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- EMDB-45370: S.c INO80 in complex with S.c 0/40 nucleosome, Class 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-45370
TitleS.c INO80 in complex with S.c 0/40 nucleosome, Class 2
Map dataClass1 of the S.c INO80 bound to S.c 0/40 nucleosome in ADP/BeFx state, the Arp8 Module Reconstruction
Sample
  • Complex: S.c INO80 in complex with S.c 0/40 nucleosome, Class2
    • Protein or peptide: x 8 types
    • DNA: x 2 types
  • Protein or peptide: x 2 types
  • Ligand: x 1 types
KeywordsChromatin Remodeler / nucleosome / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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 / regulation of TOR signaling / Swr1 complex / replication fork protection complex / telomere maintenance via recombination / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Ino80 complex / ATP-dependent chromatin remodeler activity / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / postreplication repair / box C/D snoRNP assembly / regulation of metabolic process / 3'-5' DNA helicase activity / cellular response to stress / 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 / chromosome, centromeric region / intracellular copper ion homeostasis / Ub-specific processing proteases / subtelomeric heterochromatin formation / CENP-A containing nucleosome / enzyme regulator activity / DNA helicase activity / aerobic respiration / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / rRNA processing / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / chromatin organization / 5'-3' DNA helicase activity / DNA helicase / histone binding / single-stranded 3'-5' DNA helicase activity / double-stranded DNA helicase activity / forked DNA-dependent helicase activity / four-way junction helicase activity / transcription by RNA polymerase II / chromosome, telomeric region / protein stabilization / chromatin remodeling / protein heterodimerization activity / DNA repair / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
DBINO domain / DNA helicase Ino80 / DNA-binding domain / DBINO domain profile. / INO80 complex, subunit Ies6 / INO80 complex subunit B-like conserved region / INO80 complex, subunit Ies2 / PAPA-1-like conserved region / PAPA-1 / : ...DBINO domain / DNA helicase Ino80 / DNA-binding domain / DBINO domain profile. / INO80 complex, subunit Ies6 / INO80 complex subunit B-like conserved region / INO80 complex, subunit Ies2 / PAPA-1-like conserved region / PAPA-1 / : / 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 / : / 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 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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 H2A.1 / Chromatin-remodeling complex subunit IES6 / Ino eighty subunit 2 / Chromatin-remodeling ATPase INO80 / Actin-related protein 5 / Histone H3 / Histone H4 / RuvB-like protein 1 / RuvB-like protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsWu H / Kaur U / Narlikar GJ / Cheng YF
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) United States
CitationJournal: Science / Year: 2025
Title: Autoinhibition imposed by a large conformational switch of INO80 regulates nucleosome positioning
Authors: Kaur U / Wu H / Cheng Y / Narlikar GJ
History
DepositionJun 15, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45370.png

Downloads & links

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Map

FileDownload / File: emd_45370.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationClass1 of the S.c INO80 bound to S.c 0/40 nucleosome in ADP/BeFx state, the Arp8 Module Reconstruction
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 448 pix.
= 374.08 Å		0.84 Å/pix.
x 448 pix.
= 374.08 Å		0.84 Å/pix.
x 448 pix.
= 374.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.13
Minimum - Maximum-0.35924038 - 1.1221278
Average (Standard dev.)0.004312092 (±0.03795796)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 374.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Class1 of the S.c INO80 bound to S.c...

Fileemd_45370_additional_1.map
AnnotationClass1 of the S.c INO80 bound to S.c 0/40 nucleosome in ADP/BeFx state, the Arp8 Module Reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Class1 of the S.c INO80 bound to S.c...

Fileemd_45370_half_map_1.map
AnnotationClass1 of the S.c INO80 bound to S.c 0/40 nucleosome in ADP/BeFx state, half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Class1 of the S.c INO80 bound to S.c...

Fileemd_45370_half_map_2.map
AnnotationClass1 of the S.c INO80 bound to S.c 0/40 nucleosome in ADP/BeFx state, half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : S.c INO80 in complex with S.c 0/40 nucleosome, Class2

EntireName: S.c INO80 in complex with S.c 0/40 nucleosome, Class2
Components
  • Complex: S.c INO80 in complex with S.c 0/40 nucleosome, Class2
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A.1
    • Protein or peptide: Histone H2B.1
    • DNA: DNA (227-MER)
    • DNA: DNA (227-MER)
    • Protein or peptide: Chromatin-remodeling ATPase INO80
    • Protein or peptide: Actin-related protein 5
    • Protein or peptide: Chromatin-remodeling complex subunit IES6
    • Protein or peptide: Ino eighty subunit 2
  • Protein or peptide: RuvB-like protein 1
  • Protein or peptide: RuvB-like protein 2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: S.c INO80 in complex with S.c 0/40 nucleosome, Class2

SupramoleculeName: S.c INO80 in complex with S.c 0/40 nucleosome, Class2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9, #12

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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 (brewer's yeast)
Molecular weightTheoretical: 15.391007 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LASKAARKSA PSTGGVKKPH RYKPGTVALR EIRRFQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA IGALQESVEA YLVSLFEDTN LAAIHAKRVT IQKKDIKLAR 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: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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: Chromatin-remodeling ATPase INO80

MacromoleculeName: Chromatin-remodeling ATPase INO80 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 171.693812 KDa
SequenceString: MSLAVLLNKE DKDISDFSKT TAGKSAKKNS RERVADVAPT RVLDKKQAYL SQLNSEFNRI KRRDSIEQLY QDWKFINLQE FELISEWNQ QSKDWQFDNT NDSQDLHFKK LYRDMSMINK EWAEYQSFKN ANLSDIINEK DADEDEEDDE DELEDGEEDM E EDEASTGR ...String:
MSLAVLLNKE DKDISDFSKT TAGKSAKKNS RERVADVAPT RVLDKKQAYL SQLNSEFNRI KRRDSIEQLY QDWKFINLQE FELISEWNQ QSKDWQFDNT NDSQDLHFKK LYRDMSMINK EWAEYQSFKN ANLSDIINEK DADEDEEDDE DELEDGEEDM E EDEASTGR HTNGKSMRGN GIQKSRKKDA AAAAAIGKAI KDDQTHADTV VTVNGDENED GNNGEDEDND NDNENNNDND ND NENENDN DSDNDDEEEN GEEDEEEEEI EDLDEEDFAA FEEQDDNDDE DFNPDVEKRR KRSSSSSSST KLSMNSLSLI TSK KINKNI TINSDRPKIV RELIKMCNKN KHQKIKKRRF TNCIVTDYNP IDSKLNIKIT LKQYHVKRLK KLINDAKRER EREE ALKNN VGLDGNDLDN DEDGSESHKR RKLNNNTANG ADDANKRKFN TRHGLPTYGM KMNAKEARAI QRHYDNTYTT IWKDM ARKD STKMSRLVQQ IQSIRSTNFR KTSSLCAREA KKWQSKNFKQ IKDFQTRARR GIREMSNFWK KNEREERDLK KKIEKE AME QAKKEEEEKE SKRQAKKLNF LLTQTELYSH FIGRKIKTNE LEGNNVSSND SESQKNIDIS ALAPNKNDFH AIDFDNE ND EQLRLRAAEN ASNALAETRA KAKQFDDHAN AHEEEEEEDE LNFQNPTSLG EITIEQPKIL ACTLKEYQLK GLNWLANL Y DQGINGILAD EMGLGKTVQS ISVLAHLAEN HNIWGPFLVV TPASTLHNWV NEISKFLPQF KILPYWGNAN DRKVLRKFW DRKNLRYNKN APFHVMVTSY QMVVTDANYL QKMKWQYMIL DEAQAIKSSQ SSRWKNLLSF HCRNRLLLTG TPIQNSMQEL WALLHFIMP SLFDSHDEFN EWFSKDIESH AEANTKLNQQ QLRRLHMILK PFMLRRVKKN VQSELGDKIE IDVLCDLTQR Q AKLYQVLK SQISTNYDAI ENAATNDSTS NSASNSGSDQ NLINAVMQFR KVCNHPDLFE RADVDSPFSF TTFGKTTSML TA SVANNNS SVISNSNMNL SSMSSNNISN GKFTDLIYSS RNPIKYSLPR LIYEDLILPN YNNDVDIANK LKNVKFNIFN PST NYELCL FLSKLTGEPS LNEFFRVSTT PLLKRVIERT NGPKNTDSLS FKTITQELLE VTRNAPSEGV MASLLNVEKH AYER EYLNC IQRGYHPNVS APPVTIEVLG SSHVTNSINN ELFDPLISQA LSDIPAITQY NMHVKKGIPV EDFPKTGLFP EPLNK NFSS NISMPSMDRF ITESAKLRKL DELLVKLKSE GHRVLIYFQM TKMMDLMEEY LTYRQYNHIR LDGSSKLEDR RDLVHD WQT NPEIFVFLLS TRAGGLGINL TAADTVIFYD SDWNPTIDSQ AMDRAHRLGQ TRQVTVYRLL VRGTIEERMR DRAKQKE QV QQVVMEGKTQ EKNIKTIEVG ENDSEVTREG SKSISQDGIK EAASALA

UniProtKB: Chromatin-remodeling ATPase INO80

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Macromolecule #8: Actin-related protein 5

MacromoleculeName: Actin-related protein 5 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 87.682359 KDa
SequenceString: MSSRDASLTP LKAVVIDDPP LRQTPEPFDE QSAYNPQSPI AIDFGSSKLR AGFVNHATPT HIFPNALTKF RDRKLNKNFT FVGNDTLLD QAVRSQSRSP FDGPFVTNWN LTEEILDYTF HHLGVVPDNG IPNPILLTER LATVQSQRTN WYQILFETYN V PGVTFGID ...String:
MSSRDASLTP LKAVVIDDPP LRQTPEPFDE QSAYNPQSPI AIDFGSSKLR AGFVNHATPT HIFPNALTKF RDRKLNKNFT FVGNDTLLD QAVRSQSRSP FDGPFVTNWN LTEEILDYTF HHLGVVPDNG IPNPILLTER LATVQSQRTN WYQILFETYN V PGVTFGID SLFSFYNYNP SGNKTGLVIS CGHEDTNVIP VVDGAGILTD AKRINWGGHQ AVDYLNDLMA LKYPYFPTKM SY LQYETMY KDYCYVSRNY DEDIEKILTL ENLDTNDVVV EAPFTEVLQP QKTEEELRIQ AEKRKETGKR LQEQARLKRM EKL VQKQEE FEYFSKVRDQ LIDEPKKKVL SVLQNAGFDD ERDFKKYLHS LEQSLKKAQM VEAEDDSHLD EMNEDKTAQK FDLL DIADE DLNEDQIKEK RKQRFLKASQ DARQKAKEEK ERVAKEEEEK KLKEQQWRET DLNGWIKDKR LKLNKLIKRR KEKLK LRDE MKDRKSQVSQ NRMKNLASLA EDNVKQGAKR NRHQATIDND PNDTFGANDE DWLIYTDITQ NPEAFEEALE YEYKDI VEL ERLLLEHDPN FTEEDTLEAQ YDWRNSILHL FLRGPRPHDS ENIHEQHQMH LNVERIRVPE VIFQPTMGGQ DQAGICE LS ETILLKKFGS QPGKLSQTSI DMVNNVLITG GNAKVPGLKE RIVKEFTGFL PTGTNITVNM SSDPSLDAWK GMAALARN E EQYRKTVISK KEYEEYGPEY IKEHKLGNTK YFED

UniProtKB: Actin-related protein 5

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Macromolecule #9: Chromatin-remodeling complex subunit IES6

MacromoleculeName: Chromatin-remodeling complex subunit IES6 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 18.564965 KDa
SequenceString:
MSGSRGNSSN SSVSNNSNNN NNNDGGDERL LFLRSVGERN EIGFPSRFKS AHYKKPTRRH KSARQLISDE NKRINALLTK ANKAAESST AARRLVPKAT YFSVEAPPSI RPAKKYCDVT GLKGFYKSPT NNIRYHNAEI YQLIVKPMAP GVDQEYLKLR G ANFVLK

UniProtKB: Chromatin-remodeling complex subunit IES6

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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 / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 50.516941 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 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 / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 50.539367 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 ISIAK

UniProtKB: RuvB-like protein 2

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Macromolecule #12: Ino eighty subunit 2

MacromoleculeName: Ino eighty subunit 2 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 36.210953 KDa
SequenceString: MDSEASDIEA ELSDSVSAGG EEYIDDDDYT EDIDDQIVTA KSSRRTARRS VPKGVRTSKR IRDKELSVEV DEDYDEEEDV LSPSKKRHL HTRSMDKRQV AATASEKSDI GDSKGNDGEI EDGILEEEES LEKELNRGGG KEVEKSEESY YAQNDVGQKG E EEQDGESG ...String:
MDSEASDIEA ELSDSVSAGG EEYIDDDDYT EDIDDQIVTA KSSRRTARRS VPKGVRTSKR IRDKELSVEV DEDYDEEEDV LSPSKKRHL HTRSMDKRQV AATASEKSDI GDSKGNDGEI EDGILEEEES LEKELNRGGG KEVEKSEESY YAQNDVGQKG E EEQDGESG GYEDNEPSIS KESDELVSVV NGNGNEEDDE VEATKENTTD STRSTTTRSK MLLDLLEDGG SKKKLTDEEI QL RRAENAR KRKNLSEKRL EEEKQDTINK LLKKRAGKSR SHLPNDDEKN DGSSSFVKPR RPYNSEGMTR ILRRYEEDLF CTF

UniProtKB: Ino eighty subunit 2

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Macromolecule #5: DNA (227-MER)

MacromoleculeName: DNA (227-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 70.34775 KDa
SequenceString: (DT)(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DC)(DG) (DG)(DG)(DG)(DA)(DT)(DC)(DC)(DT)(DC)(DT) (DA)(DG)(DA)(DG)(DT)(DG)(DG)(DG)(DA) (DG)(DC)(DT)(DC)(DG)(DG)(DA)(DA)(DC)(DA) (DC) (DT)(DA)(DT)(DC)(DC)(DG) ...String:
(DT)(DC)(DG)(DG)(DT)(DA)(DC)(DC)(DC)(DG) (DG)(DG)(DG)(DA)(DT)(DC)(DC)(DT)(DC)(DT) (DA)(DG)(DA)(DG)(DT)(DG)(DG)(DG)(DA) (DG)(DC)(DT)(DC)(DG)(DG)(DA)(DA)(DC)(DA) (DC) (DT)(DA)(DT)(DC)(DC)(DG)(DA)(DC) (DT)(DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG)(DC) (DA)(DA) (DG)(DG)(DT)(DC)(DG)(DC)(DT) (DG)(DT)(DT)(DC)(DA)(DA)(DT)(DA)(DC)(DA) (DT)(DG)(DC) (DA)(DC)(DA)(DG)(DG)(DA) (DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC) (DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG) (DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC)(DT) (DA)(DG)(DG)(DG)(DA) (DG)(DT)(DA)(DA) (DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC) (DG)(DG)(DT)(DT)(DA)(DA) (DA)(DA)(DC) (DG)(DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA) (DG)(DC)(DG)(DC)(DG)(DT)(DA) (DC)(DG) (DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG) (DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA) (DG) (DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA)(DC) (DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG) (DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT)(DC)(DC)(DA)(DG)

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Macromolecule #6: DNA (227-MER)

MacromoleculeName: DNA (227-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 69.840398 KDa
SequenceString: (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT) ...String:
(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DT)(DG)(DT)(DG)(DC)(DA)(DT)(DG)(DT) (DA)(DT)(DT)(DG)(DA)(DA)(DC) (DA)(DG) (DC)(DG)(DA)(DC)(DC)(DT)(DT)(DG)(DC)(DC) (DG)(DG)(DT)(DG)(DC)(DC)(DA)(DG) (DT) (DC)(DG)(DG)(DA)(DT)(DA)(DG)(DT)(DG)(DT) (DT)(DC)(DC)(DG)(DA)(DG)(DC)(DT)(DC) (DC)(DC)(DA)(DC)(DT)(DC)(DT)(DA)(DG)(DA) (DG)(DG)(DA)(DT)(DC)(DC)(DC)(DC)(DG)(DG) (DG)(DT)(DA)(DC)(DC)(DG)(DA)

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Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 13 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: OTHER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 73064
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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