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- EMDB-18498: Cryo-EM structure of the benzo[a]pyrene-bound Hsp90-XAP2-AHR complex -

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Entry
Database: EMDB / ID: EMD-18498
TitleCryo-EM structure of the benzo[a]pyrene-bound Hsp90-XAP2-AHR complex
Map data
Sample
  • Complex: Benzo[a]pyrene-bound Hsp90-XAP2-AHR complex
    • Protein or peptide: Heat shock protein HSP 90-betaHeat shock response
    • Protein or peptide: AH receptor-interacting protein
    • Protein or peptide: Aryl hydrocarbon receptor
  • Ligand: MOLYBDATE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: benzo[a]pyrene
Keywordsdetoxification / chemical pollutants / exposome / TRANSCRIPTION
Function / homology
Function and homology information


GAF domain binding / negative regulation of T cell mediated immune response to tumor cell / cytosolic aryl hydrocarbon receptor complex / regulation of B cell proliferation / cellular response to molecule of bacterial origin / regulation of adaptive immune response / : / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / nuclear aryl hydrocarbon receptor complex / HSP90-CDC37 chaperone complex ...GAF domain binding / negative regulation of T cell mediated immune response to tumor cell / cytosolic aryl hydrocarbon receptor complex / regulation of B cell proliferation / cellular response to molecule of bacterial origin / regulation of adaptive immune response / : / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / nuclear aryl hydrocarbon receptor complex / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / Aryl hydrocarbon receptor signalling / negative regulation of proteasomal protein catabolic process / dynein axonemal particle / aryl hydrocarbon receptor complex / histone methyltransferase binding / regulation of protein kinase A signaling / protein kinase regulator activity / positive regulation of protein localization to cell surface / protein targeting to mitochondrion / Xenobiotics / ATP-dependent protein binding / Phase I - Functionalization of compounds / negative regulation of protein metabolic process / protein maturation by protein folding / positive regulation of tau-protein kinase activity / telomerase holoenzyme complex assembly / Uptake and function of diphtheria toxin / blood vessel development / TPR domain binding / E-box binding / positive regulation of transforming growth factor beta receptor signaling pathway / dendritic growth cone / TFIID-class transcription factor complex binding / positive regulation of phosphoprotein phosphatase activity / aryl hydrocarbon receptor binding / cAMP-mediated signaling / Sema3A PAK dependent Axon repulsion / The NLRP3 inflammasome / regulation of protein ubiquitination / HSF1-dependent transactivation / telomere maintenance via telomerase / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / response to unfolded protein / HSF1 activation / chaperone-mediated protein complex assembly / Attenuation phase / Endogenous sterols / RHOBTB2 GTPase cycle / cis-regulatory region sequence-specific DNA binding / DNA polymerase binding / Purinergic signaling in leishmaniasis infection / supramolecular fiber organization / axonal growth cone / cellular response to forskolin / cellular response to cAMP / positive regulation of telomerase activity / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / TBP-class protein binding / cellular response to interleukin-4 / xenobiotic metabolic process / nitric-oxide synthase regulator activity / ESR-mediated signaling / placenta development / peptidyl-prolyl cis-trans isomerase activity / positive regulation of cell differentiation / peptide binding / ATP-dependent protein folding chaperone / Hsp90 protein binding / tau protein binding / circadian regulation of gene expression / DDX58/IFIH1-mediated induction of interferon-alpha/beta / transcription coactivator binding / PPARA activates gene expression / response to toxic substance / Regulation of actin dynamics for phagocytic cup formation / negative regulation of inflammatory response / kinase binding / Chaperone Mediated Autophagy / histone deacetylase binding / The role of GTSE1 in G2/M progression after G2 checkpoint / nuclear receptor activity / positive regulation of nitric oxide biosynthetic process / regulation of protein localization / disordered domain specific binding / melanosome / unfolded protein binding / sequence-specific double-stranded DNA binding / double-stranded RNA binding / protein folding / cellular response to heat / MHC class II protein complex binding / regulation of gene expression / secretory granule lumen / Estrogen-dependent gene expression / ficolin-1-rich granule lumen / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding
Similarity search - Function
Aryl hydrocarbon receptor / Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / AIP/AIPL1 / PAS fold-3 / PAS fold / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. ...Aryl hydrocarbon receptor / Aryl hydrocarbon receptor/Aryl hydrocarbon receptor repressor / AIP/AIPL1 / PAS fold-3 / PAS fold / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / TPR repeat region circular profile. / TPR repeat profile. / PAS fold / PAS fold / PAS domain / Tetratricopeptide repeat / PAS repeat profile. / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
AH receptor-interacting protein / Heat shock protein HSP 90-beta / Aryl hydrocarbon receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsKwong HS / Grandvuillemin L / Sirounian S / Ancelin A / Lai-Kee-Him J / Carivenc C / Lancey C / Ragan TJ / Hesketh EL / Bourguet W / Gruszczyk J
Funding support France, 4 items
OrganizationGrant numberCountry
ATIP-AvenirR20059SP France
Montpellier University of Excellence (MUSE)ANR-16-IDEX-0006 France
Other governmentEXPOAR23-RS03-JakubGruszczy
French National Research AgencyANR-10-INBS-04-01 France
CitationJournal: J Mol Biol / Year: 2024
Title: Structural Insights into the Activation of Human Aryl Hydrocarbon Receptor by the Environmental Contaminant Benzo[a]pyrene and Structurally Related Compounds.
Authors: Hok-Sau Kwong / Matteo Paloni / Loïc Grandvuillemin / Savannah Sirounian / Aurélie Ancelin / Josephine Lai-Kee-Him / Marina Grimaldi / Coralie Carivenc / Claudia Lancey / Timothy J Ragan / ...Authors: Hok-Sau Kwong / Matteo Paloni / Loïc Grandvuillemin / Savannah Sirounian / Aurélie Ancelin / Josephine Lai-Kee-Him / Marina Grimaldi / Coralie Carivenc / Claudia Lancey / Timothy J Ragan / Emma L Hesketh / Patrick Balaguer / Alessandro Barducci / Jakub Gruszczyk / William Bourguet /
Abstract: The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor belonging to the bHLH/PAS protein family and responding to hundreds of natural and chemical substances. It is primarily ...The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor belonging to the bHLH/PAS protein family and responding to hundreds of natural and chemical substances. It is primarily involved in the defense against chemical insults and bacterial infections or in the adaptive immune response, but also in the development of pathological conditions ranging from inflammatory to neoplastic disorders. Despite its prominent roles in many (patho)physiological processes, the lack of high-resolution structural data has precluded for thirty years an in-depth understanding of the structural mechanisms underlying ligand-binding specificity, promiscuity and activation of AHR. We recently reported a cryogenic electron microscopy (cryo-EM) structure of human AHR bound to the natural ligand indirubin, the chaperone Hsp90 and the co-chaperone XAP2 that provided the first experimental visualization of its ligand-binding PAS-B domain. Here, we report a 2.75 Å resolution structure of the AHR complex bound to the environmental pollutant benzo[a]pyrene (B[a]P). The structure substantiates the existence of a bipartite PAS-B ligand-binding pocket with a geometrically constrained primary binding site controlling ligand binding specificity and affinity, and a secondary binding site contributing to the binding promiscuity of AHR. We also report a docking study of B[a]P congeners that validates the B[a]P-bound PAS-B structure as a suitable model for accurate computational ligand binding assessment. Finally, comparison of our agonist-bound complex with the recently reported structures of mouse and fruit fly AHR PAS-B in different activation states suggests a ligand-induced loop conformational change potentially involved in the regulation of AHR function.
History
DepositionSep 24, 2023-
Header (metadata) releaseJan 10, 2024-
Map releaseJan 10, 2024-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18498.png

Downloads & links

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Map

FileDownload / File: emd_18498.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.835 Å
Density
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.074310035 - 0.223945
Average (Standard dev.)0.000104801235 (±0.0021360628)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 300.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18498_msk_1.map
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Half map: #2

Fileemd_18498_half_map_1.map
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Half map: #1

Fileemd_18498_half_map_2.map
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Sample components

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Entire : Benzo[a]pyrene-bound Hsp90-XAP2-AHR complex

EntireName: Benzo[a]pyrene-bound Hsp90-XAP2-AHR complex
Components
  • Complex: Benzo[a]pyrene-bound Hsp90-XAP2-AHR complex
    • Protein or peptide: Heat shock protein HSP 90-betaHeat shock response
    • Protein or peptide: AH receptor-interacting protein
    • Protein or peptide: Aryl hydrocarbon receptor
  • Ligand: MOLYBDATE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: benzo[a]pyrene

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Supramolecule #1: Benzo[a]pyrene-bound Hsp90-XAP2-AHR complex

SupramoleculeName: Benzo[a]pyrene-bound Hsp90-XAP2-AHR complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 254 KDa

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Macromolecule #1: Heat shock protein HSP 90-beta

MacromoleculeName: Heat shock protein HSP 90-beta / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.213141 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHPEE VHHGEEEVET FAFQAEIAQL MSLIINTFYS NKEIFLRELI SNASDALDKI RYESLTDPSK LDSGKELKID IIPNPQERT LTLVDTGIGM TKADLINNLG TIAKSGTKAF MEALQAGADI SMIGQFGVGF YSAYLVAEKV VVITKHNDDE Q YAWESSAG ...String:
MHHHHHHPEE VHHGEEEVET FAFQAEIAQL MSLIINTFYS NKEIFLRELI SNASDALDKI RYESLTDPSK LDSGKELKID IIPNPQERT LTLVDTGIGM TKADLINNLG TIAKSGTKAF MEALQAGADI SMIGQFGVGF YSAYLVAEKV VVITKHNDDE Q YAWESSAG GSFTVRADHG EPIGRGTKVI LHLKEDQTEY LEERRVKEVV KKHSQFIGYP ITLYLEKERE KEISDDEAEE EK GEKEEED KDDEEKPKIE DVGSDEEDDS GKDKKKKTKK IKEKYIDQEE LNKTKPIWTR NPDDITQEEY GEFYKSLTND WED HLAVKH FSVEGQLEFR ALLFIPRRAP FDLFENKKKK NNIKLYVRRV FIMDSCDELI PEYLNFIRGV VDSEDLPLNI SREM LQQSK ILKVIRKNIV KKCLELFSEL AEDKENYKKF YEAFSKNLKL GIHEDSTNRR RLSELLRYHT SQSGDEMTSL SEYVS RMKE TQKSIYYITG ESKEQVANSA FVERVRKRGF EVVYMTEPID EYCVQQLKEF DGKSLVSVTK EGLELPEDEE EKKKME ESK AKFENLCKLM KEILDKKVEK VTISNRLVSS PCCIVTSTYG WTANMERIMK AQALRDNSTM GYMMAKKHLE INPDHPI VE TLRQKAEADK NDKAVKDLVV LLFETALLSS GFSLEDPQTH SNRIYRMIKL GLGIDEDEVA AEEPNAAVPD EIPPLEGD E DASRMEEVD

UniProtKB: Heat shock protein HSP 90-beta

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Macromolecule #2: AH receptor-interacting protein

MacromoleculeName: AH receptor-interacting protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.691047 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MADIIARLRE DGIQKRVIQE GRGELPDFQD GTKATFHYRT LHSDDEGTVL DDSRARGKPM ELIIGKKFKL PVWETIVCTM REGEIAQFL CDIKHVVLYP LVAKSLRNIA VGKDPLEGQR HCCGVAQMRE HSSLGHADLD ALQQNPQPLI FHMEMLKVES P GTYQQDPW ...String:
MADIIARLRE DGIQKRVIQE GRGELPDFQD GTKATFHYRT LHSDDEGTVL DDSRARGKPM ELIIGKKFKL PVWETIVCTM REGEIAQFL CDIKHVVLYP LVAKSLRNIA VGKDPLEGQR HCCGVAQMRE HSSLGHADLD ALQQNPQPLI FHMEMLKVES P GTYQQDPW AMTDEEKAKA VPLIHQEGNR LYREGHVKEA AAKYYDAIAC LKNLQMKEQP GSPEWIQLDQ QITPLLLNYC QC KLVVEEY YEVLDHCSSI LNKYDDNVKA YFKRGKAHAA VWNAQEAQAD FAKVLELDPA LAPVVSRELQ ALEARIRQKD EED KARFRG IFSH

UniProtKB: AH receptor-interacting protein

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Macromolecule #3: Aryl hydrocarbon receptor

MacromoleculeName: Aryl hydrocarbon receptor / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.492559 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GAPNSSSANI TYASRKRRKP VQKTVKPIPA EGIKSNPSKR HRDRLNTELD RLASLLPFPQ DVINKLDKLS VLRLSVSYLR AKSFFDVAL KSSPTERNGG QDNCRAANFR EGLNLQEGEF LLQALNGFVL VVTTDALVFY ASSTIQDYLG FQQSDVIHQS V YELIHTED ...String:
GAPNSSSANI TYASRKRRKP VQKTVKPIPA EGIKSNPSKR HRDRLNTELD RLASLLPFPQ DVINKLDKLS VLRLSVSYLR AKSFFDVAL KSSPTERNGG QDNCRAANFR EGLNLQEGEF LLQALNGFVL VVTTDALVFY ASSTIQDYLG FQQSDVIHQS V YELIHTED RAEFQRQLHW ALNPSQCTES GQGIEEATGL PQTVVCYNPD QIPPENSPLM ERCFICRLRC LLDNSSGFLA MN FQGKLKY LHGQKKKGKD GSILPPQLAL FAIATPLQPP SILEIRTKNF IFRTKHKLDF TPIGCDAKGR IVLGYTEAEL CTR GSGYQF IHAADMLYCA ESHIRMIKTG ESGMIVFRLL TKNNRWTWVQ SNARLLYKNG RPDYIIVTQR PLTDEEGTEH LRKR NTKLP FMFTTGEAVL YEATNPFPAI MDPLPLRTKN GTSG

UniProtKB: Aryl hydrocarbon receptor

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Macromolecule #4: MOLYBDATE ION

MacromoleculeName: MOLYBDATE ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MOO
Molecular weightTheoretical: 159.938 Da
Chemical component information

ChemComp-MOO:
MOLYBDATE ION / Molybdate

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: benzo[a]pyrene

MacromoleculeName: benzo[a]pyrene / type: ligand / ID: 7 / Number of copies: 1 / Formula: W62
Molecular weightTheoretical: 252.309 Da
Chemical component information

ChemComp-W62:
benzo[a]pyrene

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.18 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
20.0 mMBis-TrisBis-tris methanebis-tris methane
50.0 mMNaClSodium chloridesodium chloride
10.0 mMKClpotassium chloride
10.0 mMMgCl2magnesium chloride
20.0 mMNa2MoO4sodium molybdate
2.0 mMBME2-mercaptoethanol
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 4.5 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 9849 / Average exposure time: 2.0 sec. / Average electron dose: 1.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6327916
Startup modelType of model: NONE
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3.1.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 210038 / Software - Name: RELION (ver. 3.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 630113
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7zub


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8qmo:
Cryo-EM structure of the benzo[a]pyrene-bound Hsp90-XAP2-AHR complex

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