[English] 日本語
Yorodumi
- EMDB-49062: 2.61 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49062
Title2.61 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex
Map dataUnsharpened map
Sample
  • Complex: Complex between nucleosome and CHD1
    • DNA: DNA Tracking Strand
    • DNA: DNA Lagging Strand
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B 1.1
    • Protein or peptide: Histone H3
    • Protein or peptide: Chromo domain-containing protein 1
Keywordschromatin / CHD1 / remodeler / ATP-dependent chromatin remodeler / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / SLIK (SAGA-like) complex / DNA double-strand break processing / nucleosome organization / ATP-dependent chromatin remodeler activity / SAGA complex ...nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / SLIK (SAGA-like) complex / DNA double-strand break processing / nucleosome organization / ATP-dependent chromatin remodeler activity / SAGA complex / sister chromatid cohesion / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / ATP-dependent activity, acting on DNA / : / helicase activity / transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / chromatin DNA binding / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / site of double-strand break / histone binding / transcription cis-regulatory region binding / chromatin remodeling / protein heterodimerization activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus
Similarity search - Function
Chromodomain helicase DNA-binding domain / Chromodomain helicase DNA-binding domain 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / : / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / ATP-dependent helicase CHD1-2/hrp3 HTH domain / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain ...Chromodomain helicase DNA-binding domain / Chromodomain helicase DNA-binding domain 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / : / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / ATP-dependent helicase CHD1-2/hrp3 HTH domain / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / : / 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. / Homeobox-like domain superfamily / 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
Histone H3 / Histone H2B 1.1 / Chromo domain-containing protein 1 / Histone H4 / Histone H2A
Similarity search - Component
Biological speciessynthetic construct (others) / Xenopus laevis (African clawed frog) / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsNodelman IM / Folkwein HJ / Armache J-P / Bowman GD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM084192 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: A competitive regulatory mechanism of the Chd1 remodeler is integral to distorting nucleosomal DNA.
Authors: Ilana M Nodelman / Heather J Folkwein / Wesley S Glime / Jean-Paul Armache / Gregory D Bowman /
Abstract: The Chd1 chromatin remodeler repositions nucleosomes into evenly spaced arrays, a characteristic of most eukaryotic genes. Here we show that the yeast Chd1 remodeler requires two activating segments ...The Chd1 chromatin remodeler repositions nucleosomes into evenly spaced arrays, a characteristic of most eukaryotic genes. Here we show that the yeast Chd1 remodeler requires two activating segments to distort nucleosomal DNA into an A-form-like conformation, a critical first step in nucleosome sliding. As shown by cryo-electron microscopy, these two activating segments together pack against the ATPase motor, where they are poised to stabilize the central ATPase cleft. These activating elements contact the ATPase at locations that are incompatible with binding of NegC, an autoinhibitory segment located between the two activators. NegC inhibits sliding by antagonizing the activators through steric competition and constraining activator placement, giving rise to directional nucleosome sliding. Given that activator reinforcement of the ATPase cleft is needed for DNA distortion, this first step in remodeling appears to provide a natural checkpoint for regulation of chromatin remodeler activity.
History
DepositionFeb 5, 2025-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49062.png

Downloads & links

-
Map

FileDownload / File: emd_49062.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 336.128 Å		1.05 Å/pix.
x 320 pix.
= 336.128 Å		1.05 Å/pix.
x 320 pix.
= 336.128 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0504 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.0 - 1.5502926
Average (Standard dev.)0.0047534793 (±0.029084938)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 336.128 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Auto-sharpened map with bfactor = -38.2

Fileemd_49062_additional_1.map
AnnotationAuto-sharpened map with bfactor = -38.2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map 1

Fileemd_49062_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map 2

Fileemd_49062_half_map_2.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex between nucleosome and CHD1

EntireName: Complex between nucleosome and CHD1
Components
  • Complex: Complex between nucleosome and CHD1
    • DNA: DNA Tracking Strand
    • DNA: DNA Lagging Strand
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B 1.1
    • Protein or peptide: Histone H3
    • Protein or peptide: Chromo domain-containing protein 1

-
Supramolecule #1: Complex between nucleosome and CHD1

SupramoleculeName: Complex between nucleosome and CHD1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 450 kDa/nm

-
Macromolecule #1: DNA Tracking Strand

MacromoleculeName: DNA Tracking Strand / type: dna / ID: 1 / Details: DNA (151-MER) / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 46.35152 KDa
SequenceString: (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) ...String:
(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) (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) (DT)(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)

-
Macromolecule #2: DNA Lagging Strand

MacromoleculeName: DNA Lagging Strand / type: dna / ID: 2 / Details: DNA (151-MER) / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 46.871832 KDa
SequenceString: (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)(DA)(DA)(DG)(DT) (DA) (DA)(DT)(DC)(DC)(DC)(DC) ...String:
(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)(DA)(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)(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)

-
Macromolecule #3: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 10.061849 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKRHRKVLRD NIQGITKPAI RRLARRGGVK RISGLIYEET RGVLKVFLEN VIRDAVTYTE HAKRKTVTAM DVVYALKRQG RTLYGFGG

UniProtKB: Histone H4

-
Macromolecule #4: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 12.082128 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVRN DEELNKLLG RVTIAQGGVL PNIQSVLLPK K

UniProtKB: Histone H2A

-
Macromolecule #5: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 10.494098 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TRKESYAIYV YKVLKQVHPD TGISCKAMSI MNSFVNDVFE RIAGEASRLA HYNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTK YTSAK

UniProtKB: Histone H2B 1.1

-
Macromolecule #6: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.760795 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KKPHRYRPGT VALREIRRYQ KSTELLIRKL PFQRLVREIA QDFKTDLRFQ SSAVMALQEA SEAYLVALFE DTNLCAIHAK RVTIMPKDI QLARRIRGER A

UniProtKB: Histone H3

-
Macromolecule #7: Chromo domain-containing protein 1

MacromoleculeName: Chromo domain-containing protein 1 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / 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: 96.77393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KIPTRFSNRQ NKTVNYNIDY SDDDLLESED DYGSEEALSE ENVHEASANP QPEDFHGIDI VINHRLKTSL EEGKVLEKTV PDLNNCKEN YEFLIKWTDE SHLHNTWETY ESIGQVRGLK RLDNYCKQFI IEDQQVRLDP YVTAEDIEIM DMERERRLDE F EEFHVPER ...String:
KIPTRFSNRQ NKTVNYNIDY SDDDLLESED DYGSEEALSE ENVHEASANP QPEDFHGIDI VINHRLKTSL EEGKVLEKTV PDLNNCKEN YEFLIKWTDE SHLHNTWETY ESIGQVRGLK RLDNYCKQFI IEDQQVRLDP YVTAEDIEIM DMERERRLDE F EEFHVPER IIDSQRASLE DGTSQLQYLV KWRRLNYDEA TWENATDIVK LAPEQVKHFQ NRENSKILPQ YSSNYTSQRP RF EKLSVQP PFIKGGELRD FQLTGINWMA FLWSKGDNGI LADEMGLGKT VQTVAFISWL IFARRQNGPH IIVVPLSTMP AWL DTFEKW APDLNCICYM GNQKSRDTIR EYEFYTNPRA KGKKTMKFNV LLTTYEYILK DRAELGSIKW QFMAVDEAHR LKNA ESSLY ESLNSFKVAN RMLITGTPLQ NNIKELAALV NFLMPGRFTI DQEIDFENQD EEQEEYIHDL HRRIQPFILR RLKKD VEKS LPSKTERILR VELSDVQTEY YKNILTKNYS ALTAGAKGGH FSLLNIMNEL KKASNHPYLF DNAEERVLQK FGDGKM TRE NVLRGLIMSS GKMVLLDQLL TRLKKDGHRV LIFSQMVRML DILGDYLSIK GINFQRLDGT VPSAQRRISI DHFNSPD SN DFVFLLSTRA GGLGINLMTA DTVVIFDSDW NPQADLQAMA RAHRIGQKNH VMVYRLVSKD TVEEEVLERA RKKMILEY A IISLGVTDGN KYTKKNEPNA GELSAILKFG AGNMFTATDN QKKGEDGNGD DVLNHAEDHV TTPDLGESHL GGEEFLKQF EVTDYKADID WDDIIPEEEL KKLQDEEQKR KDEEY

UniProtKB: Chromo domain-containing protein 1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 15463267
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 155592
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

+
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