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- EMDB-33521: Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to S... -

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Basic information

Entry
Database: EMDB / ID: EMD-33521
TitleCryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+3 position of the nucleosome
Map data
Sample
  • Complex: Complex of Fft3-nucleosome complex with Fft3 bound to SHL+3 of the nucleosome (Class II Fft3-nucleosome complex)
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: DNA (167-MER)
    • DNA: DNA (167-MER)
    • Protein or peptide: ATP-dependent helicase fft3
KeywordsDNA binding / remodeler / nucleosome / Fft3-nucleosome complex / DNA BINDING PROTEIN
Function / homology
Function and homology information


attachment of telomeric heterochromatin to nuclear envelope / ATP-dependent H3-H4 histone complex chaperone activity / HDMs demethylate histones / Interleukin-7 signaling / PKMTs methylate histone lysines / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / RCAF complex / Metalloprotease DUBs ...attachment of telomeric heterochromatin to nuclear envelope / ATP-dependent H3-H4 histone complex chaperone activity / HDMs demethylate histones / Interleukin-7 signaling / PKMTs methylate histone lysines / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / RCAF complex / Metalloprotease DUBs / Factors involved in megakaryocyte development and platelet production / E3 ubiquitin ligases ubiquitinate target proteins / RMTs methylate histone arginines / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RNA Polymerase I Promoter Escape / polytene chromosome band / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Transcriptional regulation by small RNAs / HATs acetylate histones / Ub-specific processing proteases / Estrogen-dependent gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / larval somatic muscle development / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Assembly of the ORC complex at the origin of replication / UCH proteinases / histone chaperone activity / polytene chromosome / transcription elongation-coupled chromatin remodeling / nuclear chromosome / replication fork processing / heterochromatin organization / nucleosomal DNA binding / ATP-dependent activity, acting on DNA / heterochromatin / helicase activity / structural constituent of chromatin / nucleosome / nucleosome assembly / chromosome / chromatin organization / DNA helicase / nucleic acid binding / damaged DNA binding / chromatin remodeling / protein heterodimerization activity / chromatin binding / chromatin / protein-containing complex binding / ATP hydrolysis activity / DNA binding / ATP binding / nucleus
Similarity search - Function
: / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain ...: / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / 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 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Helicase conserved C-terminal domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent helicase fft3 / Histone H2B / Histone H3 / Histone H4 / Histone H2A
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast) / Drosophila melanogaster (fruit fly) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsNan Z / Tao J / Yangao H
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800632 China
CitationJournal: To Be Published
Title: Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+3 position of the nucleosome (Class II Fft3-nucleosome complex)
Authors: Nan Z / Tao J / Yangao H
History
DepositionJun 1, 2022-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33521.png

Downloads & links

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Map

FileDownload / File: emd_33521.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 224 pix.
= 232.96 Å		1.04 Å/pix.
x 224 pix.
= 232.96 Å		1.04 Å/pix.
x 224 pix.
= 232.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017
Minimum - Maximum-0.030741896 - 0.064098805
Average (Standard dev.)0.000084282845 (±0.0037213045)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 232.95999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33521_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33521_half_map_2.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 : Complex of Fft3-nucleosome complex with Fft3 bound to SHL+3 of th...

EntireName: Complex of Fft3-nucleosome complex with Fft3 bound to SHL+3 of the nucleosome (Class II Fft3-nucleosome complex)
Components
  • Complex: Complex of Fft3-nucleosome complex with Fft3 bound to SHL+3 of the nucleosome (Class II Fft3-nucleosome complex)
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: DNA (167-MER)
    • DNA: DNA (167-MER)
    • Protein or peptide: ATP-dependent helicase fft3

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Supramolecule #1: Complex of Fft3-nucleosome complex with Fft3 bound to SHL+3 of th...

SupramoleculeName: Complex of Fft3-nucleosome complex with Fft3 bound to SHL+3 of the nucleosome (Class II Fft3-nucleosome complex)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #6-#7, #1-#5
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast)

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Macromolecule #1: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 13.257529 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKVK GKAKSRSNRA GLQFPVGRIH RLLRKGNYAE RVGAGAPVYL AAVMEYLAAE VLELAGNAAR DNKKTRIIPR HLQLAIRND EELNKLLSGV TIAQGGVLPN IQAVLLPKKT EKKA

UniProtKB: Histone H2A

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Macromolecule #2: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 13.727064 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPPKTSGKAA KKAGKAQKNI TKTDKKKKRK RKESYAIYIY KVLKQVHPDT GISSKAMSIM NSFVNDIFER IAAEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSSK

UniProtKB: Histone H2B

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Macromolecule #5: ATP-dependent helicase fft3

MacromoleculeName: ATP-dependent helicase fft3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast) / Strain: 972 / ATCC 24843
Molecular weightTheoretical: 104.629953 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDGKRKIEHT ADGTHYDATS NVKRKPIFPP FIADSLSEAT EKANVMGGGM NSRLQILSEM SKRVQATAPI SSLEHFKQLS DISPSFTSS ANSINQPYNY SGSLENLVPT PSAGTPSQFM DAQNPYGAVY NALSQFSETE PKMPSYMDDE EASDSLPLSL S SQSLSSQV ...String:
MDGKRKIEHT ADGTHYDATS NVKRKPIFPP FIADSLSEAT EKANVMGGGM NSRLQILSEM SKRVQATAPI SSLEHFKQLS DISPSFTSS ANSINQPYNY SGSLENLVPT PSAGTPSQFM DAQNPYGAVY NALSQFSETE PKMPSYMDDE EASDSLPLSL S SQSLSSQV TNQKPAPHRL TMRERYAANN LTNGLQFTLP LSSRKTYEPE ADDDSNDDMY SDDDSNADRW ASRIDTAALK EE VLKYMNR CSTQDLADMT GCTLAEAEFM VAKRPFPDLE SALVVKQPRP VIPKGRRGRR EKTPLGPRLV GICMEIMRGY FVV DALIRQ CEQLGGKIQR GIEAWGLSNT ATSDEGETSL VNFDQMKSFG TPANSSFITT PPASFSPDIK LQDYQIIGIN WLYL LYELK LAGILADEMG LGKTCQTIAF FSLLMDKNIN GPHLVIAPAS TMENWLREFA KFCPKLKIEL YYGSQVEREE IRERI NSNK DSYNVMLTTY RLAATSKADR LFLRNQKFNV CVYDEGHYLK NRASERYRHL MSIPADFRVL LTGTPLQNNL KELISL LAF ILPHVFDYGL KSLDVIFTMK KSPESDFERA LLSEQRVSRA KMMMAPFVLR RKKSQVLDAL PKKTRIIEFC EFSEEER RR YDDFASKQSV NSLLDENVMK TNLDTNANLA KKKSTAGFVL VQLRKLADHP MLFRIHYKDD ILRQMAKAIM NEPQYKKA N ELYIFEDMQY MSDIELHNLC CKFPSINSFQ LKDEPWMDAT KVRKLKKLLT NAVENGDRVV LFSQFTQVLD ILQLVMKSL NLKFLRFDGS TQVDFRQDLI DQFYADESIN VFLLSTKAGG FGINLACANM VILYDVSFNP FDDLQAEDRA HRVGQKKEVT VYKFVVKDT IEEHIQRLAN AKIALDATLS GNAETVEAED DDD

UniProtKB: ATP-dependent helicase fft3

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Macromolecule #6: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
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

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Macromolecule #7: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 11.408452 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: DNA (167-MER)

MacromoleculeName: DNA (167-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 51.783977 KDa
SequenceString: (DA)(DT)(DC)(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) ...String:
(DA)(DT)(DC)(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)(DA)(DT)

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Macromolecule #4: DNA (167-MER)

MacromoleculeName: DNA (167-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 51.325676 KDa
SequenceString: (DA)(DT)(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) ...String:
(DA)(DT)(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)(DG)(DA)(DT)

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2

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Image processing

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

5x0y

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49996

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