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- EMDB-15647: Nucleosome-bound Ino80 ATPase -

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Basic information

Entry
Database: EMDB / ID: EMD-15647
TitleNucleosome-bound Ino80 ATPase
Map datamain map
Sample
  • Complex: Chaetomium thermophilum INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA)
    • Protein or peptide: Ino80 ATPase
    • Protein or peptide: PAPA-1 domain-containing protein
    • DNA: DNA (227-MER)
    • DNA: DNA (226-MER)
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B type 1-C/E/F/G/I
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordschromatin remodeler / INO80 / Actin-related protein / DNA binding protein
Function / homology
Function and homology information


Ino80 complex / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine ...Ino80 complex / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / innate immune response in mucosa / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / antibacterial humoral response / nucleosome / E3 ubiquitin ligases ubiquitinate target proteins / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / defense response to Gram-positive bacterium / Ub-specific processing proteases / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / membrane / cytosol
Similarity search - Function
INO80 complex subunit B-like conserved region / INO80 complex, subunit Ies2 / PAPA-1-like conserved region / PAPA-1 / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. ...INO80 complex subunit B-like conserved region / INO80 complex, subunit Ies2 / PAPA-1-like conserved region / PAPA-1 / : / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H2A / INO80 complex subunit B-like conserved region domain-containing protein / Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H3.2
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus) / Homo sapiens (human) / DNA molecule (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsKunert F / Metzner FJ / Eustermann S / Jung J / Woike S / Schall K / Kostrewa D / Hopfner KP
Funding supportEuropean Union, Germany, 5 items
OrganizationGrant numberCountry
European Research Council (ERC)833613 INO3DEuropean Union
German Research Foundation (DFG)CRC1064 Germany
German Research Foundation (DFG)CRC1361 Germany
German Research Foundation (DFG)RTG1721 Germany
German Research Foundation (DFG)Gottfried-Wilhelm-Leibniz Prize Germany
CitationJournal: Sci Adv / Year: 2022
Title: Structural mechanism of extranucleosomal DNA readout by the INO80 complex.
Authors: Franziska Kunert / Felix J Metzner / James Jung / Markus Höpfler / Stephan Woike / Kevin Schall / Dirk Kostrewa / Manuela Moldt / Jia-Xuan Chen / Susanne Bantele / Boris Pfander / Sebastian ...Authors: Franziska Kunert / Felix J Metzner / James Jung / Markus Höpfler / Stephan Woike / Kevin Schall / Dirk Kostrewa / Manuela Moldt / Jia-Xuan Chen / Susanne Bantele / Boris Pfander / Sebastian Eustermann / Karl-Peter Hopfner /
Abstract: The nucleosomal landscape of chromatin depends on the concerted action of chromatin remodelers. The INO80 remodeler specifically places nucleosomes at the boundary of gene regulatory elements, which ...The nucleosomal landscape of chromatin depends on the concerted action of chromatin remodelers. The INO80 remodeler specifically places nucleosomes at the boundary of gene regulatory elements, which is proposed to be the result of an ATP-dependent nucleosome sliding activity that is regulated by extranucleosomal DNA features. Here, we use cryo-electron microscopy and functional assays to reveal how INO80 binds and is regulated by extranucleosomal DNA. Structures of the regulatory A-module bound to DNA clarify the mechanism of linker DNA binding. The A-module is connected to the motor unit via an HSA/post-HSA lever element to chemomechanically couple the motor and linker DNA sensing. Two notable sites of curved DNA recognition by coordinated action of the four actin/actin-related proteins and the motor suggest how sliding by INO80 can be regulated by extranucleosomal DNA features. Last, the structures clarify the recruitment of YY1/Ies4 subunits and reveal deep architectural similarities between the regulatory modules of INO80 and SWI/SNF complexes.
History
DepositionAug 23, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15647.png

Downloads & links

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Map

FileDownload / File: emd_15647.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 280 pix.
= 296.52 Å		1.06 Å/pix.
x 280 pix.
= 296.52 Å		1.06 Å/pix.
x 280 pix.
= 296.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.077969335 - 0.12951823
Average (Standard dev.)0.00019672693 (±0.0028946337)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 296.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_15647_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_15647_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chaetomium thermophilum INO80 A-Module (Arp4-Ies4-N-actin-Arp8-In...

EntireName: Chaetomium thermophilum INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA)
Components
  • Complex: Chaetomium thermophilum INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA)
    • Protein or peptide: Ino80 ATPase
    • Protein or peptide: PAPA-1 domain-containing protein
    • DNA: DNA (227-MER)
    • DNA: DNA (226-MER)
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B type 1-C/E/F/G/I
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Chaetomium thermophilum INO80 A-Module (Arp4-Ies4-N-actin-Arp8-In...

SupramoleculeName: Chaetomium thermophilum INO80 A-Module (Arp4-Ies4-N-actin-Arp8-Ino80HSA)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Thermochaetoides thermophila (fungus)

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Macromolecule #1: Ino80 ATPase

MacromoleculeName: Ino80 ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 131.417156 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: LELKFQSKGY NQIYDQIWRD LARKDVSKVF RLATDSYATK ASNLKKTAIL ASKEAKRWQL RTNKGTKDLQ ARAKRVMRDM MGFWKRNER EERDLRKAAE RLELENARKE EADREAARQR RKLNFLISQT ELYSHFISKK IKTHEVERST DHPDVATDEK D KIPEPTLN ...String:
LELKFQSKGY NQIYDQIWRD LARKDVSKVF RLATDSYATK ASNLKKTAIL ASKEAKRWQL RTNKGTKDLQ ARAKRVMRDM MGFWKRNER EERDLRKAAE RLELENARKE EADREAARQR RKLNFLISQT ELYSHFISKK IKTHEVERST DHPDVATDEK D KIPEPTLN INVPEPTGPI APKVTDFNSL DFDNEDESAL QAAAMANAQN AIAEAQKKAR EFNKDETKLD EDGEMNFQHP EL TEFEVAQ PKLLNCQLKE YQLKGLNWLV NLYEQGINGI LADEMGLGKT VQSISVMAYL AERYDIWGPF LVVAPASTLH NWQ QEVSKF VPDFKVLPYW GTAADRKVLR KFWDRKHTTY KKDSPFHVMI TSYQLVVSDV AYFQKMKWQY MILDEAQAIK SSQS SRWKC LLGFHCRNRL LLTGTPIQNN MQELWALLHF IMPSLFDSHD EFSEWFSKDI ESHAQSNTKL NEDQLKRLHM ILKPF MLRR VKKHVQKELG DKIEIDVFCE LSYRQRAMYQ SLRNQISIMD LIEKATVGDN EDSATLMNLV MQFRKVCNHP DLFERA DTS SPFFCGHFAE TGSFLREGTN VALGYSTRSL VEYRLPRLIW CDGGRLDKPG PGNLVAGFRS KYLNHMMNIW TPENIRS SL EGIENFTWLR FVDTSLQEAY RASHTDVFAR AVDLASKQNR LGHMQIVYDE PEDKKWTPVH ALFQICEREN PKAVAEIT T EGVLRDLMNI ARVKYRELGL CRLEKAARPR ASAPPIEVVC DSRSAVIERE NIMFHPAMRK ALFGPTPSEI KEASFGPRP VTLYPPRALL PAPDHDKQRF TNITVPSMAR FVTDSGKLAK LDELLRELKE GGHRVLLYFQ MTRMIDLMEE YLTYRNYKYC RLDGSTKLE DRRDTVADFQ TRPEIFIFLL STRAGGLGIN LTTADTVIFY DSDWNPTIDS QAMDRAHRLG QTKQVTVYRL I TRGTIEER IRKRALQKEE VQRVVITGTG SVDFSGRRPP ENRNRDIAMW LADDEQAEMI ERREKELIES GEYDKIMQQR RK GGKRKRG AANGDTVPSL EDMYHEGEGH FDDNKGSGAA TPVDADSLGR GGKRKKAGGS KKAKTTKQRL AIADGEIDDG EID IDYKDD DDKGTDYKDD DDK

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Macromolecule #2: PAPA-1 domain-containing protein

MacromoleculeName: PAPA-1 domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 53.34598 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSTRPRRHAA QRASQAITDL ADRDRESDHS HGPISSRMSS FNSSSRSRLP GKGIASVSRS EAGGASDPEH IHLTVKLPSS KLRQATSSS GIKKAGSVGS SSSSSGGGKA AVKRARGGKR SRVLESSEEE EEENEVEVLG DEDEEEEEEE DEIEVREGEG Y DEDEEDVE ...String:
MSTRPRRHAA QRASQAITDL ADRDRESDHS HGPISSRMSS FNSSSRSRLP GKGIASVSRS EAGGASDPEH IHLTVKLPSS KLRQATSSS GIKKAGSVGS SSSSSGGGKA AVKRARGGKR SRVLESSEEE EEENEVEVLG DEDEEEEEEE DEIEVREGEG Y DEDEEDVE DEDEEMQDLG EEDADGEDDE MDVDAEGEED ADGDVNMDAG VVGARATTVR AVPPAIKVTK PPKESPSNGK AA TASKAND NAVPVKRPAP DSDDESLSSL ESEPEEEVNV AGGEDAEGED DDAEGEVDAE GEEEEEEEEI EVADEDAEGE DVE QDEDED EEEEDDDDEM ISRAQTPDMS RLTARQRARL GEASGEYLKL SDEVQSKKHF TAEELSMRRA EMARRRRNLS EKRN EEIKM ETVNKLLKKQ APRTTRRAAQ AAAAAEEAEE AAKQPKRPDP MMIRWVNNKM GSVVAVPEEL LGTHAGVVFG AGPGK GLPA GKMVEEVS

UniProtKB: INO80 complex subunit B-like conserved region domain-containing protein

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Macromolecule #5: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.289904 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.2

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Macromolecule #6: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #7: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.990342 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKA RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLGK VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

UniProtKB: Histone H2A

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Macromolecule #8: Histone H2B type 1-C/E/F/G/I

MacromoleculeName: Histone H2B type 1-C/E/F/G/I / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.806018 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSVY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK

UniProtKB: Histone H2B type 1-C/E/F/G/I

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Macromolecule #3: DNA (227-MER)

MacromoleculeName: DNA (227-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (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 #4: DNA (226-MER)

MacromoleculeName: DNA (226-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 70.018547 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)

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Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / 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 stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 44.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.1 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: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 137900
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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