[English] 日本語
Yorodumi
- EMDB-33520: Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-33520
TitleCryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+2 position of the nucleosome
Map data
Sample
  • Complex: Complex of Fft3-nucleosome complex with Fft3 bound to SHL+2 of the nucleosome (Class I Fft3-nucleosome complex)
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
  • Protein or peptide: ATP-dependent helicase fft3
  • DNA: DNA (167-MER)
  • DNA: DNA (167-MER)
KeywordsDNA binding / remodeler / nucleosome / Fft3-nucleosome complex / DNA BINDING PROTEIN
Function / homology
Function and homology information


attachment of telomeric heterochromatin to nuclear envelope / HDMs demethylate histones / PKMTs methylate histone lysines / Interleukin-7 signaling / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / Factors involved in megakaryocyte development and platelet production ...attachment of telomeric heterochromatin to nuclear envelope / HDMs demethylate histones / PKMTs methylate histone lysines / Interleukin-7 signaling / Chromatin modifying enzymes / Condensation of Prophase Chromosomes / SUMOylation of chromatin organization proteins / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / Factors involved in megakaryocyte development and platelet production / RCAF complex / RMTs methylate histone arginines / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / polytene chromosome band / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Ub-specific processing proteases / RNA Polymerase I Promoter Escape / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Regulation of endogenous retroelements by KRAB-ZFP proteins / larval somatic muscle development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / HATs acetylate histones / UCH proteinases / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / ATP-dependent H3-H4 histone complex chaperone activity / polytene chromosome / histone chaperone activity / DNA double-strand break processing / nucleosome array spacer activity / nucleosomal DNA binding / transcription elongation-coupled chromatin remodeling / nuclear chromosome / DNA repair-dependent chromatin remodeling / replication fork processing / heterochromatin / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / chromatin organization / chromosome / DNA helicase / damaged DNA binding / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / chromatin remodeling / protein heterodimerization activity / chromatin binding / protein-containing complex binding / chromatin / positive regulation of transcription by RNA polymerase II / 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. ...: / 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 / 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 / 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: 3.8 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+2 position of the nucleosome (Class I Fft3-nucleosome complex)
Authors: Nan Z / Tao J / Yangao H
History
DepositionJun 1, 2022-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_33520.png

Downloads & links

-
Map

FileDownload / File: emd_33520.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: 0.0158
Minimum - Maximum-0.048071787 - 0.096245974
Average (Standard dev.)-0.00013146765 (±0.0041596717)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #2

Fileemd_33520_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_33520_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of Fft3-nucleosome complex with Fft3 bound to SHL+2 of th...

EntireName: Complex of Fft3-nucleosome complex with Fft3 bound to SHL+2 of the nucleosome (Class I Fft3-nucleosome complex)
Components
  • Complex: Complex of Fft3-nucleosome complex with Fft3 bound to SHL+2 of the nucleosome (Class I Fft3-nucleosome complex)
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
  • Protein or peptide: ATP-dependent helicase fft3
  • DNA: DNA (167-MER)
  • DNA: DNA (167-MER)

-
Supramolecule #1: Complex of Fft3-nucleosome complex with Fft3 bound to SHL+2 of th...

SupramoleculeName: Complex of Fft3-nucleosome complex with Fft3 bound to SHL+2 of the nucleosome (Class I Fft3-nucleosome complex)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #6-#7, #1-#2
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast)

-
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: 11.552494 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKSRSNRAGL QFPVGRIHRL LRKGNYAERV GAGAPVYLAA VMEYLAAEVL ELAGNAARDN KKTRIIPRHL QLAIRNDEEL NKLLSGVTI AQGGVLPNIQ AVLLPKK

UniProtKB: Histone H2A

-
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: 10.721382 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RKRKESYAIY IYKVLKQVHP DTGISSKAMS IMNSFVNDIF ERIAAEASRL AHYNKRSTIT SREIQTAVRL LLPGELAKHA VSEGTKAVT KYTSSK

UniProtKB: Histone H2B

-
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: 78.351766 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: IDTAALKEEV LKY(MSE)NRCSTQ DLAD(MSE)TGCTL AEAEF(MSE)VAKR PFPDLESALV VKQPRPVIPK GRRGRREK T PLGPRLVGIC (MSE)EI(MSE)RGYFVV DALIRQCEQL GGKIQRGIEA WGLSNTATSD EGETSLVNFD Q(MSE)KSFGT PA NSSFITTPPA ...String:
IDTAALKEEV LKY(MSE)NRCSTQ DLAD(MSE)TGCTL AEAEF(MSE)VAKR PFPDLESALV VKQPRPVIPK GRRGRREK T PLGPRLVGIC (MSE)EI(MSE)RGYFVV DALIRQCEQL GGKIQRGIEA WGLSNTATSD EGETSLVNFD Q(MSE)KSFGT PA NSSFITTPPA SFSPDIKLQD YQIIGINWLY LLYELKLAGI LADE(MSE)GLGKT CQTIAFFSLL (MSE)DKNINGPHL VIAPAST(MSE)E NWLREFAKFC PKLKIELYYG SQVEREEIRE RINSNKDSYN V(MSE)LTTYRLAA TSKADRLFLR NQK FNVCVY DEGHYLKNRA SERYRHL(MSE)SI PADFRVLLTG TPLQNNLKEL ISLLAFILPH VFDYGLKSLD VIFT(MSE)K KSP ESDFERALLS EQRVSRAK(MSE)(MSE) (MSE)APFVLRRKK SQVLDALPKK TRIIEFCEFS EEERRRYDDF ASKQS VNSL LDENV(MSE)KTNL DTNANLAKKK STAGFVLVQL RKLADHP(MSE)LF RIHYKDDILR Q(MSE)AKAI(MSE)NEP QYKKANELY IFED(MSE)QY(MSE)SD IELHNLCCKF PSINSFQLKD EPW(MSE)DATKVR KLKKLLTNAV ENGDRVVLF SQFTQVLDIL QLV(MSE)KSLNLK FLRFDGSTQV DFRQDLIDQF YADESINVFL LSTKAGGFGI NLACAN(MSE)VIL YD VSFNPFD DLQAEDRAHR VGQKKEVTVY KFVVKDTIEE HIQRLANAKI A

UniProtKB: ATP-dependent helicase fft3

-
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: 11.48841 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PHRYRPGTVA LREIRRYQKS TELLIRKLPF QRLVREIAQD FKTDLRFQSS AVMALQEASE AYLVGLFEDT NLCAIHAKRV TIMPKDIQL ARRIRGERA

UniProtKB: Histone H3

-
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: 9.86159 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMDV VYALKRQGRT LYGFGG

UniProtKB: Histone H4

-
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: 45.27484 KDa
SequenceString: (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) ...String:
(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)

-
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: 44.85657 KDa
SequenceString: (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) ...String:
(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)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

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

-
Image processing

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

5x0y

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 178242
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more