[English] 日本語
Yorodumi
- EMDB-44074: Cryo-EM structure of native SWR1 bound to DNA (composite structure) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-44074
TitleCryo-EM structure of native SWR1 bound to DNA (composite structure)
Map dataComposite cryo-EM map of SWR1-DNA complex.
Sample
  • Complex: Native SWR1 bound to DNA.
    • Complex: Native SWR1 complex
      • Protein or peptide: x 6 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


ATP-dependent H2AZ histone chaperone activity / R2TP complex / Swr1 complex / protein targeting to vacuole / Ino80 complex / box C/D snoRNP assembly / 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / nucleosome binding / DNA helicase activity ...ATP-dependent H2AZ histone chaperone activity / R2TP complex / Swr1 complex / protein targeting to vacuole / Ino80 complex / box C/D snoRNP assembly / 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / nucleosome binding / DNA helicase activity / nuclear periphery / transcription initiation-coupled chromatin remodeling / rRNA processing / histone binding / 5'-3' DNA helicase activity / DNA helicase / protein stabilization / chromatin remodeling / DNA repair / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / ATP binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
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 ...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 / ATPase, nucleotide binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
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) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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

-
Structure visualization

Supplemental images

emd_44074.png

Downloads & links

-
Map

FileDownload / File: emd_44074.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite cryo-EM map of SWR1-DNA 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: 0.15
Minimum - Maximum-0.039235763 - 1.9881451
Average (Standard dev.)0.0012745858 (±0.025840033)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Sample components

+
Entire : Native SWR1 bound to DNA.

EntireName: Native SWR1 bound to DNA.
Components
  • Complex: Native SWR1 bound to DNA.
    • 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
    • DNA: DNA (147-MER)
    • DNA: DNA (147-MER)
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

+
Supramolecule #1: Native SWR1 bound to DNA.

SupramoleculeName: Native SWR1 bound to DNA. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Details: Endogenously purified yeast SWR1 complex bound to 147-bp dsDNA fragment in the presence of ATPgS.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303
Molecular weightTheoretical: 1.19 MDa

+
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

+
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

+
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

+
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

+
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

+
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

+
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

+
Macromolecule #7: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.145754 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) (DC)(DA)(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) (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)

+
Macromolecule #8: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.604047 KDa
SequenceString: (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) ...String:
(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)

+
Macromolecule #9: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 9 / Number of copies: 4 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

+
Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #12: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 12 / Number of copies: 4 / 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

Concentration0.125 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
3.5 %glycerol
0.25 mMTCEP
1.0 mMATP-gamma-s
0.05 %glutaraldehyde

Details: 20 mM HEPES pH 7.6, 0.2 mM EDTA, 2 mM MgCl2, 100 mM NaCl, 0.01% IGEPAL CA-630, 3.5% glycerol, and 0.25 mM TCEP, 1 mM ATP-gamma-s, 0.05% glutaraldehyde.
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / 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: 6 second blot time and blot force of 12..

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
SoftwareName: SerialEM (ver. 3.7.6)
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5379 / 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: 386667
Details: 2D classification was used to remove graphene edges.
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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3)
Details: Refined maps were post-processed using DeepEMhancer
Number images used: 101246
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final 3D classificationSoftware - Name: RELION (ver. 3.1.3)

-
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
SoftwareName: ISOLDE (ver. 1.7)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 84 / Target criteria: Cross-correlation coefficient
Output model

PDB-9b1d:
Cryo-EM structure of native SWR1 bound to DNA (composite structure)

+
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