[English] 日本語
Yorodumi
- EMDB-68935: Cryo-EM structure of Chaetomium thermophilum RSC bound to a nucleosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-68935
TitleCryo-EM structure of Chaetomium thermophilum RSC bound to a nucleosome
Map dataThe composite cryo-EM map for the Chaetomium thermophilum RSC-NCP complex
Sample
  • Complex: RSC
    • Protein or peptide: x 15 types
    • DNA: x 2 types
  • Ligand: x 1 types
KeywordsSWI/SNF-family chromatin remodeling / RSC / PBAF / DNA BINDING PROTEIN / nucleosome / NUCLEAR PROTEIN/DNA / NUCLEAR PROTEIN-DNA complex
Function / homology
Function and homology information


RSC-type complex / SWI/SNF complex / nuclear chromosome / helicase activity / transcription elongation by RNA polymerase II / chromatin DNA binding / transcription by RNA polymerase II / nucleosomal DNA binding / innate immune response in mucosa / structural constituent of chromatin ...RSC-type complex / SWI/SNF complex / nuclear chromosome / helicase activity / transcription elongation by RNA polymerase II / chromatin DNA binding / transcription by RNA polymerase II / nucleosomal DNA binding / innate immune response in mucosa / structural constituent of chromatin / nucleosome / nucleosome assembly / antimicrobial humoral immune response mediated by antimicrobial peptide / heterochromatin formation / histone binding / antibacterial humoral response / chromatin organization / chromatin remodeling / protein heterodimerization activity / hydrolase activity / DNA repair / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / : / DNA-templated transcription / zinc ion binding / ATP binding / nucleus
Similarity search - Function
: / : / Domain of unknown function (DUF7785) / Domain of unknown function (DUF7877) / SWI/SNF and RSC complexes subunit Ssr4, N-terminal / SWI/SNF and RSC complexes subunit Ssr4, C-terminal / SWI/SNF and RSC complexes subunit Ssr4 N-terminal / SWI/SNF and RSC complexes subunit Ssr4 C-terminal / Rsc8/Ssr1/Ssr2, zinc finger, ZZ-type / : ...: / : / Domain of unknown function (DUF7785) / Domain of unknown function (DUF7877) / SWI/SNF and RSC complexes subunit Ssr4, N-terminal / SWI/SNF and RSC complexes subunit Ssr4, C-terminal / SWI/SNF and RSC complexes subunit Ssr4 N-terminal / SWI/SNF and RSC complexes subunit Ssr4 C-terminal / Rsc8/Ssr1/Ssr2, zinc finger, ZZ-type / : / DNA-binding RFX-type winged-helix domain / Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Chromatin remodelling complex Rsc7/Swp82 subunit / RFX-type winged-helix DNA-binding domain profile. / SWIB domain / SWI complex, BAF60b domains / SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / Remodelling complex subunit Rsc/polybromo / SNF5 / SMARCB1 / INI1 / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / Glutamine-Leucine-Glutamine, QLQ / QLQ domain profile. / QLQ / Myb-like domain profile. / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / ARID/BRIGHT DNA binding domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / HSA domain / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / Helicase/SANT-associated domain / HSA domain profile. / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / SWIB/MDM2 domain superfamily / SANT domain profile. / SANT domain / Myb-like DNA-binding domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Actin, conserved site / Actins signature 2. / Actin / Actin family / Actin / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Homeobox-like domain superfamily / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Helicase conserved C-terminal domain / Zinc finger, NHR/GATA-type / Histone H3 signature 1. / ATPase, nucleotide binding domain / Histone H3 signature 2. / Bromodomain, conserved site / Bromodomain signature. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile.
Similarity search - Domain/homology
Histone H3 / Histone H2B / DM2 domain-containing protein / Uncharacterized protein / Chromatin structure-remodeling complex protein / Uncharacterized protein / Uncharacterized protein / Chromatin structure remodeling complex protein / Chromatin structure-remodeling complex protein / Uncharacterized protein ...Histone H3 / Histone H2B / DM2 domain-containing protein / Uncharacterized protein / Chromatin structure-remodeling complex protein / Uncharacterized protein / Uncharacterized protein / Chromatin structure remodeling complex protein / Chromatin structure-remodeling complex protein / Uncharacterized protein / Actin-related protein 4 / DUF1750-domain-containing protein / WD40 repeat-containing protein / Histone H4 / Histone H2A
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.45 Å
AuthorsMa SS / Liu MD / Shen QT / Chen Y
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2023YFA1800403 China
CitationJournal: Sci Adv / Year: 2026
Title: Structural principles underlying the evolution of SWI/SNF chromatin remodelers
Authors: Ma SS / Liu MD / Xu WC / Wang QM / Wang XM / Huang YG / Li MC / Li CH / Shen QT / Chen Y
History
DepositionFeb 5, 2026-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_68935.png

Downloads & links

-
Map

FileDownload / File: emd_68935.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe composite cryo-EM map for the Chaetomium thermophilum RSC-NCP complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 420 pix.
= 445.2 Å		1.06 Å/pix.
x 420 pix.
= 445.2 Å		1.06 Å/pix.
x 420 pix.
= 445.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.06691751 - 4.472262
Average (Standard dev.)0.0017741899 (±0.06071368)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 445.19998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : RSC

EntireName: RSC
Components
  • Complex: RSC
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: DNA (167-MER)
    • DNA: DNA (167-MER)
    • Protein or peptide: WD40 repeat-containing protein
    • Protein or peptide: Putative chromatin structure remodeling complex protein
    • Protein or peptide: Actin-related protein 4
    • Protein or peptide: Ssr1
    • Protein or peptide: DM2 domain-containing protein
    • Protein or peptide: DUF1750-domain-containing protein
    • Protein or peptide: Putative chromatin structure-remodeling complex protein
    • Protein or peptide: Putative chromatin structure-remodeling complex protein
    • Protein or peptide: Rsc7
    • Protein or peptide: Rsc1
    • Protein or peptide: Rsc58
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

+
Supramolecule #1: RSC

SupramoleculeName: RSC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Details: The RSC complex is overexpressed in 293F cells and purified by affinity chromatography, anion exchange chromatography, Grafix, etc.
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)

+
Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.30393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3

+
Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

+
Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.978241 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

UniProtKB: Histone H2A

+
Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.848097 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK TQKKDGKKRR KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Histone H2B

+
Macromolecule #7: WD40 repeat-containing protein

MacromoleculeName: WD40 repeat-containing protein / type: protein_or_peptide / ID: 7
Details: THE N-TERMINAL 62AA CONTAINS 3XFLAG TAG, 3C SITE, AND THE CLONING LINKER
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 179.692891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSPQQNKTAA LAQHDEADYK DHDGDYKDHD IDYKDDDDKG GSGGSLEVLF QGPGGSGGSG TMTSVQVPQV PPAVQLPGTA IPANMTQQQ AQEVYKRWRQ MKESGVPPTD PEFIKTQNIL SALQRQSDMR KQMQMQQQMQ LQQQQQQQQQ QQQQQQQQQQ Q QQQVMQNG ...String:
GSPQQNKTAA LAQHDEADYK DHDGDYKDHD IDYKDDDDKG GSGGSLEVLF QGPGGSGGSG TMTSVQVPQV PPAVQLPGTA IPANMTQQQ AQEVYKRWRQ MKESGVPPTD PEFIKTQNIL SALQRQSDMR KQMQMQQQMQ LQQQQQQQQQ QQQQQQQQQQ Q QQQVMQNG ANGVVNGTQF GRVAQPGAAP ASMPPATGAL GASALPAGSA APAQNAAGAS ALPPQLQGHP HFTQAQLNLL MN QIKAFRM LGKNAGVPIQ MQKAIFEHRA RRRQSLGKQE PQPAATSVTP TTSAETPAPD ASKPAVNGPE AIKAAAPATT TAS LSDPQS KTFKTVKSPF DAGFIRKTIS YIDHSRRKNR QLVPGLFPTG IDFEQLRADR EKIIFNRMSQ RYQELKSLPG NLAH WDASK DELVADDTAK RKAIIEMKKL ALYSKQRALR EKIGRQMMHY DNLAMTTNRA QYRRMKKHNV REARITEKLE KQQRD AREN RERKKHIDFL QAIQNHRNEV LNAGAAQRLK MSKLSRHMYN HHFNIEKEEQ KRIERTAKQR LQALKANDEE AYLKLL DQA KDTRITHLLK QTDGFLKQLA ASVREQQRQA AEKYGEPMDI PSSEDEDEDD ENGRSKIDYY AVAHRIKEEV TEQASIL VG GTLKEYQLKG LQWMLSLYNN NLNGILADEM GLGKTIQTIS LITYLIEKKK QNGPYLVIVP LSTLTNWNLE FEKWAPSV T KVVYKGPPNA RKMQQEKIRQ GKFQVLLTTY EYIIKDRPLL SKIKWFHMII DEGHRMKNTN SKLSATIQQY YTTRFRLIL TGTPLQNNLA ELWAMLNFVL PNIFKSAKTF DEWFNTPFAN TGGQDKMELT EEEQILVIRR LHKVLRPFLL RRLKKDVEKD LPDKTEKVI KCKFSALQAR LYKQMVTHQK IIVSDGKGGK TGARGLSNMI MQLRKLCNHP FVFDEVENQM NPQNISNDLL W RTAGKFEL LDRILPKYKA TGHRVLMFFQ MTAIMDIMED YLRYRGLHYL RLDGTTKSED RSELLKLFNA PDSPYFMFLL ST RAGGLGL NLQTADTVII YDSDWNPHQD LQAQDRAHRI GQKNEVRILR LITSNSVEEK ILERARFKLD MDGKVIQAGR FDN KSSETD RDAMLRTLLE TADLAESGEQ EEMDDEELNM VLARNEEELA IFQKIDEERN RDPIYGTAPG CKGVPRLMTE DELP EIYLH EGNPAEEENE VHLGRGARER KQIRYDDGLT EEQWLMAVDD DEDTPEAAAA RKQARREKRE QNKLKRLAML NASME NSPS ASRASTEDVE TPKKRGRKPG SKNQEKRKAE DGDDEPPAKK RRGPQGRPKA VGTSSGGSAL APELRDKLQK ACRRIF DGL MNLAVDDDEP PEKPEGENDD ESEDEGPPKR LIIGPFVKLP PKREWQDYYV IIQNPICMND IQKKIKREEY NSLGDMR KD LDLLVTNCRT FNEETSGICQ DANTIEAYFK EHFAKELAED PDLRALEDPN SPNLVGLNVD GVNSSASSSS AEASGPAT T GESSAAQSSQ PASSTTSTTP APAPAPAAPT GPPRIKLVSS ANKENKGDTN TSANGSAAQT NGGVNGVANG NSEA

UniProtKB: WD40 repeat-containing protein

+
Macromolecule #8: Putative chromatin structure remodeling complex protein

MacromoleculeName: Putative chromatin structure remodeling complex protein
type: protein_or_peptide / ID: 8 / Details: THE C TERMINAL CONTAINS 6XHIS TAG / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 80.29125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSGQSGKWRE DQVLVICPGS QTTLAQLGCN ELTPPARRFP TRMFRDPEDP SKWRPYHTYK RKKEGTTGEG EDKDEWEWVE DVDSIEGAV YPMQAGRIVQ MDAFLALLEH VHSQMTTTYH NTPILLMASP QWTRPDHEAI ARYIFEKTKT PALCLIHSGL A TQYGLKWP ...String:
MSGQSGKWRE DQVLVICPGS QTTLAQLGCN ELTPPARRFP TRMFRDPEDP SKWRPYHTYK RKKEGTTGEG EDKDEWEWVE DVDSIEGAV YPMQAGRIVQ MDAFLALLEH VHSQMTTTYH NTPILLMASP QWTRPDHEAI ARYIFEKTKT PALCLIHSGL A TQYGLKWP NMTVVDIGYE KVDVTCIYDG RIVSQKNVGP RPGVGGPEET DISGGEVFTR SLLKLLESKG FNYDMAEQLK RS NICEVLP YAPEHPDLME IPPEIDPNAP NAPQIVEPGD DVDTGADTKE VEDGVLDVAN IVASGQTREF LAKREREKAE REA AKKKKG KDKEAGSGDA PPKPVKLPNS KRYKNIFHYE ELVTEEVPVQ PSPPPPPPAA TDSNGDVTMA DAAPAENKEG EQAS KPEGE QPKAEGEQPK TEGEQPKTAE ESSETKPEEA ADSEKKLEEQ QQQSSEQKDG QTEQKDQAQP QADQQQANGA AQQTE RITR RVRRDIEVGP ERFQFASRRE IDRIATAIYR AIQSIDDIYM RPALWENIVF VGNGARIRGL KDNIIQTLTH RYLISP SSA SMFVGDLPSN IGTPSGTGSQ TPNSAVGAGG PPHQLPGAGA GSGVNPLLQA ATTAAAAQSN LTVPGQTPGG DANNAGG GT SQSFHSQTPT VIKTAQLPTY LSEWSKHGFE EAMFLGSLVA ARLAFCIHNL DAQGLEAQKG MSLTRVDYNE LGPKGIRS H SMLALEHHHH HH

UniProtKB: Chromatin structure remodeling complex protein

+
Macromolecule #9: Actin-related protein 4

MacromoleculeName: Actin-related protein 4 / type: protein_or_peptide / ID: 9 / Details: THE C TERMINAL CONTAINS 6XHIS TAG / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 52.83234 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 RCKLEHHHHH H

UniProtKB: Actin-related protein 4

+
Macromolecule #10: Ssr1

MacromoleculeName: Ssr1 / type: protein_or_peptide / ID: 10 / Details: THE C-TERMINAL 8AA ENCODE A FLAG TAG / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 75.831109 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEEGSVSYGT PTTGASPGAN PILAQPPLPD AGDQSEDIQM SESPAIKQDS TTPAPGAENA AERAQAARED TEMGDAPKNE AGHADATGQ NEGNGETKTK DFIENAAREH LIAQTHAIIL PSYSTWFDMN TIHDIERKAL PEFFNNRNRS KTPAVYKDYR D FMINAYRL ...String:
MEEGSVSYGT PTTGASPGAN PILAQPPLPD AGDQSEDIQM SESPAIKQDS TTPAPGAENA AERAQAARED TEMGDAPKNE AGHADATGQ NEGNGETKTK DFIENAAREH LIAQTHAIIL PSYSTWFDMN TIHDIERKAL PEFFNNRNRS KTPAVYKDYR D FMINAYRL NPTEYLTVTA CRRNLAGDVC AIMRVHAFLE QWGLINYQVD ADQRPSHVGP PFTGHFKIIV DTPRGLQPWQ PA ADPVITE GKPNKDTEAK ASATPAPKTE LNLEVGRNIY EANAKHNKIN KSDKPNGEAS AAATNGVTGA DELPKAPIMK VNC YNCGTD CTRIYYHSPQ SDPNSKVKYD LCSTCYLEGR FPGNQTSAHY TRMENPTYSS TLDRDAPWSD AEILRLLEAL ERYD EDWNQ IAEYVGTRTR EECVLQFLQL DIEDKYLESE RLDAPIGLQM LGSHGGQLPF SQSDNPVMSV VSFLASLADP ASTAA AANK SAEILKQNLR NKLEGGSKTA ETANGKGKEK EGTVSSGDSM DVDNKETGSG NGSSEKLTPS QLANIPLAAM GARASA LAS HEEREMTRLV SAAVNVMLEK LELKLKYFNE MEAMLQAERR ELERARQQLF LDRLTFKRRV REVQEVLRQA AATGGEQ GF RMAQEVLAGA AAPGAGNGMT FQPAPAASAV QPLSAEGPVK SYEADYKDDD DK

UniProtKB: Uncharacterized protein

+
Macromolecule #11: DM2 domain-containing protein

MacromoleculeName: DM2 domain-containing protein / type: protein_or_peptide / ID: 11 / Details: THE C-TERMINAL 8AA ENCODES A FLAG TAG / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 61.496863 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQQQFRGYGQ HAPTPPRPGS GPHGVPPRRG GIGPMMSAGP HPQAPLSAAQ LNQQHQAQQQ ANHLAKLRSR KPTDKNLPDG VEEIVIDHG YVVDAYRQLR DFERRLDATM TRKRLDIVDS LSRNTKRYKT MRVWISNTVE DQYWQNNSLN VDTFDFSSNL E ASYRLKIE ...String:
MQQQFRGYGQ HAPTPPRPGS GPHGVPPRRG GIGPMMSAGP HPQAPLSAAQ LNQQHQAQQQ ANHLAKLRSR KPTDKNLPDG VEEIVIDHG YVVDAYRQLR DFERRLDATM TRKRLDIVDS LSRNTKRYKT MRVWISNTVE DQYWQNNSLN VDTFDFSSNL E ASYRLKIE GRLLEDEEDP SSDDDEPSAN GGDKMDTDSV PAAKPAKPAK AVPAKHGQRY RFSHFFKALT VEFDKSRVAA AA AAGRETT IEWKKPERTP AGAANLPAMA DFDEITFKRP GDENVNVIIN LYRHEDPERF ELSPELAEIV DMKEATRQEA VMA VWEYIK LNKLQEDEEK RNFRCDDMLK KIIPRDSGFI PHLNEYLTPH LRPLSPIKLP YTIRVDEEFH KNPSPTIYDI RVLV DDPLR TRQSSSPYLP FPSNPSYATT LKEIAALDDQ LATLMQAVAH SKAKHAFLSG MARDPVGFVK GWLSSQKRDL DIILG EANR AGRDGVTGGL GAGGGEEAVT AGDEWRRGGK ESVWASQNAR ESVNVLLAKQ PLVLRDYKDD DDK

UniProtKB: DM2 domain-containing protein

+
Macromolecule #12: DUF1750-domain-containing protein

MacromoleculeName: DUF1750-domain-containing protein / type: protein_or_peptide / ID: 12 / Details: THE C-TERMINAL 8AA ENCODES A FLAG TAG / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 81.947281 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAVVDPSQNV HGDLLPHIHL ISTFRYATMP RVELQEVTKW LLQAPKIARD TSPFYWTYLD CPADGSILLT WQPTARRGTE FATDGYIWA GPEVQFQQNM GNGLLLEIYF QRAGYRMGEQ YAVHSRRRFR LLLAPGQAPN PNLQVDPNLW IVHYGPAEKN D RLPVSAIV ...String:
MAVVDPSQNV HGDLLPHIHL ISTFRYATMP RVELQEVTKW LLQAPKIARD TSPFYWTYLD CPADGSILLT WQPTARRGTE FATDGYIWA GPEVQFQQNM GNGLLLEIYF QRAGYRMGEQ YAVHSRRRFR LLLAPGQAPN PNLQVDPNLW IVHYGPAEKN D RLPVSAIV LPPPIHQLLN FRQHLLSMGQ IIRKEFMLSD RVNWPQIPFP TRATSMYAPP IPQRHIPQAM AYPPHPGQPI AP APKRRGG QSSSSSSAAA AAAAAAAQAA QMAGAAAGYH PDVFNDEEDV SAGDMFDHLT PRELSLARYQ QNHEWMEEIL LSP YQIGQI EVSDLGLGKK GELAALTEGI FEAQGFDALQ RGPKKPYTGK LDPGLADEFR KRVEERNAAV KAEIEEMKAK HEKM MAKFK RSAVIKQAEQ ELRFAVQETG TEFWRLEGKI DEGEEAPSQK IITKSLDEIV ARVEELVGKH ATVVKDVHRI QDGGY QEPQ PEPPAPTAAP SAGAVGDMSC QASHAGSNGS GVLIGSDHDI DMGGTAGSLL DQMHSSAGFS STSTPMNNFP TPQAHL PVS SIPSSAATPG VVSVSSPNPV PPTAGVPAAQ VQQQQDVQMG GTEPAAVVPA KEATTATEQG ISSGEGDWVV VGKEGIP PA PGPSNITQPP AAPATAPLAT TPAATGPGGA PTPGSTALIE TDFADLDTAG DALASYEAAA AGSGSQNGDD HEGGRLED E EDMDMMVGGE ESAFGEAFEG VEAANAAVGQ GGVEGGGDVS DYKDDDDK

UniProtKB: DUF1750-domain-containing protein

+
Macromolecule #13: Putative chromatin structure-remodeling complex protein

MacromoleculeName: Putative chromatin structure-remodeling complex protein
type: protein_or_peptide / ID: 13 / Details: THE C TERMINAL CONTAINS 6XHIS TAG / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 86.517656 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPPPIQQVPL RIVDTPASNP ELFARKQRQL RYPQPSAPNP GALVRATLGA TALEGPNIYE RCLLALRSSL RAEQAFALNH LVKISYERG DKYKFSQFSG LAEGLTEFAL GVTKLFYGVE MFISHDFDLD CDDPTALDGI NGTDDLDRRL AEVKKVNPDI Q DSIQPAEF ...String:
MPPPIQQVPL RIVDTPASNP ELFARKQRQL RYPQPSAPNP GALVRATLGA TALEGPNIYE RCLLALRSSL RAEQAFALNH LVKISYERG DKYKFSQFSG LAEGLTEFAL GVTKLFYGVE MFISHDFDLD CDDPTALDGI NGTDDLDRRL AEVKKVNPDI Q DSIQPAEF ADQLTLIIEA VLTIRNMVML PDNAWFLSEY PPVKDLLVII LHLPEMDMLV ELKHLALEIA EQLTPYMLLS ES DPLYFIM MRTLERSEDR GMILSALRAL GRIAMQHPTE TNKLKGVGQH PNILPKMASW LLLNDDELLD ACLDFLYQYT AEP DNIDLM LRTINVEHVV AHLVRLLSHG AKRSQREIVL KAAQVAYEAA PEQILALPKD LQERLLAMEE PDRCQAWLRC LFEE DPGSH VTQIAIWQAY NGAFAEALKM QGRPMIGAQE YIKNISNVYQ SGGAQVVREQ GPTGEIQKFI MSGIRPRTRP IALDG RSYL KCHWKYDGPT PPGIPVPQHC GSWHLTAETM WRHILVDHLR EPITSDGKFQ NREAAFSCHW DGCTKYRTPT KQRLAQ LMA HVKTHLRAEE AQQHKMSQLT GPNDPNQPLT ASPTVSKRHP PHQPHASRQG RVIRPATTIT ITYEETASAR DERNPNA PP QAAGIPLSAV LILRNIARNV PHTNLEREER ERAAEAAGQG EQQAQVVVSN DREKEIDDDA GSRIKAIWNE RLFRPVLP R LWEVFTENRL LAPYVASLFS LLERDDRDYS SEGYFFHHHH HH

UniProtKB: Chromatin structure-remodeling complex protein

+
Macromolecule #14: Putative chromatin structure-remodeling complex protein

MacromoleculeName: Putative chromatin structure-remodeling complex protein
type: protein_or_peptide / ID: 14 / Details: THE C-TERMINAL 8AA ENCODES A FLAG TAG / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 66.694156 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAVRSDSQQA VFSSYAPRLR TYNNALLQPI LPGSGQGPLS RTTKRGTAII NYAEDGYDDL DDDEDDGRRR PTGLRSLRRD DSTSKVDPS EKVGKDTSVP VEMQGYWRDW MGKNKPNRSD VHNYVQACLP LTLIPIRIDL DIPSFTPQPP LPPVPGGSVD N THPLYKPQ ...String:
MAVRSDSQQA VFSSYAPRLR TYNNALLQPI LPGSGQGPLS RTTKRGTAII NYAEDGYDDL DDDEDDGRRR PTGLRSLRRD DSTSKVDPS EKVGKDTSVP VEMQGYWRDW MGKNKPNRSD VHNYVQACLP LTLIPIRIDL DIPSFTPQPP LPPVPGGSVD N THPLYKPQ EPTVPYRLRD TFLWNLHESL ITTDYFATQL VQDLDLPNKQ QTIAEISKQI RTQLEEYAGV ALHPLFHART NR AKATADN TTKGTTPAPN QAQGASRADT PNAPITSFKP GAAGSSVVQT AQGEVSARAT PIPPEAGDDS PDDTYRCIIN LNI TLSSQV YTDKFEWSLL HPPGTAEIFA KQTCADLGLY GEWVPALTHA IYEAVLKLKK EACEAGGLVA GWTAFGSGTL AGGA GTEFP NDAAPTAGGE GAGWRYDPEH LAEEWEPKLE TLSKEEIEKR EGDRERQIRR LRRETARFSS NTGMAGGIPI GFAFG SLIE QEQEERLAKL RRRRRFRSPS PGRDSVAPGR GTPAAGGAGG GGAEGYGGGG GTLTEAERTT WRCSHCRVWG TSVWAV RDG PFGPRSLCNN CGFMYERDRK LPRWTKMLHA NDPRPFDYKD DDDK

UniProtKB: Chromatin structure-remodeling complex protein

+
Macromolecule #15: Rsc7

MacromoleculeName: Rsc7 / type: protein_or_peptide / ID: 15 / Details: THE C-TERMINAL 8AA ENCODES A FLAG TAG / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 60.565992 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPSRRSGRAA AKRAQQALES TPKTFEGIDD EDEPMPDAAE QEDAEAKDDA DEDGDKDDGS VVEEEAVEED EEESAKSPTP PPEPVVRRR RLGRPPKNRP PDWDQLPIEP PNPDATPRRR GRGGWRGRGG RKGQQQQPQQ QAVEVDGVFY NIVDDELDLP E DPEGEEKV ...String:
MPSRRSGRAA AKRAQQALES TPKTFEGIDD EDEPMPDAAE QEDAEAKDDA DEDGDKDDGS VVEEEAVEED EEESAKSPTP PPEPVVRRR RLGRPPKNRP PDWDQLPIEP PNPDATPRRR GRGGWRGRGG RKGQQQQPQQ QAVEVDGVFY NIVDDELDLP E DPEGEEKV DKLGNLKGGR EYRCRTFTVL GRGERLYMLS TEPARCVGFR DSYLFFTKHK RLHKIIVNDE EKRDMIERDI IP HSYKGRS IGIVTARSVF REFGAQIIVG GRRIIDDYEV AKARADGVVE GELADPNDIF DPDKPYNKNQ YVAWHGASSV YHS GGPSVP QQNVKADTKK RRVAVNDVNW QLEHAREASH FNSVLSAVRR QNLNGVYDIH TNTMFYPRTM QPTHARIVQV NDSE VSPDA HKSKVFPPLK PSISRNFLVL DTHLETPPAG ISPAAYDVPF RTSRADYENW LATDFTAPFK GLMAVSDEIR DLLPP ECRA AFDRAREQEE NWFAKWGDEK DCTSRREPII DKAIVPYSMT LGDYKDDDDK

UniProtKB: Uncharacterized protein

+
Macromolecule #16: Rsc1

MacromoleculeName: Rsc1 / type: protein_or_peptide / ID: 16 / Details: THE C-TERMINAL 8AA ENCODES A FLAG TAG / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 112.634406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPTLRERPSR GEASPAKSAS TAATRSTPRT RRTSMPGDAI EVRESIEAKG DVDEDIEMED ADGSATPRKN KDKNKDKDAD GDIKMGGAS GTGDVDADGE PDDEVAQTQQ DDSQRDLLQL IRETSEYLCR YTIKIDGEEH EIASGFQRLV SKRSLPDYFE V IKEPMAFS ...String:
MPTLRERPSR GEASPAKSAS TAATRSTPRT RRTSMPGDAI EVRESIEAKG DVDEDIEMED ADGSATPRKN KDKNKDKDAD GDIKMGGAS GTGDVDADGE PDDEVAQTQQ DDSQRDLLQL IRETSEYLCR YTIKIDGEEH EIASGFQRLV SKRSLPDYFE V IKEPMAFS TIRAKIGKKT YQKFSEFVHD VTRICHNAQV YNRPSAPIFA DAAKLLEVFK EKLDELVKEG AITAEEAQIP DL GPLPEFE ESPPPEEEEE EEEEEEEEEE EEEDDDSDDD GRRRSRRRNR KGASRRGGDD DDDDDYKKQR PGRPPKVLTP MEA RIESLL KGLRKFKNEN GQPRVVYFDR LPEKGEPISL DIIKKNHKRK KYQNVDEVLQ DLLRMFNNAK QHHDENSQVY KDAV ELEKQ ARLLAEIEKA RPDEDFRGED GKLPLASIEH KGEIWKVGDW VHIRNPNDLS KPIVAQIFRT WSDKSGQKWV NACWY YRPE QTVHRFDKHF YENEVVKTGQ YRDHRIDDIE DRCFVMFITR YPRGRPRGLP PDKAVYVCES RYNEETFKFN KIKTWS GCL PDEVREKDYE MDLFDVPRVM RKFPSPIKHL LQADAKETDP LPKPTWRSPN APPLIGAVHR RPREPNESPP PEPHPVP VP VAPGAVPLPM APQVPIKANV PGVTGPPPPS YHHPAVLTPA PAPSPAHYQV QHFAPRQAPP PVPQQVPGPP MPHFQPQP Q PMPMHVPPQP GMMPHPMQQM PPAPHFPPAP HAYPPQYGAQ PPQAPPPPNY YQPAPNHIAS VPYEQHHRPV HAAPPPVTP SRPPPPMAPA PPNITTMPPH ASPHVSAPPP APAPHVYNAP RAPEVYTLAD NIDAAIPKEV REQFQCDENG RILFFTGAPL DRPANRVAE AYSQLGHSVR HLASIKQLRE ERARKRKERD EALARERAAQ EEEAKRQRLA QEQDSNDAAT LEQKKAEARE L LEKVLRDW AAEIDRGTQL LREDLDYKDD DDK

UniProtKB: Uncharacterized protein

+
Macromolecule #17: Rsc58

MacromoleculeName: Rsc58 / type: protein_or_peptide / ID: 17 / Details: THE C TERMINAL CONTAINS 6XHIS TAG / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 107.232539 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASPDVAPPQ ANGVAALSRP DSPASSIASQ STKRKREPAD EAAVDPSLSA ISDSQKPTLN GQRAASECMP LIRDFFAVLE SFDSSESPI LKRHLPEPVS HGEPSTKRAK SEDPSKPLTI ADKVTQNAYE NLDDFVVDVA RATDARIKDL EAAGATADEN A IAEAAAFK ...String:
MASPDVAPPQ ANGVAALSRP DSPASSIASQ STKRKREPAD EAAVDPSLSA ISDSQKPTLN GQRAASECMP LIRDFFAVLE SFDSSESPI LKRHLPEPVS HGEPSTKRAK SEDPSKPLTI ADKVTQNAYE NLDDFVVDVA RATDARIKDL EAAGATADEN A IAEAAAFK TKALELYRRE LAYPNVPPPS SSGKVSSIST RTGGVVLSTV GMAPTMRPLF TSLRQAPDGS NKPLPETALP NG VSVTRVL QEPPLTGDKS GRTPTLGELF PSPRNLPPLQ PPKAPKTTTK SNVLTFYHPE FIEKSKYRTG TYFSQVLSQG VWL DYTNAT PTVHTKTKQR ERAQSLAGVK PSSIELEMTE LEALFRGAFS SFAPSRDDSG AIVPAQQVSR IWYQRIGRRN LNKM VEEIE PEVAEEDGVP ARADSAVIME VDEERVKEVI ENWDDSLIDP NLDSVLGKKS DEEKQVDDIL EEISDMIETL ASYQR NRNL TLPTSQDRYS ADPVNGDMLR NGSASHQPSE EEMMAYQALK SQLALIIQTL PPWAVARLNS DKLAELAVST KIEVRS DDY RGVMEEDEPA RQARLAAQVA TTNQRQSQRA PSVAAAQYAN HQYQPQFTHS ARPVPNAPHY QPQTPVRPQP NVYSRAP SA VPIPQPHHQA RPQPPPAQYR PQMYAPQLAK AQGPYGHSGM PQQYVPSPAQ QPRMPPQQPP PPHYNNMVPA GAPPNSRF P QAYPAGYPQQ QPIHPQHMPP HAQSVPMPPQ HHPPMTQQPM PAPYSPYPNG APMPRTMSPQ VPPQPPHTYA QSPTPQHQQ MPRPPPPYGP GTTQPGMPPN TIPRPPPQQY VPGSPGPAGM MPARPPQHQP VAPTPPPGQH PLPAAAMPSY APVMTTTADN LQPRPATPG HQAPPPGGVV GLAGIGLAGQ MDVHKLAAAK MQMAQAQQRT QTPVPVPQVP GQVPPPQLVN GTGVRTVAPS P SPVPGTPT VAPAPVPVPP QQQPSAHHHH HH

UniProtKB: Uncharacterized protein

+
Macromolecule #5: DNA (167-MER)

MacromoleculeName: DNA (167-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 51.333703 KDa
SequenceString: (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT) ...String:
(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DT)(DG)(DT)(DG)(DC)(DA)(DT)(DG)(DT) (DA)(DT)(DT)(DG)(DA)(DA)(DC) (DA)(DG) (DC)(DG)(DA)(DC)(DC)

+
Macromolecule #6: DNA (167-MER)

MacromoleculeName: DNA (167-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 51.773973 KDa
SequenceString: (DG)(DG)(DT)(DC)(DG)(DC)(DT)(DG)(DT)(DT) (DC)(DA)(DA)(DT)(DA)(DC)(DA)(DT)(DG)(DC) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA) (DC) (DA)(DC)(DG)(DT)(DG)(DC) ...String:
(DG)(DG)(DT)(DC)(DG)(DC)(DT)(DG)(DT)(DT) (DC)(DA)(DA)(DT)(DA)(DC)(DA)(DT)(DG)(DC) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA) (DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT) (DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG) (DG)(DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC) (DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT) (DT)(DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG) (DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG) (DC)(DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC) (DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG) (DT)(DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC) (DT)(DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC) (DC)(DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC) (DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA) (DC)(DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC) (DT)(DC)(DC)(DA)(DG)

+
Macromolecule #18: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 18 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
30.0 mMKClPotassium chloride
2.0 mMMgCl2Magnesium chloride
20.0 mMC8H18N2O4SHEPEs
0.5 mMC10H15N5O10P2ADP
1.0 mMBeSO4Beryllium sulfate
8.0 mMNaFsodium fluoride
VitrificationCryogen name: ETHANE
DetailsThis sample was homogenous and monodisperse.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 754609
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0) / Number images used: 117380
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-23fu:
Cryo-EM structure of Chaetomium thermophilum RSC bound to a nucleosome

+
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