[English] 日本語
Yorodumi
- EMDB-29068: Cryo-EM structure of the GR-Hsp90-FKBP52 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-29068
TitleCryo-EM structure of the GR-Hsp90-FKBP52 complex
Map dataSharpened consensus GR-Hsp90-FKBP52 map
Sample
  • Complex: Complex of the Glucocorticoid Receptor ligand binding domain, Hsp90 alpha dimer, and the co-chaperone FKBP52
    • Protein or peptide: Heat shock protein HSP 90-alphaHeat shock response
    • Protein or peptide: Glucocorticoid receptor
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed
  • 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


steroid hormone receptor complex assembly / negative regulation of microtubule polymerization or depolymerization / male sex differentiation / copper-dependent protein binding / Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / prostate gland development / steroid hormone binding / PTK6 Expression ...steroid hormone receptor complex assembly / negative regulation of microtubule polymerization or depolymerization / male sex differentiation / copper-dependent protein binding / Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / prostate gland development / steroid hormone binding / PTK6 Expression / neuroinflammatory response / glucocorticoid metabolic process / copper ion transport / microglia differentiation / nuclear glucocorticoid receptor binding / mammary gland duct morphogenesis / maternal behavior / protein-containing complex 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 / negative regulation of microtubule polymerization / positive regulation of tau-protein kinase activity / protein insertion into mitochondrial outer membrane / regulation of gluconeogenesis / chaperone-mediated autophagy / telomerase holoenzyme complex assembly / adrenal gland development / Rho GDP-dissociation inhibitor binding / cellular response to steroid hormone stimulus / Uptake and function of diphtheria toxin / FK506 binding / 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 / androgen receptor signaling pathway / dendritic growth cone / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / skeletal muscle contraction / positive regulation of cell size / HSF1-dependent transactivation / telomere maintenance via telomerase / response to unfolded protein / chaperone-mediated protein complex assembly / protein unfolding / HSF1 activation / regulation of protein-containing complex assembly / Attenuation phase / estrogen response element binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / RHOBTB2 GTPase cycle / positive regulation of lamellipodium assembly / eNOS activation / axonal growth cone / DNA polymerase binding / chaperone-mediated protein folding / intracellular steroid hormone receptor signaling pathway / core promoter sequence-specific DNA binding / 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 / Recruitment of mitotic centrosome proteins and complexes / cardiac muscle cell apoptotic process / positive regulation of telomerase activity / Signaling by ERBB2 / positive regulation of defense response to virus by host / cellular response to transforming growth factor beta stimulus / endocytic vesicle lumen / response to salt stress / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / TBP-class protein binding / embryo implantation / steroid binding / activation of innate immune response
Similarity search - Function
Tetratricopeptide repeat 2 / Tetratricopeptide repeat / Glucocorticoid receptor / Glucocorticoid receptor / 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 ...Tetratricopeptide repeat 2 / Tetratricopeptide repeat / Glucocorticoid receptor / Glucocorticoid receptor / 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 FKBP4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 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

-
Structure visualization

Supplemental images

emd_29068.png

Downloads & links

-
Map

FileDownload / File: emd_29068.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened consensus GR-Hsp90-FKBP52 map
Voxel sizeX=Y=Z: 0.835 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.49168167 - 2.19702
Average (Standard dev.)0.0023564885 (±0.040498532)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_29068_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_29068_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #3

Fileemd_29068_msk_3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened consensus GR-Hsp90-FKBP52 map

Fileemd_29068_additional_1.map
AnnotationUnsharpened consensus GR-Hsp90-FKBP52 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Focused map on Hsp90 in the GR-Hsp90-FKBP52 complex

Fileemd_29068_additional_2.map
AnnotationFocused map on Hsp90 in the GR-Hsp90-FKBP52 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Focused map on GR-FKBP52 in the GR-Hsp90-FKBP52 complex

Fileemd_29068_additional_3.map
AnnotationFocused map on GR-FKBP52 in the GR-Hsp90-FKBP52 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Composite map for GR-Hsp90-FKBP52 with combined focused maps...

Fileemd_29068_additional_4.map
AnnotationComposite map for GR-Hsp90-FKBP52 with combined focused maps on Hsp90 and GR-FKBP52
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: GR-Hsp90-FKBP52 Half Map 1

Fileemd_29068_half_map_1.map
AnnotationGR-Hsp90-FKBP52 Half Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: GR-Hsp90-FKBP52 Half Map 2

Fileemd_29068_half_map_2.map
AnnotationGR-Hsp90-FKBP52 Half Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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 FKBP52
Components
  • Complex: Complex of the Glucocorticoid Receptor ligand binding domain, Hsp90 alpha dimer, and the co-chaperone FKBP52
    • Protein or peptide: Heat shock protein HSP 90-alphaHeat shock response
    • Protein or peptide: Glucocorticoid receptor
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: DEXAMETHASONE

-
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 FKBP52
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 307 KDa

-
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

-
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

-
Macromolecule #3: Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.87652 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTAEEMKATE SGAQSAPLPM EGVDISPKQD EGVLKVIKRE GTGTEMPMIG DRVFVHYTGW LLDGTKFDSS LDRKDKFSFD LGKGEVIKA WDIAIATMKV GEVCHITCKP EYAYGSAGSP PKIPPNATLV FEVELFEFKG EDLTEEEDGG IIRRIQTRGE G YAKPNEGA ...String:
MTAEEMKATE SGAQSAPLPM EGVDISPKQD EGVLKVIKRE GTGTEMPMIG DRVFVHYTGW LLDGTKFDSS LDRKDKFSFD LGKGEVIKA WDIAIATMKV GEVCHITCKP EYAYGSAGSP PKIPPNATLV FEVELFEFKG EDLTEEEDGG IIRRIQTRGE G YAKPNEGA IVEVALEGYY KDKLFDQREL RFEIGEGENL DLPYGLERAI QRMEKGEHSI VYLKPSYAFG SVGKEKFQIP PN AELKYEL HLKSFEKAKE SWEMNSEEKL EQSTIVKERG TVYFKEGKYK QALLQYKKIV SWLEYESSFS NEEAQKAQAL RLA SHLNLA MCHLKLQAFS AAIESCNKAL ELDSNNEKGL FRRGEAHLAV NDFELARADF QKVLQLYPNN KAAKTQLAVC QQRI RRQLA REKKLYANMF ERLAEEENKA KAEASSGDHP TDTEMKEEQK SNTAGSQSQV ETEA

UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP4

-
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

-
Macromolecule #5: MAGNESIUM ION

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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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 recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 11162 / Average exposure time: 5.9 sec. / Average electron dose: 67.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
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: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 307109
FSC plot (resolution estimation)

-
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-8ffv:
Cryo-EM structure of the GR-Hsp90-FKBP52 complex

+
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