[English] 日本語
Yorodumi
- EMDB-15180: Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15180
TitleStructure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of Chaetomium thermophilum INO80 on curved DNA
Map datamain map
Sample
  • Complex: INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA) on curved DNA
    • Protein or peptide: Ino80 ATPase
    • DNA: DNA (36-MER)
    • DNA: DNA (36-MER)
    • Protein or peptide: Actin-related protein 8
    • Protein or peptide: Actin
    • Protein or peptide: Actin related protein 4 (Arp4)
    • Protein or peptide: Ies4
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


Ino80 complex / SWI/SNF complex / NuA4 histone acetyltransferase complex / double-strand break repair / nervous system development / cytoskeleton / hydrolase activity / chromatin remodeling / DNA repair / chromatin binding ...Ino80 complex / SWI/SNF complex / NuA4 histone acetyltransferase complex / double-strand break repair / nervous system development / cytoskeleton / hydrolase activity / chromatin remodeling / DNA repair / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP binding
Similarity search - Function
INO80 complex subunit Ies4 / INO80 complex, subunit Ies4 / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Actin-related protein 8 / Actin-related protein 4 / INO80 complex subunit 4 / Actin
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsKunert F / Metzner FJ / Eustermann S / Jung J / Woike S / Schall K / Kostrewa D / Hopfner KP
Funding supportEuropean Union, Germany, 5 items
OrganizationGrant numberCountry
European Research Council (ERC)833613 INO3DEuropean Union
German Research Foundation (DFG)CRC1064 Germany
German Research Foundation (DFG)CRC1361 Germany
German Research Foundation (DFG)RTG1721 Germany
German Research Foundation (DFG)Gottfried-Wilhelm-Leibniz Prize Germany
CitationJournal: Sci Adv / Year: 2022
Title: Structural mechanism of extranucleosomal DNA readout by the INO80 complex.
Authors: Franziska Kunert / Felix J Metzner / James Jung / Markus Höpfler / Stephan Woike / Kevin Schall / Dirk Kostrewa / Manuela Moldt / Jia-Xuan Chen / Susanne Bantele / Boris Pfander / Sebastian ...Authors: Franziska Kunert / Felix J Metzner / James Jung / Markus Höpfler / Stephan Woike / Kevin Schall / Dirk Kostrewa / Manuela Moldt / Jia-Xuan Chen / Susanne Bantele / Boris Pfander / Sebastian Eustermann / Karl-Peter Hopfner /
Abstract: The nucleosomal landscape of chromatin depends on the concerted action of chromatin remodelers. The INO80 remodeler specifically places nucleosomes at the boundary of gene regulatory elements, which ...The nucleosomal landscape of chromatin depends on the concerted action of chromatin remodelers. The INO80 remodeler specifically places nucleosomes at the boundary of gene regulatory elements, which is proposed to be the result of an ATP-dependent nucleosome sliding activity that is regulated by extranucleosomal DNA features. Here, we use cryo-electron microscopy and functional assays to reveal how INO80 binds and is regulated by extranucleosomal DNA. Structures of the regulatory A-module bound to DNA clarify the mechanism of linker DNA binding. The A-module is connected to the motor unit via an HSA/post-HSA lever element to chemomechanically couple the motor and linker DNA sensing. Two notable sites of curved DNA recognition by coordinated action of the four actin/actin-related proteins and the motor suggest how sliding by INO80 can be regulated by extranucleosomal DNA features. Last, the structures clarify the recruitment of YY1/Ies4 subunits and reveal deep architectural similarities between the regulatory modules of INO80 and SWI/SNF complexes.
History
DepositionJun 15, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateDec 28, 2022-
Current statusDec 28, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15180.png

Downloads & links

-
Map

FileDownload / File: emd_15180.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 192 pix.
= 257.28 Å		1.34 Å/pix.
x 192 pix.
= 257.28 Å		1.34 Å/pix.
x 192 pix.
= 257.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.024422472 - 0.087524004
Average (Standard dev.)-6.3362204e-05 (±0.0032898618)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 257.28 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: sharpened map

Fileemd_15180_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_15180_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_15180_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA) on curved DNA

EntireName: INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA) on curved DNA
Components
  • Complex: INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA) on curved DNA
    • Protein or peptide: Ino80 ATPase
    • DNA: DNA (36-MER)
    • DNA: DNA (36-MER)
    • Protein or peptide: Actin-related protein 8
    • Protein or peptide: Actin
    • Protein or peptide: Actin related protein 4 (Arp4)
    • Protein or peptide: Ies4
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

+
Supramolecule #1: INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA) on curved DNA

SupramoleculeName: INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA) on curved DNA
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Thermochaetoides thermophila (fungus)

+
Macromolecule #1: Ino80 ATPase

MacromoleculeName: Ino80 ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 210.443344 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDHFPTVLQR PPHFDEDGSA GTGRMRSNVV GNGSSNGARD DRGLRGGLRD ILNPVGSASQ TMPSASHGGT HSTPGTPGAP APPRPHSSF SLRSPTQTGN HHASPYSAPT SSAAATSSQQ PAGACSMLNN PFVTASTPFP PPPLQAPPSL ASSRTSPSGL Q HPPRSPLH ...String:
MDHFPTVLQR PPHFDEDGSA GTGRMRSNVV GNGSSNGARD DRGLRGGLRD ILNPVGSASQ TMPSASHGGT HSTPGTPGAP APPRPHSSF SLRSPTQTGN HHASPYSAPT SSAAATSSQQ PAGACSMLNN PFVTASTPFP PPPLQAPPSL ASSRTSPSGL Q HPPRSPLH APPVYYPSDV RDRDLVRDQQ TSLSFYDPTT DSKRDRDRER DRERERTGSD PESGAWSTST QNSPPKIRDS YN YSRSPSF NNSGNYPSAT GSYPPRSPVV RPHPAPPAGS MSPSAGSRTV TSPSLRHLAM PSTHSSQSAS TVLPPLARTE TPA PSARAT PASNTPSRAS GVMSFSNILS SSEPISKPRP TSPISLDNNP AMVARTEPAE RPDKGEKDKK QSRKIIKTRV SDIK SAEST PKMTRKSAVK PETPTMLRIP TKRTANGSMK HKAFSADKEK TIRDIMDQFD YESIDETEFE DELLAWKERA RRRRQ EMNR RDFIHRQSRR SDFAETEALK LQIHANLGKA RYSDLHYDEA LQEVREQELW AEKERKKDMQ RKRRREKSMA ATLEQQ AAA LQKASQAEDE AERLKYIREA ERANKKVQQT KYILQKGIKG PARNLPPIEP NLEGGTMATF SAENMEPGKV KGKGRGG RL KKSKEQKQAE KEQAELAQAA IDAGEEPPSK EETKIRIKLS KAKASAKEEA EKDKENKEPK QPKEPEKPVE EPKDPLEL K FQSKGYNQIY DQIWRDLARK DVSKVFRLAT DSYATKASNL KKTAILASKE AKRWQLRTNK GTKDLQARAK RVMRDMMGF WKRNEREERD LRKAAERLEL ENARKEEADR EAARQRRKLN FLISQTELYS HFISKKIKTH EVERSTDHPD VATDEKDKIP EPTLNINVP EPTGPIAPKV TDFNSLDFDN EDESALQAAA MANAQNAIAE AQKKAREFNK DETKLDEDGE MNFQHPELTE F EVAQPKLL NCQLKEYQLK GLNWLVNLYE QGINGILADE MGLGKTVQSI SVMAYLAERY DIWGPFLVVA PASTLHNWQQ EV SKFVPDF KVLPYWGTAA DRKVLRKFWD RKHTTYKKDS PFHVMITSYQ LVVSDVAYFQ KMKWQYMILD EAQAIKSSQS SRW KCLLGF HCRNRLLLTG TPIQNNMQEL WALLHFIMPS LFDSHDEFSE WFSKDIESHA QSNTKLNEDQ LKRLHMILKP FMLR RVKKH VQKELGDKIE IDVFCELSYR QRAMYQSLRN QISIMDLIEK ATVGDNEDSA TLMNLVMQFR KVCNHPDLFE RADTS SPFF CGHFAETGSF LREGTNVALG YSTRSLVEYR LPRLIWCDGG RLDKPGPGNL VAGFRSKYLN HMMNIWTPEN IRSSLE GIE NFTWLRFVDT SLQEAYRASH TDVFARAVDL ASKQNRLGHM QIVYDEPEDK KWTPVHALFQ ICERENPKAV AEITTEG VL RDLMNIARVK YRELGLCRLE KAARPRASAP PIEVVCDSRS AVIERENIMF HPAMRKALFG PTPSEIKEAS FGPRPVTL Y PPRALLPAPD HDKQRFTNIT VPSMARFVTD SGKLAKLDEL LRELKEGGHR VLLYFQMTRM IDLMEEYLTY RNYKYCRLD GSTKLEDRRD TVADFQTRPE IFIFLLSTRA GGLGINLTTA DTVIFYDSDW NPTIDSQAMD RAHRLGQTKQ VTVYRLITRG TIEERIRKR ALQKEEVQRV VITGTGSVDF SGRRPPENRN RDIAMWLADD EQAEMIERRE KELIESGEYD KIMQQRRKGG K RKRGAANG DTVPSLEDMY HEGEGHFDDN KGSGAATPVD ADSLGRGGKR KKAGGSKKAK TTKQRLAIAD GEIDDGEIDI DY KDDDDKG TDYKDDDDK

+
Macromolecule #4: Actin-related protein 8

MacromoleculeName: Actin-related protein 8 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 84.139266 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVGKVSERVL AREGLERTDN GMRQTSWPEV QPINQKNYYT DYMKRDDQIL SLRLQNEANR ERLVKTAQDR DRALNTNTNG EVPLPLDEL QEDAPPAPSA AMDPSKIIVI HPGSQNLRIG FASDALPKTI PMVLGTQYSQ TESEMHEALP RRQFEGRTME Q QYGEEWVK ...String:
MVGKVSERVL AREGLERTDN GMRQTSWPEV QPINQKNYYT DYMKRDDQIL SLRLQNEANR ERLVKTAQDR DRALNTNTNG EVPLPLDEL QEDAPPAPSA AMDPSKIIVI HPGSQNLRIG FASDALPKTI PMVLGTQYSQ TESEMHEALP RRQFEGRTME Q QYGEEWVK KYQKMCSDLK VTMRANKLKV LPNSKDLVVN FNRRTEPEII SQHNDPLQVE WTNVNKAPED GTTQKVFIGQ QA LRIAEDS SPKYKLWWPI QHGWLNEDDY PTRAHLFDDL EMLLDRALRR ELGLTKKADW KQYSCVIVIP DLYDKRYVEL LLH LCIEFF DLSRVAFIQE SMAATFGAGY TQACVVDVGA QKTSISCVED GLVIEDSRVN LKYGGYDVTE TFIKMMLYDN FPYQ DINLR RRHDFLLAEE LKMKYCTLSQ ANISVQAFDF HLRAPNQPTR KYQFKFYDEV ILAPMGFYDP SIFDNSTKLR GRRKL IDRS YNAYDVDMPD DPTSSAQLAI LAMVQPSLAA PTATASFNGD PTATPSKERT QPFNFLSRPD ATGTPGTSKA PSPAPD GAS TPVPGPYIFG ASSREANGGS PAPSGRNGGT PAPANGTTVL PATSFDNPTS QQPQQRSAKE IAAERDAVLP IAPLDVA IL TSIQHAAKGD EKKVRELVGS IMVVGGGAKI PHFAPFLEEK LKIRRPDLAD RILVSRSARE MDEQVVVWKG ASVFAKLS T NDSWVTNYEY KMLGSRCIYM KLLWHY

+
Macromolecule #5: Actin

MacromoleculeName: Actin / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 41.735512 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEEEVAALVI DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH HGIMIGMGQK DSYVGDEAQS KRGILTLRYP IEHGVVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP INPKSNREKM TQIVFETFNA PAFYVSIQAV LSLYASGRTT GIVLDSGDGV T HVVPIYEG ...String:
MEEEVAALVI DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH HGIMIGMGQK DSYVGDEAQS KRGILTLRYP IEHGVVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP INPKSNREKM TQIVFETFNA PAFYVSIQAV LSLYASGRTT GIVLDSGDGV T HVVPIYEG FSLPHAIARL DMAGRDLTDY LMKILAERGY TFSTTAEREI VRDIKEKLCY VALDFEQEIQ TAAQSSHLEK SY ELPDGQV ITIGNERFRA PEALFQPSVL GLESGGIHVT TFNSIMKCDV DVRKDLYGNI VMSGGTTMYP GLSDRMQKEI TAL APSSMK VKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF

+
Macromolecule #6: Actin related protein 4 (Arp4)

MacromoleculeName: Actin related protein 4 (Arp4) / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 51.761199 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSQQPLSSSV QPADIYGGDE VSALVLDPGY CNTRAGFAGE EMPKQVIPSF YGHVDGRDLF GDEVIVPRAG FEVRNYMNRD SMVEDWDAA TRVWEYLLVQ RLQPPRPTPA SKNGLNVSDD GDVQMEDSAP NEDALDALEK PLTENPLLMT EAPWNTPKAR E KAIEVVME ...String:
MSQQPLSSSV QPADIYGGDE VSALVLDPGY CNTRAGFAGE EMPKQVIPSF YGHVDGRDLF GDEVIVPRAG FEVRNYMNRD SMVEDWDAA TRVWEYLLVQ RLQPPRPTPA SKNGLNVSDD GDVQMEDSAP NEDALDALEK PLTENPLLMT EAPWNTPKAR E KAIEVVME NWGTPAFWLS RTPVLAAFAA GKATALVIDV GGANTSVTAI HDGMVLKRSI QRSPAAGVWL SGQIRSMWKS QD PPVNVVP TFMVENKKPV EAGAPPDCRL RNFGFPIHDS FRAFEEERVL TEFKESVVEV WRGPGKYLNP GNEDFAKTQP GRV FEFPDG SNQMWREQRY RVAEGMWDET AAYPSLNPDE AAITKAQTIP ALIKAALDGV DVDLRPNLLG NVVVTGSTSL LNGF NDRLN HELTNMYPGL KIKLHAAGLT SERRFGAWIG GSILASLGTF HQMWISRKEY EENGAGIVEK RCK

+
Macromolecule #7: Ies4

MacromoleculeName: Ies4 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 29.015457 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAPSSKNATP SNKDRRKSGI AAAGNGNAAA SSKIVTLKVT PERLRAIFDP DILMEDAPAS KASPAAANSN TENATESNPN SPSASTPAG QSVMGPPAEG PKKKGVKRGA AALGPNGEPK PRGKPGPKKK QRLEDGTIVE EPSRKLGPKA NQGAINAGLR A LDRSGKPC ...String:
MAPSSKNATP SNKDRRKSGI AAAGNGNAAA SSKIVTLKVT PERLRAIFDP DILMEDAPAS KASPAAANSN TENATESNPN SPSASTPAG QSVMGPPAEG PKKKGVKRGA AALGPNGEPK PRGKPGPKKK QRLEDGTIVE EPSRKLGPKA NQGAINAGLR A LDRSGKPC RKWTRGTFQM KSFTGVVWEI PRWTAPPRPK PETAAPDDAA ATVAVNGNGA TPASTAADNN SNKENNNPSI AA AKVEDAS SQTAVKSEMS TGSGDIEMQS VAPSIAPSPA PVPIAVA

+
Macromolecule #2: DNA (36-MER)

MacromoleculeName: DNA (36-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 11.094113 KDa
SequenceString:
(DC)(DA)(DT)(DG)(DT)(DA)(DT)(DT)(DG)(DA) (DA)(DC)(DA)(DG)(DC)(DG)(DA)(DC)(DC)(DT) (DT)(DG)(DC)(DC)(DG)(DG)(DT)(DG)(DC) (DC)(DA)(DG)(DT)(DC)(DG)(DG)

+
Macromolecule #3: DNA (36-MER)

MacromoleculeName: DNA (36-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 11.063104 KDa
SequenceString:
(DC)(DC)(DG)(DA)(DC)(DT)(DG)(DG)(DC)(DA) (DC)(DC)(DG)(DG)(DC)(DA)(DA)(DG)(DG)(DT) (DC)(DG)(DC)(DT)(DG)(DT)(DT)(DC)(DA) (DA)(DT)(DA)(DC)(DA)(DT)(DG)

+
Macromolecule #8: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

+
Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 325000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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://pdbjlvh1.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