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- EMDB-28613: Class2 of the INO80-Nucleosome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-28613
TitleClass2 of the INO80-Nucleosome complex
Map dataClass2,INO80-Ncp,overall
Sample
  • Complex: INO80-Ncp
    • 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
KeywordsChromatin Remodeler / hexasome / DNA BINDING PROTEIN / DNA BINDING PROTEIN-Hydrolase complex
Function / homology
Function and homology information


R2TP complex / regulation of TOR signaling / Swr1 complex / telomere maintenance via recombination / Ino80 complex / regulation of metabolic process / box C/D snoRNP assembly / DNA duplex unwinding / ATP-dependent chromatin remodeler activity / 3'-5' DNA helicase activity ...R2TP complex / regulation of TOR signaling / Swr1 complex / telomere maintenance via recombination / Ino80 complex / regulation of metabolic process / box C/D snoRNP assembly / DNA duplex unwinding / ATP-dependent chromatin remodeler activity / 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / chromosome, centromeric region / subtelomeric heterochromatin formation / enzyme regulator activity / DNA helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / rRNA processing / histone binding / 5'-3' DNA helicase activity / DNA helicase / transcription by RNA polymerase II / chromosome, telomeric region / protein stabilization / chromatin remodeling / DNA repair / regulation of DNA-templated transcription / chromatin / 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 B-like conserved region / INO80 complex, subunit Ies2 / INO80 complex, subunit Ies6 / PAPA-1-like conserved region / PAPA-1 / : ...DBINO domain / DNA helicase Ino80 / DNA-binding domain / DBINO domain profile. / INO80 complex subunit B-like conserved region / INO80 complex, subunit Ies2 / INO80 complex, subunit Ies6 / 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 / Helicase conserved C-terminal domain / ATPase, nucleotide binding domain / 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
Chromatin-remodeling complex subunit IES6 / Ino eighty subunit 2 / Chromatin-remodeling ATPase INO80 / Actin-related protein 5 / RuvB-like protein 1 / RuvB-like protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsWu H / Munoz E / Gourdet M / Narlikar G / 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: 2023
Title: Reorientation of INO80 on hexasomes reveals basis for mechanistic versatility.
Authors: Hao Wu / Elise N Muñoz / Laura J Hsieh / Un Seng Chio / Muryam A Gourdet / Geeta J Narlikar / Yifan Cheng /
Abstract: Unlike other chromatin remodelers, INO80 preferentially mobilizes hexasomes, which can form during transcription. Why INO80 prefers hexasomes over nucleosomes remains unclear. Here, we report ...Unlike other chromatin remodelers, INO80 preferentially mobilizes hexasomes, which can form during transcription. Why INO80 prefers hexasomes over nucleosomes remains unclear. Here, we report structures of INO80 bound to a hexasome or a nucleosome. INO80 binds the two substrates in substantially different orientations. On a hexasome, INO80 places its ATPase subunit, Ino80, at superhelical location -2 (SHL -2), in contrast to SHL -6 and SHL -7, as previously seen on nucleosomes. Our results suggest that INO80 action on hexasomes resembles action by other remodelers on nucleosomes such that Ino80 is maximally active near SHL -2. The SHL -2 position also plays a critical role for nucleosome remodeling by INO80. Overall, the mechanistic adaptations used by INO80 for preferential hexasome sliding imply that subnucleosomal particles play considerable regulatory roles.
History
DepositionOct 18, 2022-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateAug 16, 2023-
Current statusAug 16, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28613.png

Downloads & links

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Map

FileDownload / File: emd_28613.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationClass2,INO80-Ncp,overall
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 480 pix.
= 400.8 Å		0.84 Å/pix.
x 480 pix.
= 400.8 Å		0.84 Å/pix.
x 480 pix.
= 400.8 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 AUTHOR: 0.174
Minimum - Maximum-0.02355003 - 1.7818509
Average (Standard dev.)0.0013354458 (±0.024070915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 400.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Class2,INO80-Ncp,ncp

Fileemd_28613_additional_1.map
AnnotationClass2,INO80-Ncp,ncp
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Class2,INO80-Ncp,overall,halfmap1

Fileemd_28613_half_map_1.map
AnnotationClass2,INO80-Ncp,overall,halfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Class2,INO80-Ncp,overall,halfmap2

Fileemd_28613_half_map_2.map
AnnotationClass2,INO80-Ncp,overall,halfmap2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : INO80-Ncp

EntireName: INO80-Ncp
Components
  • Complex: INO80-Ncp
    • 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: INO80-Ncp

SupramoleculeName: INO80-Ncp / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3, #6
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Chromatin-remodeling ATPase INO80

MacromoleculeName: Chromatin-remodeling ATPase INO80 / type: protein_or_peptide / ID: 1 / 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 S288C (yeast) / Strain: ATCC 204508 / S288c
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 #2: Actin-related protein 5

MacromoleculeName: Actin-related protein 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
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 #3: Chromatin-remodeling complex subunit IES6

MacromoleculeName: Chromatin-remodeling complex subunit IES6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
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 #4: RuvB-like protein 1

MacromoleculeName: RuvB-like protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
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 #5: RuvB-like protein 2

MacromoleculeName: RuvB-like protein 2 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
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 #6: Ino eighty subunit 2

MacromoleculeName: Ino eighty subunit 2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
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 #7: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / 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: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44535
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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