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- EMDB-29069: Cryo-EM structure of the GR-Hsp90-FKBP51 complex -

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Entry
Database: EMDB / ID: EMD-29069
TitleCryo-EM structure of the GR-Hsp90-FKBP51 complex
Map dataSharpened consensus map for the GR-Hsp90-FKBP51 complex
Sample
  • Complex: Complex of the Glucocorticoid Receptor ligand binding domain, Hsp90 alpha dimer, and the co-chaperone FKBP51
    • Protein or peptide: Heat shock protein HSP 90-alphaHeat shock response
    • Protein or peptide: Glucocorticoid receptor
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP5
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: DEXAMETHASONE
Keywordschaperone / steroid hormone receptor / ligand binding / ATP binding / protein folding
Function / homology
Function and homology information


Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / glucocorticoid metabolic process / neuroinflammatory response / microglia differentiation / maternal behavior / mammary gland duct morphogenesis ...Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / glucocorticoid metabolic process / neuroinflammatory response / microglia differentiation / maternal behavior / mammary gland duct morphogenesis / nucleus localization / astrocyte differentiation / cellular response to glucocorticoid stimulus / motor behavior / sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane / positive regulation of tau-protein kinase activity / protein insertion into mitochondrial outer membrane / regulation of gluconeogenesis / adrenal gland development / telomerase holoenzyme complex assembly / chaperone-mediated autophagy / Rho GDP-dissociation inhibitor binding / FK506 binding / cellular response to steroid hormone stimulus / Uptake and function of diphtheria toxin / mitochondrial transport / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / PIWI-interacting RNA (piRNA) biogenesis / TPR domain binding / non-chaperonin molecular chaperone ATPase / regulation of postsynaptic membrane neurotransmitter receptor levels / dendritic growth cone / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / positive regulation of cell size / skeletal muscle contraction / protein unfolding / regulation of protein-containing complex assembly / HSF1-dependent transactivation / telomere maintenance via telomerase / response to unfolded protein / HSF1 activation / chaperone-mediated protein complex assembly / Attenuation phase / estrogen response element binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / RHOBTB2 GTPase cycle / DNA polymerase binding / positive regulation of lamellipodium assembly / axonal growth cone / chaperone-mediated protein folding / eNOS activation / intracellular steroid hormone receptor signaling pathway / MECP2 regulates neuronal receptors and channels / core promoter sequence-specific DNA binding / endocytic vesicle lumen / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of cardiac muscle contraction / positive regulation of defense response to virus by host / Signaling by ERBB2 / Recruitment of mitotic centrosome proteins and complexes / cardiac muscle cell apoptotic process / response to salt stress / positive regulation of telomerase activity / cellular response to transforming growth factor beta stimulus / Recruitment of NuMA to mitotic centrosomes / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein tyrosine kinase binding / Anchoring of the basal body to the plasma membrane / TBP-class protein binding / positive regulation of interferon-beta production / activation of innate immune response / steroid binding / response to cold / nitric-oxide synthase regulator activity / cellular response to dexamethasone stimulus / lysosomal lumen / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / AURKA Activation by TPX2
Similarity search - Function
Glucocorticoid receptor / Glucocorticoid receptor / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / 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 ...Glucocorticoid receptor / Glucocorticoid receptor / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / 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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 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 / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Glucocorticoid receptor / Heat shock protein HSP 90-alpha / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsNoddings CM / Agard DA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118099 United States
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Cryo-EM reveals how Hsp90 and FKBP immunophilins co-regulate the glucocorticoid receptor.
Authors: Chari M Noddings / Jill L Johnson / David A Agard /
Abstract: Hsp90 is an essential molecular chaperone responsible for the folding and activation of hundreds of 'client' proteins, including the glucocorticoid receptor (GR). Previously, we revealed that Hsp70 ...Hsp90 is an essential molecular chaperone responsible for the folding and activation of hundreds of 'client' proteins, including the glucocorticoid receptor (GR). Previously, we revealed that Hsp70 and Hsp90 remodel the conformation of GR to regulate ligand binding, aided by co-chaperones. In vivo, the co-chaperones FKBP51 and FKBP52 antagonistically regulate GR activity, but a molecular understanding is lacking. Here we present a 3.01 Å cryogenic electron microscopy structure of the human GR:Hsp90:FKBP52 complex, revealing how FKBP52 integrates into the GR chaperone cycle and directly binds to the active client, potentiating GR activity in vitro and in vivo. We also present a 3.23 Å cryogenic electron microscopy structure of the human GR:Hsp90:FKBP51 complex, revealing how FKBP51 competes with FKBP52 for GR:Hsp90 binding and demonstrating how FKBP51 can act as a potent antagonist to FKBP52. Altogether, we demonstrate how FKBP51 and FKBP52 integrate into the GR chaperone cycle to advance GR to the next stage of maturation.
History
DepositionDec 10, 2022-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29069.png

Downloads & links

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Map

FileDownload / File: emd_29069.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened consensus map for the GR-Hsp90-FKBP51 complex
Voxel sizeX=Y=Z: 0.835 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.4372388 - 1.3152113
Average (Standard dev.)0.002901532 (±0.032506146)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 267.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_29069_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Mask #2

Fileemd_29069_msk_2.map
Projections & Slices
AxesZYX

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Histogram

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Mask #3

Fileemd_29069_msk_3.map
Projections & Slices
AxesZYX

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Histogram

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Additional map: Focused map on GR-FKBP51 in the GR-Hsp90-FKBP51 complex

Fileemd_29069_additional_1.map
AnnotationFocused map on GR-FKBP51 in the GR-Hsp90-FKBP51 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Unsharpened consensus map for GR-Hsp90-FKBP51

Fileemd_29069_additional_2.map
AnnotationUnsharpened consensus map for GR-Hsp90-FKBP51
Projections & Slices
AxesZYX

Projections

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focused map on Hsp90 in the GR-Hsp90-FKBP51 complex

Fileemd_29069_additional_3.map
AnnotationFocused map on Hsp90 in the GR-Hsp90-FKBP51 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Composite map for the GR-Hsp90-FKBP51 complex made from...

Fileemd_29069_additional_4.map
AnnotationComposite map for the GR-Hsp90-FKBP51 complex made from the Hsp90 focused map and GR-FKBP51 focused map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 for the GR-Hsp90-FKBP51 consensus map

Fileemd_29069_half_map_1.map
AnnotationHalf map 1 for the GR-Hsp90-FKBP51 consensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 for the GR-Hsp90-FKBP51 consensus map

Fileemd_29069_half_map_2.map
AnnotationHalf map 2 for the GR-Hsp90-FKBP51 consensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of the Glucocorticoid Receptor ligand binding domain, Hsp...

EntireName: Complex of the Glucocorticoid Receptor ligand binding domain, Hsp90 alpha dimer, and the co-chaperone FKBP51
Components
  • Complex: Complex of the Glucocorticoid Receptor ligand binding domain, Hsp90 alpha dimer, and the co-chaperone FKBP51
    • Protein or peptide: Heat shock protein HSP 90-alphaHeat shock response
    • Protein or peptide: Glucocorticoid receptor
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP5
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: DEXAMETHASONE

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Supramolecule #1: Complex of the Glucocorticoid Receptor ligand binding domain, Hsp...

SupramoleculeName: Complex of the Glucocorticoid Receptor ligand binding domain, Hsp90 alpha dimer, and the co-chaperone FKBP51
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 306.5 KDa

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Macromolecule #1: Heat shock protein HSP 90-alpha

MacromoleculeName: Heat shock protein HSP 90-alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-chaperonin molecular chaperone ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.650531 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: PEETQTQDQP MEEEEVETFA FQAEIAQLMS LIINTFYSNK EIFLRELISN SSDALDKIRY ESLTDPSKLD SGKELHINLI PNKQDRTLT IVDTGIGMTK ADLINNLGTI AKSGTKAFME ALQAGADISM IGQFGVGFYS AYLVAEKVTV ITKHNDDEQY A WESSAGGS ...String:
PEETQTQDQP MEEEEVETFA FQAEIAQLMS LIINTFYSNK EIFLRELISN SSDALDKIRY ESLTDPSKLD SGKELHINLI PNKQDRTLT IVDTGIGMTK ADLINNLGTI AKSGTKAFME ALQAGADISM IGQFGVGFYS AYLVAEKVTV ITKHNDDEQY A WESSAGGS FTVRTDTGEP MGRGTKVILH LKEDQTEYLE ERRIKEIVKK HSQFIGYPIT LFVEKERDKE VSDDEAEEKE DK EEEKEKE EKESEDKPEI EDVGSDEEEE KKDGDKKKKK KIKEKYIDQE ELNKTKPIWT RNPDDITNEE YGEFYKSLTN DWE DHLAVK HFSVEGQLEF RALLFVPRRA PFDLFENRKK KNNIKLYVRR VFIMDNCEEL IPEYLNFIRG VVDSEDLPLN ISRE MLQQS KILKVIRKNL VKKCLELFTE LAEDKENYKK FYEQFSKNIK LGIHEDSQNR KKLSELLRYY TSASGDEMVS LKDYC TRMK ENQKHIYYIT GETKDQVANS AFVERLRKHG LEVIYMIEPI DEYCVQQLKE FEGKTLVSVT KEGLELPEDE EEKKKQ EEK KTKFENLCKI MKDILEKKVE KVVVSNRLVT SPCCIVTSTY GWTANMERIM KAQALRDNST MGYMAAKKHL EINPDHS II ETLRQKAEAD KNDKSVKDLV ILLYETALLS SGFSLEDPQT HANRIYRMIK LGLGIDEDDP TADDTSAAVT EEMPPLEG D DDTSRMEEVD

UniProtKB: Heat shock protein HSP 90-alpha

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Macromolecule #2: Glucocorticoid receptor

MacromoleculeName: Glucocorticoid receptor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.198973 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: PKLCLVCSDE ASGCHYGVLT CGSCKVFFKR AVEGQHNYLC AGRNDCIIDK IRRKNCPACR YRKCLQAGMN LEARKTKKKI KGIQQATTG VSQETSENPG NKTIVPATLP QLTPTLVSLL EVIEPEVLYA GYDSSVPDST WRIMTTLNML GGRQVIAAVK W AKAIPGFR ...String:
PKLCLVCSDE ASGCHYGVLT CGSCKVFFKR AVEGQHNYLC AGRNDCIIDK IRRKNCPACR YRKCLQAGMN LEARKTKKKI KGIQQATTG VSQETSENPG NKTIVPATLP QLTPTLVSLL EVIEPEVLYA GYDSSVPDST WRIMTTLNML GGRQVIAAVK W AKAIPGFR NLHLDDQMTL LQYSWMSLMA FALGWRSYRQ SSANLLCFAP DLIINEQRMT LPCMYDQCKH MLYVSSELHR LQ VSYEEYL CMKTLLLLSS VPKDGLKSQE LFDEIRMTYI KELGKAIVKR EGNSSQNWQR FYQLTKLLDS MHEVVENLLN YCF QTFLDK TMSIEFPEML AEIITNQIPK YSNGNIKKLL FHQK

UniProtKB: Glucocorticoid receptor

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Macromolecule #3: Peptidyl-prolyl cis-trans isomerase FKBP5

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase FKBP5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.158992 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: TTDEGAKNNE ESPTATVAEQ GEDITSKKDR GVLKIVKRVG NGEETPMIGD KVYVHYKGKL SNGKKFDSSH DRNEPFVFSL GKGQVIKAW DIGVATMKKG EICHLLCKPE YAYGSAGSLP KIPSNATLFF EIELLDFKGE DLFEDGGIIR RTKRKGEGYS N PNEGATVE ...String:
TTDEGAKNNE ESPTATVAEQ GEDITSKKDR GVLKIVKRVG NGEETPMIGD KVYVHYKGKL SNGKKFDSSH DRNEPFVFSL GKGQVIKAW DIGVATMKKG EICHLLCKPE YAYGSAGSLP KIPSNATLFF EIELLDFKGE DLFEDGGIIR RTKRKGEGYS N PNEGATVE IHLEGRCGGR MFDCRDVAFT VGEGEDHDIP IGIDKALEKM QREEQCILYL GPRYGFGEAG KPKFGIEPNA EL IYEVTLK SFEKAKESWE MDTKEKLEQA AIVKEKGTVY FKGGKYMQAV IQYGKIVSWL EMEYGLSEKE SKASESFLLA AFL NLAMCY LKLREYTKAV ECCDKALGLD SANEKGLYRR GEAQLLMNEF ESAKGDFEKV LEVNPQNKAA RLQISMCQKK AKEH NERDR RIYANMFKKF AEQDAKEEAN KAMGKKTSEG VTNEKGTDSQ AMEEEKPEGH V

UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP5

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: DEXAMETHASONE

MacromoleculeName: DEXAMETHASONE / type: ligand / ID: 6 / Number of copies: 1 / Formula: DEX
Molecular weightTheoretical: 392.461 Da
Chemical component information

ChemComp-DEX:
DEXAMETHASONE / medication, antibiotic*YM / Dexamethasone

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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

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 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 opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #0 - Number grids imaged: 1 / #0 - Number real images: 5489 / #0 - Average exposure time: 3.0 sec. / #0 - Average electron dose: 69.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #1 - Number grids imaged: 1 / #1 - Number real images: 20924 / #1 - Average exposure time: 2.0 sec. / #1 - Average electron dose: 45.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7krj

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final 3D classificationSoftware - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 171778
Image recording ID1
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5fwk

chain_id: A, source_name: PDB, initial_model_type: experimental model

5fwk

chain_id: B, source_name: PDB, initial_model_type: experimental model

1m2z

chain_id: A, source_name: PDB, initial_model_type: experimental model

1ejf

chain_id: A, source_name: PDB, initial_model_type: experimental model
Output model

PDB-8ffw:
Cryo-EM structure of the GR-Hsp90-FKBP51 complex

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