30955150935
245.308951008260.5784293100065.125950930529.11951203584.643850985378.390069357980.661674698974-0.212463533144-0.6713972197970.8310565225350.07354175529451.039546632682.23569822468-3.43320227915-0.8495012589970.957030575622-0.277996987547-0.05986742541671.268488553180.5032876583410.500495974713-8.7866850435-9.318271784981.8418907471
256.71325415267-1.74455379283-2.862356575937.76241001599-3.366218810017.29916063854-0.2527608789940.266570577669-0.0644814365319-0.3623171740190.2588110179870.01018524122560.7470898941641.222174845870.0310408299870.4645543723280.0341267382561-0.1996310999280.475811409959-0.02445049716140.391844420247-0.987983087299-4.61383132206-1.95009315467
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 183 through 198 )
2X-RAY DIFFRACTION2chain 'A' and (resid 199 through 221 )
3X-RAY DIFFRACTION3chain 'A' and (resid 222 through 245 )
4X-RAY DIFFRACTION4chain 'A' and (resid 246 through 275 )
5X-RAY DIFFRACTION5chain 'A' and (resid 276 through 285 )
6X-RAY DIFFRACTION6chain 'A' and (resid 286 through 319 )
7X-RAY DIFFRACTION7chain 'A' and (resid 320 through 344 )
8X-RAY DIFFRACTION8chain 'A' and (resid 345 through 372 )
9X-RAY DIFFRACTION9chain 'A' and (resid 373 through 401 )
10X-RAY DIFFRACTION10chain 'A' and (resid 402 through 415 )
11X-RAY DIFFRACTION11chain 'B' and (resid 182 through 198 )
12X-RAY DIFFRACTION12chain 'B' and (resid 199 through 221 )
13X-RAY DIFFRACTION13chain 'B' and (resid 222 through 276 )
14X-RAY DIFFRACTION14chain 'B' and (resid 277 through 290 )
15X-RAY DIFFRACTION15chain 'B' and (resid 291 through 319 )
16X-RAY DIFFRACTION16chain 'B' and (resid 320 through 344 )
17X-RAY DIFFRACTION17chain 'B' and (resid 345 through 372 )
18X-RAY DIFFRACTION18chain 'B' and (resid 373 through 401 )
19X-RAY DIFFRACTION19chain 'B' and (resid 402 through 416 )
20X-RAY DIFFRACTION20chain 'C' and (resid 687 through 694 )
21X-RAY DIFFRACTION21chain 'C' and (resid 695 through 700 )
22X-RAY DIFFRACTION22chain 'C' and (resid 701 through 712 )
23X-RAY DIFFRACTION23chain 'D' and (resid 687 through 694 )
24X-RAY DIFFRACTION24chain 'D' and (resid 695 through 700 )
25X-RAY DIFFRACTION25chain 'D' and (resid 701 through 654 )

+
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