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- EMDB-18764: SWR1-hexasome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-18764
TitleSWR1-hexasome complex
Map data
Sample
  • Complex: SWR1-hexasome complex
    • Protein or peptide: x 11 types
    • DNA: x 2 types
  • Ligand: x 4 types
KeywordsChromatin remodelling complex / hexasome / DNA BINDING PROTEIN
Function / homology
Function and homology information


sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / R2TP complex / Assembly of the ORC complex at the origin of replication ...sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / R2TP complex / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / Swr1 complex / protein targeting to vacuole / Ino80 complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / box C/D snoRNP assembly / Oxidative Stress Induced Senescence / replication fork protection complex / RMTs methylate histone arginines / postreplication repair / SUMOylation of chromatin organization proteins / recombinational repair / 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / RNA Polymerase I Promoter Escape / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / rRNA transcription / intracellular copper ion homeostasis / Ub-specific processing proteases / DNA helicase activity / CENP-A containing nucleosome / nucleosome binding / nuclear periphery / aerobic respiration / heterochromatin formation / nucleosome assembly / rRNA processing / structural constituent of chromatin / nucleosome / chromatin organization / 5'-3' DNA helicase activity / DNA helicase / molecular adaptor activity / histone binding / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / protein stabilization / chromatin remodeling / protein heterodimerization activity / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader activity / DNA repair / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / structural molecule activity / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
BCNT-C domain / SWR1-complex protein 5/Craniofacial development protein 1/2 / Bucentaur or craniofacial development / Bucentaur C-terminal (BCNT-C) domain profile. / Vps71/ZNHIT1 / Zinc finger HIT-type profile. / Vps72/YL1, N-terminal / YL1 nuclear protein / Zinc finger, HIT-type / : ...BCNT-C domain / SWR1-complex protein 5/Craniofacial development protein 1/2 / Bucentaur or craniofacial development / Bucentaur C-terminal (BCNT-C) domain profile. / Vps71/ZNHIT1 / Zinc finger HIT-type profile. / 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 / domain in helicases and associated with SANT domains / 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 / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Actin / Actin family / Actin / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / 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 / 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 / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H2B.1 / Histone H4 / Histone H2A.1 / SWR1-complex protein 5 / Histone H3 / Vacuolar protein sorting-associated protein 72 / Vacuolar protein sorting-associated protein 71 / RuvB-like protein 1 / Helicase SWR1 / RuvB-like protein 2 / Actin-like protein ARP6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsJalal ASB / Wigley DB
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust095519/Z/11/Z & 209327/Z/17/Z United Kingdom
Cancer Research UKC6913/A21608 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N009258/1 & MR/R009023/1 United Kingdom
CitationJournal: Mol Cell / Year: 2024
Title: Stabilization of the hexasome intermediate during histone exchange by yeast SWR1 complex.
Authors: Adam S B Jalal / Paul Girvan / Eugene Y D Chua / Lexin Liu / Shijie Wang / Elizabeth A McCormack / Michael T Skehan / Carol L Knight / David S Rueda / Dale B Wigley /
Abstract: The yeast SWR1 complex catalyzes the exchange of histone H2A/H2B dimers in nucleosomes with Htz1/H2B dimers. We use cryoelectron microscopy to determine the structure of an enzyme-bound hexasome ...The yeast SWR1 complex catalyzes the exchange of histone H2A/H2B dimers in nucleosomes with Htz1/H2B dimers. We use cryoelectron microscopy to determine the structure of an enzyme-bound hexasome intermediate in the reaction pathway of histone exchange, in which an H2A/H2B dimer has been extracted from a nucleosome prior to the insertion of a dimer comprising Htz1/H2B. The structure reveals a key role for the Swc5 subunit in stabilizing the unwrapping of DNA from the histone core of the hexasome. By engineering a crosslink between an Htz1/H2B dimer and its chaperone protein Chz1, we show that this blocks histone exchange by SWR1 but allows the incoming chaperone-dimer complex to insert into the hexasome. We use this reagent to trap an SWR1/hexasome complex with an incoming Htz1/H2B dimer that shows how the reaction progresses to the next step. Taken together the structures reveal insights into the mechanism of histone exchange by SWR1 complex.
History
DepositionOct 26, 2023-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18764.png

Downloads & links

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Map

FileDownload / File: emd_18764.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 480 pix.
= 408. Å		0.85 Å/pix.
x 480 pix.
= 408. Å		0.85 Å/pix.
x 480 pix.
= 408. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00197
Minimum - Maximum-0.019897453 - 0.047192484
Average (Standard dev.)0.000089580084 (±0.0010216002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18764_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_18764_half_map_2.map
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Sample components

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Entire : SWR1-hexasome complex

EntireName: SWR1-hexasome complex
Components
  • Complex: SWR1-hexasome complex
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A.1
    • Protein or peptide: Histone H2B.1
    • DNA: DNA (118-MER)
    • DNA: DNA (118-MER)
    • Protein or peptide: Helicase SWR1
    • Protein or peptide: SWR1-complex protein 5
    • 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: Vacuolar protein sorting-associated protein 72
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: SWR1-hexasome complex

SupramoleculeName: SWR1-hexasome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 15.374983 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LASKAARKSA PSTGGVKKPH RYKPGTVALR EIRRFQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA IGALQESVEA YLVSLFEDTN LAAIHAKRVT IMPKEIQLAR RLRGERS

UniProtKB: Histone H3

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 11.39539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KILRDNIQGI TKPAIRRLAR RGGVKRISGL IYEEVRAVLK SFLESVIRDS VTYTEHAKRK TVTSLDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A.1

MacromoleculeName: Histone H2A.1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 14.013177 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGGKGGKAG SAAKASQSRS AKAGLTFPVG RVHRLLRRGN YAQRIGSGAP VYLTAVLEYL AAEILELAGN AARDNKKTRI IPRHLQLAI RNDDELNKLL GNVTIAQGGV LPNIHQNLLP KKSAKATKAS QEL

UniProtKB: Histone H2A.1

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Macromolecule #4: Histone H2B.1

MacromoleculeName: Histone H2B.1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 14.280362 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSAKAEKKPA SKAPAEKKPA AKKTSTSTDG KKRSKARKET YSSYIYKVLK QTHPDTGISQ KSMSILNSFV NDIFERIATE ASKLAAYNK KSTISAREIQ TAVRLILPGE LAKHAVSEGT RAVTKYSSST QA

UniProtKB: Histone H2B.1

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Macromolecule #7: Helicase SWR1

MacromoleculeName: Helicase SWR1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 174.792969 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 YY

UniProtKB: Helicase SWR1

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Macromolecule #8: SWR1-complex protein 5

MacromoleculeName: SWR1-complex protein 5 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 34.395734 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MPEVETKIIP NEKEDEDEDG YIEEEDEDFQ PEKDKLGGGS DDSDASDGGD DYDDGVNRDK GRNKVDYSRI ESESGGLIKT RRARQAEEE YAKTHKYESL TVESIPAKVN SIWEELQEAS KNRLLSSSGK VGSVLDGSKE ARSTTAAQQE DKILIERNYK F AGETVHEK ...String:
MPEVETKIIP NEKEDEDEDG YIEEEDEDFQ PEKDKLGGGS DDSDASDGGD DYDDGVNRDK GRNKVDYSRI ESESGGLIKT RRARQAEEE YAKTHKYESL TVESIPAKVN SIWEELQEAS KNRLLSSSGK VGSVLDGSKE ARSTTAAQQE DKILIERNYK F AGETVHEK KWVSRSSAEG QEYLNSLKFK QQAPAAPVQL EKAVRTKSNE SRQHLRRPLK RPPLLEQIIS GGLRPKLTTL EK SQLDWAS YVDRAGLNDE LVLHNKDGFL ARQEFLQRVG SAEDERYKEL RRQQLAQQLQ QDSEAS

UniProtKB: SWR1-complex protein 5

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Macromolecule #9: Actin-like protein ARP6

MacromoleculeName: Actin-like protein ARP6 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 50.100582 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 #10: Vacuolar protein sorting-associated protein 71

MacromoleculeName: Vacuolar protein sorting-associated protein 71 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 32.073479 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 #11: RuvB-like protein 1

MacromoleculeName: RuvB-like protein 1 / type: protein_or_peptide / ID: 11 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 50.516941 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 LETSANYL

UniProtKB: RuvB-like protein 1

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Macromolecule #12: RuvB-like protein 2

MacromoleculeName: RuvB-like protein 2 / type: protein_or_peptide / ID: 12 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 51.673488 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 #13: Vacuolar protein sorting-associated protein 72

MacromoleculeName: Vacuolar protein sorting-associated protein 72 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 90.709008 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 #5: DNA (118-MER)

MacromoleculeName: DNA (118-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 36.192051 KDa
SequenceString: (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)(DA)(DC)(DA)(DG) ...String:
(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)(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)

+
Macromolecule #6: DNA (118-MER)

MacromoleculeName: DNA (118-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 36.64132 KDa
SequenceString: (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) ...String:
(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)(DG)(DG)

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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

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6gej

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30312
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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