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- EMDB-18471: SWR1-nucleosome complex in configuration 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-18471
TitleSWR1-nucleosome complex in configuration 1
Map data
Sample
  • Complex: SWR1-nucleosome complex
    • Protein or peptide: x 10 types
    • DNA: x 2 types
  • Ligand: x 4 types
KeywordsChromatin remodelling complex / nucleosome / protein-DNA complex / DNA BINDING PROTEIN
Function / homology
Function and homology information


sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / TTT Hsp90 cochaperone complex / 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 ...sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / TTT Hsp90 cochaperone complex / 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 / Oxidative Stress Induced Senescence / replication fork protection complex / box C/D snoRNP assembly / 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 / rRNA transcription / Estrogen-dependent gene expression / intracellular copper ion homeostasis / Ub-specific processing proteases / DNA helicase activity / CENP-A containing nucleosome / nucleosome binding / nuclear periphery / aerobic respiration / rRNA processing / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / chromatin organization / 5'-3' DNA helicase activity / molecular adaptor activity / DNA helicase / 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 / 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 / zinc ion binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Vps71/ZNHIT1 / Zinc finger HIT-type profile. / Zinc finger, HIT-type / Vps72/YL1, N-terminal / YL1 nuclear protein / : / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain / domain in helicases and associated with SANT domains ...Vps71/ZNHIT1 / Zinc finger HIT-type profile. / Zinc finger, HIT-type / Vps72/YL1, N-terminal / YL1 nuclear protein / : / 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 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. / 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.2 / 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 (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsJalal ASB / Wigley DB
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust095519/Z/11/Z and 209327/Z/17/Z United Kingdom
Cancer Research UKC6913/A21608 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N009258/1 and MR/R009023/1 United Kingdom
CitationJournal: Nature / Year: 2024
Title: Nucleosome flipping drives kinetic proofreading and processivity by SWR1.
Authors: Paul Girvan / Adam S B Jalal / Elizabeth A McCormack / Michael T Skehan / Carol L Knight / Dale B Wigley / David S Rueda /
Abstract: The yeast SWR1 complex catalyses the exchange of histone H2A-H2B dimers in nucleosomes, with Htz1-H2B dimers. Here we used single-molecule analysis to demonstrate two-step double exchange of the two ...The yeast SWR1 complex catalyses the exchange of histone H2A-H2B dimers in nucleosomes, with Htz1-H2B dimers. Here we used single-molecule analysis to demonstrate two-step double exchange of the two H2A-H2B dimers in a canonical yeast nucleosome with Htz1-H2B dimers, and showed that double exchange can be processive without release of the nucleosome from the SWR1 complex. Further analysis showed that bound nucleosomes flip between two states, with each presenting a different face, and hence histone dimer, to SWR1. The bound dwell time is longer when an H2A-H2B dimer is presented for exchange than when presented with an Htz1-H2B dimer. A hexasome intermediate in the reaction is bound to the SWR1 complex in a single orientation with the 'empty' site presented for dimer insertion. Cryo-electron microscopy analysis revealed different populations of complexes showing nucleosomes caught 'flipping' between different conformations without release, each placing a different dimer into position for exchange, with the Swc2 subunit having a key role in this process. Together, the data reveal a processive mechanism for double dimer exchange that explains how SWR1 can 'proofread' the dimer identities within nucleosomes.
History
DepositionSep 18, 2023-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18471.png

Downloads & links

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Map

FileDownload / File: emd_18471.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.00197
Minimum - Maximum-0.02587688 - 0.0727605
Average (Standard dev.)0.0002548435 (±0.0023558945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18471_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_18471_half_map_2.map
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Sample components

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Entire : SWR1-nucleosome complex

EntireName: SWR1-nucleosome complex
Components
  • Complex: SWR1-nucleosome complex
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A.2
    • Protein or peptide: Histone H2B.1
    • DNA: DNA (177-MER)
    • DNA: DNA (177-MER)
    • Protein or peptide: Helicase SWR1
    • 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-nucleosome complex

SupramoleculeName: SWR1-nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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: 15.405032 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LASKAARKSA PSTGGVKKPH RYKPGTVALR EIRRFQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA IGALQESVEA YLVSLFEDTN LAAIHAKRVT IQKKEIKLAR RLRGERS

UniProtKB: Histone H3

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2
Details: MARTKQTARKSTGGKAPRKQLASKAARKSAPSTGGVKKPHRYKPGTVALREIRRFQKSTE LLIRKLPFQRLVREIAQDFKTDLRFQSSAIGALQESVEAYLVSLFEDTNLAAIHAKRVTI QKKDIKLARRLRGERS
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.2

MacromoleculeName: Histone H2A.2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 17.064666 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGGKGGKAG SAAKASQSRS AKAGLTFPVG RVHRLLRRGN YAQRIGSGAP VYLTAVLEYL AAEILELAGN AARDNKKTRI IPRHLQLAI RNDDELNKLL GNVTIAQGGV LPNIHQNLLP KKSAKTAKEV CQDCQSFSRT VRTELKRNKA NQTFLSFGV

UniProtKB: Histone H2A.2

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Macromolecule #4: Histone H2B.1

MacromoleculeName: Histone H2B.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / 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: Actin-like protein ARP6

MacromoleculeName: Actin-like protein ARP6 / type: protein_or_peptide / ID: 8 / 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 #9: Vacuolar protein sorting-associated protein 71

MacromoleculeName: Vacuolar protein sorting-associated protein 71 / type: protein_or_peptide / ID: 9 / 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 #10: RuvB-like protein 1

MacromoleculeName: RuvB-like protein 1 / type: protein_or_peptide / ID: 10 / 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 #11: RuvB-like protein 2

MacromoleculeName: RuvB-like protein 2 / type: protein_or_peptide / ID: 11 / 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 #12: Vacuolar protein sorting-associated protein 72

MacromoleculeName: Vacuolar protein sorting-associated protein 72 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 21.970316 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
KRSSVMENTM KVYEKLSKAE KKRKIIQERI RKHKEQESQH MLTQEERLRI AKETEKLNIL SLDKFKEQEV WKKENRLALQ KRQKQKFQP NETILQFLST AWLMTPAMEL EDRKYWQEQL NKRDKKKKKY PRKPKKTQTY EGPEQLTSRN FVTLYDFPNA P PNLKDFNT NLFGDRWSYT NG

UniProtKB: Vacuolar protein sorting-associated protein 72, Vacuolar protein sorting-associated protein 72

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Macromolecule #5: DNA (177-MER)

MacromoleculeName: DNA (177-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 54.375605 KDa
SequenceString: (DG)(DC)(DA)(DT)(DT)(DA)(DA)(DT)(DG)(DC) (DA)(DT)(DC)(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) ...String:
(DG)(DC)(DA)(DT)(DT)(DA)(DA)(DT)(DG)(DC) (DA)(DT)(DC)(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)(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)

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Macromolecule #6: DNA (177-MER)

MacromoleculeName: DNA (177-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 54.913961 KDa
SequenceString: (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) ...String:
(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)(DG)(DG)(DC)(DG)(DG)(DC) (DC)(DG) (DC)(DG)(DG)(DA)(DT)(DG)(DC)(DA)(DT)(DT) (DA)(DA)(DT)(DG)(DC)

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Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 13 / 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 #14: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 14 / Number of copies: 2 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #15: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 15 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #16: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 16 / 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.7000000000000001 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:

6gen

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 123591
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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