[English] 日本語
Yorodumi
- PDB-9b1e: Cryo-EM structure of native SWR1 bound to nucleosome (composite s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9b1e
TitleCryo-EM structure of native SWR1 bound to nucleosome (composite structure)
Components
  • (DNA (214-MER)) x 2
  • (RuvB-like protein ...) x 2
  • (Vacuolar protein sorting-associated protein ...) x 2
  • Actin-like protein ARP6
  • Helicase SWR1
  • Histone H2A
  • Histone H2B
  • Histone H3
  • Histone H4
  • SWR1-complex protein 3
KeywordsGENE REGULATION / Chromatin Remodeler / Snf2 family ATPase / histone exchange / H2A.Z
Function / homology
Function and homology information


Interleukin-7 signaling / Chromatin modifying enzymes / RCAF complex / Factors involved in megakaryocyte development and platelet production / ATP-dependent H2AZ histone chaperone activity / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RNA Polymerase I Promoter Escape / Regulation of endogenous retroelements by KRAB-ZFP proteins ...Interleukin-7 signaling / Chromatin modifying enzymes / RCAF complex / Factors involved in megakaryocyte development and platelet production / ATP-dependent H2AZ histone chaperone activity / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RNA Polymerase I Promoter Escape / Regulation of endogenous retroelements by KRAB-ZFP proteins / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / HATs acetylate histones / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / polytene chromosome / R2TP complex / protein targeting to vacuole / Swr1 complex / Ino80 complex / endoplasmic reticulum organization / box C/D snoRNP assembly / 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / nucleosome binding / nucleosomal DNA binding / DNA helicase activity / transcription initiation-coupled chromatin remodeling / nuclear periphery / structural constituent of chromatin / rRNA processing / nucleosome / nucleosome assembly / chromatin organization / histone binding / 5'-3' DNA helicase activity / DNA helicase / protein stabilization / chromatin remodeling / protein heterodimerization activity / DNA repair / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
SWR1-complex protein 3 / Vps71/ZNHIT1 / Zinc finger HIT-type profile. / Vps72/YL1, N-terminal / Vps72/YL1 family / YL1 nuclear protein / Zinc finger, HIT-type / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain ...SWR1-complex protein 3 / Vps71/ZNHIT1 / Zinc finger HIT-type profile. / Vps72/YL1, N-terminal / Vps72/YL1 family / YL1 nuclear protein / Zinc finger, HIT-type / 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 / Actin / Actin family / Actin / 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. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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 / ATPase, nucleotide binding domain / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H4 / Histone H2B / Histone H2A / Histone H3 / SWR1-complex protein 3 ...ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H4 / Histone H2B / Histone H2A / Histone H3 / SWR1-complex protein 3 / Vacuolar protein sorting-associated protein 72 / Vacuolar protein sorting-associated protein 71 / RuvB-like protein 2 / Actin-like protein ARP6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Drosophila melanogaster (fruit fly)
Saccharomyces cerevisiae W303 (yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsLouder, R.K. / Park, G. / Wu, C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM149291 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM125831 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM133151 United States
CitationJournal: Cell(Cambridge,Mass.) / Year: 2024
Title: Molecular basis of global promoter sensing and nucleosome capture by the SWR1 chromatin remodeler
Authors: Louder, R.K. / Park, G. / Ye, Z. / Cha, J.S. / Gardner, A.M. / Lei, Q. / Ranjan, A. / Hollmuller, E. / Stengel, F. / Pugh, B.F. / Wu, C.
History
DepositionMar 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Helicase SWR1
B: Vacuolar protein sorting-associated protein 72
C: Actin-like protein ARP6
D: Vacuolar protein sorting-associated protein 71
E: RuvB-like protein 1
F: RuvB-like protein 2
G: RuvB-like protein 1
H: RuvB-like protein 2
I: RuvB-like protein 1
J: RuvB-like protein 2
K: SWR1-complex protein 3
Q: Histone H2A
R: Histone H2B
S: Histone H2A
T: Histone H2B
U: Histone H3
V: Histone H4
W: Histone H3
X: Histone H4
Y: DNA (214-MER)
Z: DNA (214-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,099,12241
Polymers1,095,24721
Non-polymers3,87520
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Protein , 7 types, 11 molecules ACKQSRTUWVX

#1: Protein Helicase SWR1


Mass: 178058.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Fusion protein with C-terminal 3xFLAG / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / Variant: W1558-4C / References: DNA helicase
#3: Protein Actin-like protein ARP6


Mass: 50100.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / Variant: W1558-4C / References: UniProt: Q12509
#7: Protein SWR1-complex protein 3


Mass: 72648.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / Variant: W1558-4C / References: UniProt: P31376
#8: Protein Histone H2A


Mass: 14013.177 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HTA1, GI527_G0001155 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A6A5Q1K4
#9: Protein Histone H2B


Mass: 14280.362 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HTB1, GI527_G0001154 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A6A5PZQ7
#10: Protein Histone H3


Mass: 15421.101 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: His3, His3:CG31613, CG31613, His3:CG33803, CG33803, His3:CG33806, CG33806, His3:CG33809, CG33809, His3:CG33812, CG33812, His3:CG33815, CG33815, His3:CG33818, CG33818, His3:CG33821, CG33821, ...Gene: His3, His3:CG31613, CG31613, His3:CG33803, CG33803, His3:CG33806, CG33806, His3:CG33809, CG33809, His3:CG33812, CG33812, His3:CG33815, CG33815, His3:CG33818, CG33818, His3:CG33821, CG33821, His3:CG33824, CG33824, His3:CG33827, CG33827, His3:CG33830, CG33830, His3:CG33833, CG33833, His3:CG33836, CG33836, His3:CG33839, CG33839, His3:CG33842, CG33842, His3:CG33845, CG33845, His3:CG33848, CG33848, His3:CG33851, CG33851, His3:CG33854, CG33854, His3:CG33857, CG33857, His3:CG33860, CG33860, His3:CG33863, CG33863, His3:CG33866, CG33866
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P02299
#11: Protein Histone H4


Mass: 11408.452 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: His4r, BcDNA:RH52884, CG3379, Dmel\CG3379, FBtr0082962, H4r, His4-88CD, His4R, CG3379, Dmel_CG3379
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0B4KFZ9

-
Vacuolar protein sorting-associated protein ... , 2 types, 2 molecules BD

#2: Protein Vacuolar protein sorting-associated protein 72 / SWR complex protein 2


Mass: 90709.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / Variant: W1558-4C / References: UniProt: Q03388
#4: Protein Vacuolar protein sorting-associated protein 71 / SWR complex protein 6


Mass: 32073.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / Variant: W1558-4C / References: UniProt: Q03433

-
RuvB-like protein ... , 2 types, 6 molecules EGIFHJ

#5: Protein RuvB-like protein 1


Mass: 91413.242 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: Fusion protein with C-terminal maltose-binding protein
Source: (natural) Saccharomyces cerevisiae W303 (yeast) / Variant: W1558-4C / References: DNA helicase
#6: Protein RuvB-like protein 2 / RUVBL2 / TIP49-homology protein 2 / TIP49b homolog


Mass: 51673.488 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / Variant: W1558-4C / References: UniProt: Q12464, DNA helicase

-
DNA chain , 2 types, 2 molecules YZ

#12: DNA chain DNA (214-MER)


Mass: 65672.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#13: DNA chain DNA (214-MER)


Mass: 66478.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 20 molecules

#14: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#15: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#16: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#17: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Native SWR1 bound to nucleosome.COMPLEXEndogenously purified yeast SWR1 complex bound to 60-N-7 nucleosome fragment in the presence of ADP-BeF3.#1-#130NATURAL
2Native SWR1 complexCOMPLEXEndogenously purified yeast SWR1 complex#1-#61NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
111.43 MDaNO
211.19 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Saccharomyces cerevisiae (brewer's yeast)4932W303
32Saccharomyces cerevisiae (brewer's yeast)4932W303
Buffer solutionpH: 7.6
Details: 80 nM SWR1, 160 nM nucleosomes, 1 mM ADP, 10 mM NaF, 8 mM BeCl2, 0.05% glutaraldehyde, 20 mM HEPES-KOH pH 7.6, 1.5 mM MgCl2, 0.25 mM TCEP, 0.01% IGEPAL CA-630, 1% glycerol
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES1
20.2 mMEDTA1
32 mMmagnesium chlorideMgCl21
4100 mMsodium chlorideNaCl1
50.01 %IGEPAL CA-6301
61 %glycerol1
70.25 mMTCEP1
81 mMADP1
910 mMsodium flourideNaF1
108 mMberyllium chlorideBeCl21
110.05 %glutaraldehyde1
SpecimenConc.: 0.08 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 3 second blot time and blot force of 10.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 48543 X / Nominal defocus max: 3600 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4 sec. / Electron dose: 54 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7260
Details: Each micrograph was fractionated into 64 frames within a 4 second exposure.

-
Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 525782
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16524 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 200 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16GEJ

6gej

16GEJ1PDBexperimental model
21AlphaFoldin silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 187.65 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003151416
ELECTRON MICROSCOPYf_angle_d0.672570830
ELECTRON MICROSCOPYf_chiral_restr0.04797976
ELECTRON MICROSCOPYf_plane_restr0.00667788
ELECTRON MICROSCOPYf_dihedral_angle_d23.34719827

+
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://pdbjlvh1.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