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- EMDB-44075: Cryo-EM structure of native SWR1 bound to nucleosome (composite s... -

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Basic information

Entry
Database: EMDB / ID: EMD-44075
TitleCryo-EM structure of native SWR1 bound to nucleosome (composite structure)
Map dataComposite cryo-EM structure of SWR1-nucleosome complex
Sample
  • Complex: Native SWR1 bound to nucleosome.
    • Complex: Native SWR1 complex
      • Protein or peptide: x 6 types
    • Protein or peptide: x 5 types
    • DNA: x 2 types
  • Ligand: x 4 types
KeywordsChromatin Remodeler / Snf2 family ATPase / histone exchange / H2A.Z / GENE REGULATION
Function / homology
Function and homology information


Interleukin-7 signaling / Chromatin modifying enzymes / Factors involved in megakaryocyte development and platelet production / RCAF complex / ATP-dependent H2AZ histone chaperone activity / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RNA Polymerase I Promoter Escape / Formation of the beta-catenin:TCF transactivating complex ...Interleukin-7 signaling / Chromatin modifying enzymes / Factors involved in megakaryocyte development and platelet production / RCAF complex / ATP-dependent H2AZ histone chaperone activity / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RNA Polymerase I Promoter Escape / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Regulation of endogenous retroelements by KRAB-ZFP proteins / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / HATs acetylate histones / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / polytene chromosome / R2TP complex / Swr1 complex / protein targeting to vacuole / Ino80 complex / endoplasmic reticulum organization / box C/D snoRNP assembly / 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / nucleosome binding / nucleosomal DNA binding / DNA helicase activity / nuclear periphery / transcription initiation-coupled chromatin remodeling / structural constituent of chromatin / rRNA processing / nucleosome / nucleosome assembly / chromatin organization / histone binding / 5'-3' DNA helicase activity / DNA helicase / protein stabilization / chromatin remodeling / protein heterodimerization activity / DNA repair / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
SWR1-complex protein 3 / Vps71/ZNHIT1 / Zinc finger HIT-type profile. / Vps72/YL1 family / Vps72/YL1, N-terminal / YL1 nuclear protein / Zinc finger, HIT-type / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain ...SWR1-complex protein 3 / Vps71/ZNHIT1 / Zinc finger HIT-type profile. / Vps72/YL1 family / Vps72/YL1, N-terminal / YL1 nuclear protein / Zinc finger, HIT-type / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / Actin / Actin family / Actin / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / ATPase, nucleotide binding domain / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H4 / Histone H2B / Histone H2A / Histone H3 / SWR1-complex protein 3 / Vacuolar protein sorting-associated protein 72 / Vacuolar protein sorting-associated protein 71 / RuvB-like protein 2 / Actin-like protein ARP6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae W303 (yeast) / Drosophila melanogaster (fruit fly) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsLouder RK / Park G / Wu C
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM149291 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM125831 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM133151 United States
CitationJournal: Cell / Year: 2024
Title: Molecular basis of global promoter sensing and nucleosome capture by the SWR1 chromatin remodeler.
Authors: Robert K Louder / Giho Park / Ziyang Ye / Justin S Cha / Anne M Gardner / Qin Lei / Anand Ranjan / Eva Höllmüller / Florian Stengel / B Franklin Pugh / Carl Wu /
Abstract: The SWR1 chromatin remodeling complex is recruited to +1 nucleosomes downstream of transcription start sites of eukaryotic promoters, where it exchanges histone H2A for the specialized variant H2A.Z. ...The SWR1 chromatin remodeling complex is recruited to +1 nucleosomes downstream of transcription start sites of eukaryotic promoters, where it exchanges histone H2A for the specialized variant H2A.Z. Here, we use cryoelectron microscopy (cryo-EM) to resolve the structural basis of the SWR1 interaction with free DNA, revealing a distinct open conformation of the Swr1 ATPase that enables sliding from accessible DNA to nucleosomes. A complete structural model of the SWR1-nucleosome complex illustrates critical roles for Swc2 and Swc3 subunits in oriented nucleosome engagement by SWR1. Moreover, an extended DNA-binding α helix within the Swc3 subunit enables sensing of nucleosome linker length and is essential for SWR1-promoter-specific recruitment and activity. The previously unresolved N-SWR1 subcomplex forms a flexible extended structure, enabling multivalent recognition of acetylated histone tails by reader domains to further direct SWR1 toward the +1 nucleosome. Altogether, our findings provide a generalizable mechanism for promoter-specific targeting of chromatin and transcription complexes.
History
DepositionMar 13, 2024-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44075.png

Downloads & links

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Map

FileDownload / File: emd_44075.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite cryo-EM structure of SWR1-nucleosome complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 384 pix.
= 395.52 Å		1.03 Å/pix.
x 384 pix.
= 395.52 Å		1.03 Å/pix.
x 384 pix.
= 395.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.0054022768 - 2.1138809
Average (Standard dev.)0.0021323424 (±0.03182059)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 395.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Native SWR1 bound to nucleosome.

EntireName: Native SWR1 bound to nucleosome.
Components
  • Complex: Native SWR1 bound to nucleosome.
    • Complex: Native SWR1 complex
      • Protein or peptide: Helicase SWR1
      • Protein or peptide: Vacuolar protein sorting-associated protein 72
      • Protein or peptide: Actin-like protein ARP6
      • Protein or peptide: Vacuolar protein sorting-associated protein 71
      • Protein or peptide: RuvB-like protein 1
      • Protein or peptide: RuvB-like protein 2
    • Protein or peptide: SWR1-complex protein 3
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • DNA: DNA (214-MER)
    • DNA: DNA (214-MER)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Native SWR1 bound to nucleosome.

SupramoleculeName: Native SWR1 bound to nucleosome. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Details: Endogenously purified yeast SWR1 complex bound to 60-N-7 nucleosome fragment in the presence of ADP-BeF3.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303
Molecular weightTheoretical: 1.19 MDa

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Supramolecule #2: Native SWR1 complex

SupramoleculeName: Native SWR1 complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6 / Details: Endogenously purified yeast SWR1 complex
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303

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Macromolecule #1: Helicase SWR1

MacromoleculeName: Helicase SWR1 / type: protein_or_peptide / ID: 1 / Details: Fusion protein with C-terminal 3xFLAG / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)
Molecular weightTheoretical: 178.058172 KDa
SequenceString: MTTSRKSHAK DKKAGGEQDL ADLKFRYDLL TNELFHLREF VSLVDYDPTH FNDSESFQKF LRETHLSLEE RGEKFTDDVA KKGTNGDLT RRRRNLRTST VVSSETTNEK KGDIELKLES IAPLVRNKCE ELKYKLSDHS NRKSIVPQKR PIQHLKKREA A KSLKFKSE ...String:
MTTSRKSHAK DKKAGGEQDL ADLKFRYDLL TNELFHLREF VSLVDYDPTH FNDSESFQKF LRETHLSLEE RGEKFTDDVA KKGTNGDLT RRRRNLRTST VVSSETTNEK KGDIELKLES IAPLVRNKCE ELKYKLSDHS NRKSIVPQKR PIQHLKKREA A KSLKFKSE RKENPLPLHE HIAEERYDHI AKVEEPSEAF TIKCPSDDSS FENTSEHYSD NFYFTTSSEE EDIKKKRGRK KK KPRIKLV VHPPKQTITN PLHVVKPGYE SLHEYIASFK SLEDDLTLEE YNKYIDEQRR LLSRLKKGIE NGALKYDKET DSL QPITSK EIKTIITYKP DPISYFYKQQ DLQIHTDHLI NQGIHMSKLF RSSTKARIAR AKKVSQMIEQ HFKHVAGAEE RKAK EEERH KKSLARFAVQ AVKKRWNMAE KAYRILRKDE EEQLKRIEGK QHLSKMLEKS TQLLEAQLNQ VNDDGRSSTP SSDSN DVLS ESDDDMDDEL STSSDEDEEV DADVGLENSP ASTEATPTDE SLNLIQLKEK YGHFNGSSTV YDSRNKDEKF PTLDKH ESS SSESSVMTGE ESSIYSSSEN ESQNENDRES DDKTPSVGLS ALFGKGEESD GDLDLDDSED FTVNSSSVEG EELEKDQ VD NSAATFERAG DFVHTQNENR DDIKDVEEDA ETKVQEEQLS VVDVPVPSLL RGNLRTYQKQ GLNWLASLYN NHTNGILA D EMGLGKTIQT ISLLAYLACE KENWGPHLIV VPTSVLLNWE MEFKRFAPGF KVLTYYGSPQ QRKEKRKGWN KPDAFHVCI VSYQLVVQDQ HSFKRKRWQY MVLDEAHNIK NFRSTRWQAL LNFNTQRRLL LTGTPLQNNL AELWSLLYFL MPQTVIDGKK VSGFADLDA FQQWFGRPVD KIIETGQNFG QDKETKKTVA KLHQVLRPYL LRRLKADVEK QMPAKYEHIV YCKLSKRQRF L YDDFMSRA QTKATLASGN FMSIVNCLMQ LRKVCNHPNL FEVRPILTSF VLEHCVASDY KDVERTLLKL FKKNNQVNRV DL DFLNLVF TLNDKDLTSY HAEEISKLTC VKNFVEEVNK LRETNKQLQE EFGEASFLNF QDANQYFKYS NKQKLEGTVD MLN FLKMVN KLRCDRRPIF GKNLIDLLTK DRRVKYDKSS IIDNELIKPL QTRVLDNRKI IDTFAVLTPS AVSLDMRKLA LGLN DDSSV GENTRLKVMQ NCFEVSNPLH QLQTKLTIAF PDKSLLQYDC GKLQKLAILL QQLKDNGHRA LIFTQMTKVL DVLEQ FLNY HGYLYMRLDG ATKIEDRQIL TERFNTDSRI TVFILSSRSG GLGINLTGAD TVIFYDSDWN PAMDKQCQDR CHRIGQ TRD VHIYRFVSEH TIESNILKKA NQKRQLDNVV IQEGDFTTDY FSKLSVRDLL GSELPENASG GDKPLIADAD VAAKDPR QL ERLLAQAEDE DDVKAANLAM REVEIDNDDF DESTEKKAAN EEEENHAELD EYEGTAHVDE YMIRFIANGY YYGSGGSG D YKDHDGDYKD HDIDYKDDDD KGS

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Macromolecule #2: Vacuolar protein sorting-associated protein 72

MacromoleculeName: Vacuolar protein sorting-associated protein 72 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)
Molecular weightTheoretical: 90.709008 KDa
SequenceString: MSDEGADKSL DTNTEFIIQT RSRRSNAGNK LQKLLEQELR DIESTKRQIS SYKNGNDDEE DEIGLLFQED EDDEDFEMMA KDDDDEGEE KEDETQSIRK EPSQASSEQA ADDLMFSSSE SEDSSNENDE DAEEKEIRRQ ELLSRKKRNK RLQKGPVVIK K QKPKPKSG ...String:
MSDEGADKSL DTNTEFIIQT RSRRSNAGNK LQKLLEQELR DIESTKRQIS SYKNGNDDEE DEIGLLFQED EDDEDFEMMA KDDDDEGEE KEDETQSIRK EPSQASSEQA ADDLMFSSSE SEDSSNENDE DAEEKEIRRQ ELLSRKKRNK RLQKGPVVIK K QKPKPKSG EAIPRSHHTH EQLNAETLLL NTRRTSKRSS VMENTMKVYE KLSKAEKKRK IIQERIRKHK EQESQHMLTQ EE RLRIAKE TEKLNILSLD KFKEQEVWKK ENRLALQKRQ KQKFQPNETI LQFLSTAWLM TPAMELEDRK YWQEQLNKRD KKK KKYPRK PKKNLNLGKQ DASDDKKRES EESIKNDGDV NSLGENSSSV HNQKRIEETS TNDTVEGESS PDAAVSRVNS DELK PTALP DVTLDAIANK QSTVDEAPNS QPQKNIITNE QKITNVGEPI QNLHNEEIKD EMVSALESRE NTFENSSPAA QVVSQ RDNS ATPTPSNSTG TEDTILISPD TDIKGEPEPC LKTEGIENLS HNVPQETKSN TDVSFLKQVT FTDHPQVAII DTEESP SKK DTANVDESSA ENSLSTQTYE GPEQLTSRNF VTLYDFPNAP PNLKDFNTNL FGDRWSYTNG LSATQRPQDM KTVFHSI LP SPPQSSVPSP TVDISLDLSA LANFPSFGEY DKKIVHQINT EINKDLEIKI KTQPPTGVFL ANGIRKKCLI TNKECQYF D PRTGVPYSDV EAYKIIQRIQ DPISKEEGRS DIKRDETTNE DSDDQVRFKW FGFKNGGIYL DLSQRPAKGV PEGF

UniProtKB: Vacuolar protein sorting-associated protein 72

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Macromolecule #3: Actin-like protein ARP6

MacromoleculeName: Actin-like protein ARP6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)
Molecular weightTheoretical: 50.100582 KDa
SequenceString: METPPIVIDN GSYEIKFGPS TNKKPFRALN ALAKDKFGTS YLSNHIKNIK DISSITFRRP HELGQLTLWE LESCIWDYCL FNPSEFDGF DLKEGKGHHL VASESCMTLP ELSKHADQVI FEEYEFDSLF KSPVAVFVPF TKSYKGEMRT ISGKDEDIDI V RGNSDSTN ...String:
METPPIVIDN GSYEIKFGPS TNKKPFRALN ALAKDKFGTS YLSNHIKNIK DISSITFRRP HELGQLTLWE LESCIWDYCL FNPSEFDGF DLKEGKGHHL VASESCMTLP ELSKHADQVI FEEYEFDSLF KSPVAVFVPF TKSYKGEMRT ISGKDEDIDI V RGNSDSTN STSSESKNAQ DSGSDYHDFQ LVIDSGFNCT WIIPVLKGIP YYKAVKKLDI GGRFLTGLLK ETLSFRHYNM MD ETILVNN IKEQCLFVSP VSYFDSFKTK DKHALEYVLP DFQTSFLGYV RNPRKENVPL PEDAQIITLT DELFTIPETF FHP EISQIT KPGIVEAILE SLSMLPEIVR PLMVGNIVCT GGNFNLPNFA QRLAAELQRQ LPTDWTCHVS VPEGDCALFG WEVM SQFAK TDSYRKARVT REEYYEHGPD WCTKHRFGYQ NWI

UniProtKB: Actin-like protein ARP6

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Macromolecule #4: Vacuolar protein sorting-associated protein 71

MacromoleculeName: Vacuolar protein sorting-associated protein 71 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)
Molecular weightTheoretical: 32.073479 KDa
SequenceString: MKALVEEIDK KTYNPDIYFT SLDPQARRYT SKKINKQGTI STSRPVKRIN YSLADLEARL YTSRSEGDGN SISRQDDRNS KNSHSFEER YTQQEILQSD RRFMELNTEN FSDLPNVPTL LSDLTGVPRD RIESTTKPIS QTSDGLSALM GGSSFVKEHS K YGHGWVLK ...String:
MKALVEEIDK KTYNPDIYFT SLDPQARRYT SKKINKQGTI STSRPVKRIN YSLADLEARL YTSRSEGDGN SISRQDDRNS KNSHSFEER YTQQEILQSD RRFMELNTEN FSDLPNVPTL LSDLTGVPRD RIESTTKPIS QTSDGLSALM GGSSFVKEHS K YGHGWVLK PETLREIQLS YKSTKLPKPK RKNTNRIVAL KKVLSSKRNL HSFLDSALLN LMDKNVIYHN VYNKRYFKVL PL ITTCSIC GGYDSISSCV NCGNKICSVS CFKLHNETRC RNR

UniProtKB: Vacuolar protein sorting-associated protein 71

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Macromolecule #5: RuvB-like protein 1

MacromoleculeName: RuvB-like protein 1 / type: protein_or_peptide / ID: 5
Details: Fusion protein with C-terminal maltose-binding protein
Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)
Molecular weightTheoretical: 91.413242 KDa
SequenceString: MVAISEVKEN PGVNSSNSGA VTRTAAHTHI KGLGLDESGV AKRVEGGFVG QIEAREACGV IVDLIKAKKM SGRAILLAGG PSTGKTALA LAISQELGPK VPFCPLVGSE LYSVEVKKTE TLMENFRRAI GLRIKETKEV YEGEVTELTP EDAENPLGGY G KTISHVIV ...String:
MVAISEVKEN PGVNSSNSGA VTRTAAHTHI KGLGLDESGV AKRVEGGFVG QIEAREACGV IVDLIKAKKM SGRAILLAGG PSTGKTALA LAISQELGPK VPFCPLVGSE LYSVEVKKTE TLMENFRRAI GLRIKETKEV YEGEVTELTP EDAENPLGGY G KTISHVIV GLKSAKGTKT LRLDPTIYES IQREKVSIGD VIYIEANTGA VKRVGRSDAY ATEFDLETEE YVPLPKGEVH KK KEIVQDV TLHDLDVANA RPQGGQDVIS MMGQLLKPKK TEITEKLRQE VNKVVAKYID QGVAELIPGV LFIDEVNMLD IEI FTYLNK ALESNIAPVV VLASNRGMTT VRGTEDVISP HGVPPDLIDR LLIVRTLPYD KDEIRTIIER RATVERLQVE SSAL DLLAT MGTETSLRYA LQLLAPCGIL AQTSNRKEIV VNDVNEAKLL FLDAKRSTKI LETSANYLSG GGASMKIEEG KLVIW INGD KGYNGLAEVG KKFEKDTGIK VTVEHPDKLE EKFPQVAATG DGPDIIFWAH DRFGGYAQSG LLAEITPDKA FQDKLY PFT WDAVRYNGKL IAYPIAVEAL SLIYNKDLLP NPPKTWEEIP ALDKELKAKG KSALMFNLQE PYFTWPLIAA DGGYAFK YE NGKYDIKDVG VDNAGAKAGL TFLVDLIKNK HMNADTDYSI AEAAFNKGET AMTINGPWAW SNIDTSKVNY GVTVLPTF K GQPSKPFVGV LSAGINAASP NKELAKEFLE NYLLTDEGLE AVNKDKPLGA VALKSYEEEL AKDPRIAATM ENAQKGEIM PNIPQMSAFW YAVRTAVINA ASGRQTVDEA LKDAQTN

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Macromolecule #6: RuvB-like protein 2

MacromoleculeName: RuvB-like protein 2 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)
Molecular weightTheoretical: 51.673488 KDa
SequenceString: MSIQTSDPNE TSDLKSLSLI AAHSHITGLG LDENLQPRPT SEGMVGQLQA RRAAGVILKM VQNGTIAGRA VLVAGPPSTG KTALAMGVS QSLGKDVPFT AIAGSEIFSL ELSKTEALTQ AFRKSIGIKI KEETELIEGE VVEIQIDRSI TGGHKQGKLT I KTTDMETI ...String:
MSIQTSDPNE TSDLKSLSLI AAHSHITGLG LDENLQPRPT SEGMVGQLQA RRAAGVILKM VQNGTIAGRA VLVAGPPSTG KTALAMGVS QSLGKDVPFT AIAGSEIFSL ELSKTEALTQ AFRKSIGIKI KEETELIEGE VVEIQIDRSI TGGHKQGKLT I KTTDMETI YELGNKMIDG LTKEKVLAGD VISIDKASGK ITKLGRSFAR SRDYDAMGAD TRFVQCPEGE LQKRKTVVHT VS LHEIDVI NSRTQGFLAL FTGDTGEIRS EVRDQINTKV AEWKEEGKAE IVPGVLFIDE VHMLDIECFS FINRALEDEF API VMMATN RGVSKTRGTN YKSPHGLPLD LLDRSIIITT KSYNEQEIKT ILSIRAQEEE VELSSDALDL LTKTGVETSL RYSS NLISV AQQIAMKRKN NTVEVEDVKR AYLLFLDSAR SVKYVQENES QYIDDQGNVQ ISIAKSADPD AMDTTE

UniProtKB: RuvB-like protein 2

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Macromolecule #7: SWR1-complex protein 3

MacromoleculeName: SWR1-complex protein 3 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)
Molecular weightTheoretical: 72.648656 KDa
SequenceString: MPAVLRTRSK ESSIEQKPAS RTRTRSRRGK RGRDDDDDDD DEESDDAYDE VGNDYDEYAS RAKLATNRPF EIVAGLPASV ELPNYNSSL THPQSIKNSG VLYDSLVSSR RTWVQGEMFE LYWRRPKKIV SESTPAATES PTSGTIPLIR DKMQKMCDCV M SGGPHTFK ...String:
MPAVLRTRSK ESSIEQKPAS RTRTRSRRGK RGRDDDDDDD DEESDDAYDE VGNDYDEYAS RAKLATNRPF EIVAGLPASV ELPNYNSSL THPQSIKNSG VLYDSLVSSR RTWVQGEMFE LYWRRPKKIV SESTPAATES PTSGTIPLIR DKMQKMCDCV M SGGPHTFK VRLFILKNDK IEQKWQDEQE LKKKEKELKR KNDAEAKRLR MEERKRQQMQ KKIAKEQKLQ LQKENKAKQK LE QEALKLK RKEEMKKLKE QNKNKQGSPS SSMHDPRMIM NLNLMAQEDP KLNTLMETVA KGLANNSQLE EFKKFIEIAK KRS LEENPV NKRPSVTTTR PAPPSKAKDV AEDHRLNSIT LVKSSKTAAT EPEPKKADDE NAEKQQSKEA KTTAESTQVD VKKE EEDVK EKGVKSEDTQ KKEDNQVVPK RKRRKNAIKE DKDMQLTAFQ QKYVQGAEII LEYLEFTHSR YYLPKKSVVE FLEDT DEII ISWIVIHNSK EIEKFKTKKI KAKLKADQKL NKEDAKPGSD VEKEVSFNPL FEADCPTPLY TPMTMKLSGI HKRFNQ IIR NSVSPMEEVV KEMEKILQIG TRLSGYNLWY QLDGYDDEAL SESLRFELNE WEHAMRSRRH KR

UniProtKB: SWR1-complex protein 3

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Macromolecule #8: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.013177 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MSGGKGGKAG SAAKASQSRS AKAGLTFPVG RVHRLLRRGN YAQRIGSGAP VYLTAVLEYL AAEILELAGN AARDNKKTRI IPRHLQLAI RNDDELNKLL GNVTIAQGGV LPNIHQNLLP KKSAKATKAS QEL

UniProtKB: Histone H2A

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Macromolecule #9: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.280362 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MSAKAEKKPA SKAPAEKKPA AKKTSTSTDG KKRSKARKET YSSYIYKVLK QTHPDTGISQ KSMSILNSFV NDIFERIATE ASKLAAYNK KSTISAREIQ TAVRLILPGE LAKHAVSEGT RAVTKYSSST QA

UniProtKB: Histone H2B

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Macromolecule #10: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 15.421101 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3

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Macromolecule #11: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 11.408452 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MTGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #12: DNA (214-MER)

MacromoleculeName: DNA (214-MER) / type: dna / ID: 12 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 65.672789 KDa
SequenceString: (DA)(DT)(DC)(DG)(DC)(DA)(DT)(DC)(DG)(DA) (DT)(DC)(DT)(DT)(DC)(DA)(DC)(DA)(DC)(DC) (DG)(DA)(DG)(DT)(DT)(DC)(DA)(DT)(DC) (DC)(DC)(DT)(DT)(DA)(DT)(DG)(DT)(DG)(DA) (DT) (DG)(DG)(DA)(DC)(DC)(DC) ...String:
(DA)(DT)(DC)(DG)(DC)(DA)(DT)(DC)(DG)(DA) (DT)(DC)(DT)(DT)(DC)(DA)(DC)(DA)(DC)(DC) (DG)(DA)(DG)(DT)(DT)(DC)(DA)(DT)(DC) (DC)(DC)(DT)(DT)(DA)(DT)(DG)(DT)(DG)(DA) (DT) (DG)(DG)(DA)(DC)(DC)(DC)(DT)(DA) (DT)(DA)(DC)(DG)(DC)(DG)(DG)(DC)(DC)(DG) (DC)(DC) (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) (DC)(DA)(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)(DA)(DT)

+
Macromolecule #13: DNA (214-MER)

MacromoleculeName: DNA (214-MER) / type: dna / ID: 13 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 66.478328 KDa
SequenceString: (DA)(DT)(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) ...String:
(DA)(DT)(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)(DT)(DG)(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)(DG)(DG)(DC)(DG)(DG)(DC) (DC)(DG) (DC)(DG)(DT)(DA)(DT)(DA)(DG)(DG)(DG)(DT) (DC)(DC)(DA)(DT)(DC)(DA)(DC)(DA) (DT) (DA)(DA)(DG)(DG)(DG)(DA)(DT)(DG)(DA)(DA) (DC)(DT)(DC)(DG)(DG)(DT)(DG)(DT)(DG) (DA)(DA)(DG)(DA)(DT)(DC)(DG)(DA)(DT)(DG) (DC)(DG)(DA)(DT)

+
Macromolecule #14: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 14 / Number of copies: 8 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

+
Macromolecule #15: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 15 / Number of copies: 2 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

+
Macromolecule #16: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 16 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #17: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 17 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.08 mg/mL
BufferpH: 7.6
Component:
ConcentrationNameFormula
20.0 mMHEPES
0.2 mMEDTA
2.0 mMmagnesium chlorideMgCl2
100.0 mMsodium chlorideNaCl
0.01 %IGEPAL CA-630
1.0 %glycerol
0.25 mMTCEP
1.0 mMADP
10.0 mMsodium flourideNaF
8.0 mMberyllium chlorideBeCl2
0.05 %glutaraldehyde

Details: 80 nM SWR1, 160 nM nucleosomes, 1 mM ADP, 10 mM NaF, 8 mM BeCl2, 0.05% glutaraldehyde, 20 mM HEPES-KOH pH 7.6, 1.5 mM MgCl2, 0.25 mM TCEP, 0.01% IGEPAL CA-630, 1% glycerol
GridModel: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 3 second blot time and blot force of 10..

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7260 / Average exposure time: 4.0 sec. / Average electron dose: 54.0 e/Å2
Details: Each micrograph was fractionated into 64 frames within a 4 second exposure.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 48543 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 2.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 525782
Startup modelType of model: EMDB MAP
EMDB ID:

4395

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16524
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

Initial model
PDB IDChain

6gej

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 200 / Target criteria: Cross-correlation coefficient
Output model

PDB-9b1e:
Cryo-EM structure of native SWR1 bound to nucleosome (composite structure)

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