[English] 日本語
Yorodumi
- EMDB-6700: Complex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 6700
TitleComplex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the nucleosome
Map dataDensity map of Snf2-nucleosome complex with Snf2 binding to SHL2 of the nucleosome. The map was sharpened by RELION post-processing, and the resolution was reported at 4.69A.
SampleSHL2 complex:
Histone H3.2 / Histone H4 / Histone H2A / Histone H2B 1.1 / (nucleic-acidNucleic acid) x 2 / Transcription regulatory protein SNF2
Function / homologyHistone-fold / Helicase/SANT-associated domain / SNF2-related, N-terminal domain / Histone H2B / Bromodomain / Helicase, C-terminal / Histone H4 / Histone H2A / TATA box binding protein associated factor (TAF) / Histone H2A/H2B/H3 ...Histone-fold / Helicase/SANT-associated domain / SNF2-related, N-terminal domain / Histone H2B / Bromodomain / Helicase, C-terminal / Histone H4 / Histone H2A / TATA box binding protein associated factor (TAF) / Histone H2A/H2B/H3 / Helicase superfamily 1/2, ATP-binding domain / Glutamine-Leucine-Glutamine, QLQ / SNF2 family N-terminal domain / AT hook, DNA-binding motif / Bromodomain, conserved site / Histone H4, conserved site / P-loop containing nucleoside triphosphate hydrolase / Snf2, ATP coupling domain / Histone H2A, C-terminal domain / Histone H2A conserved site / CENP-T/Histone H4, histone fold / Bromodomain-like superfamily / SNF2-like, N-terminal domain superfamily / Histone H3/CENP-A / Helicase conserved C-terminal domain / Bromodomain / C-terminus of histone H2A / QLQ domain profile. / HSA domain profile. / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Bromodomain profile. / Histone H3 signature 2. / Bromodomain signature. / Histone H2B signature. / Histone H3 signature 1. / Histone H4 signature. / Histone H2A signature. / Core histone H2A/H2B/H3/H4 / Centromere kinetochore component CENP-T histone fold / Snf2-ATP coupling, chromatin remodelling complex / QLQ / HSA / positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of transcription from RNA polymerase II promoter in response to amino acid starvation / cellular alcohol catabolic process / positive regulation of invasive growth in response to glucose limitation / positive regulation of mating type switching / sucrose catabolic process / nucleosome mobilization / SWI/SNF complex / strand invasion / rDNA binding / ATP-dependent chromatin remodeling / ec:3.6.4.-: / DNA-dependent ATPase activity / RNA polymerase II activating transcription factor binding / nucleosomal DNA binding / DNA-templated transcription, initiation / lysine-acetylated histone binding / double-strand break repair / nucleosome / helicase activity / DNA-dependent DNA replication / nucleosome assembly / chromatin remodeling / protein heterodimerization activity / positive regulation of transcription by RNA polymerase II / transcription, DNA-templated / DNA binding / nucleoplasm / ATP binding / nucleus / Histone H2B 1.1 / Histone H2A type 1 / Transcription regulatory protein SNF2 / Histone H4 / Histone H3.2 / Histone H2A
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 4.69 Å resolution
AuthorsLi M / Liu X / Xia X / Cheng Z / Li X
CitationJournal: Nature / Year: 2017
Title: Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure.
Authors: Xiaoyu Liu / Meijing Li / Xian Xia / Xueming Li / Zhucheng Chen
Validation ReportPDB-ID: 5x0y

SummaryFull reportAbout validation report
DateDeposition: Jan 23, 2017 / Header (metadata) release: Apr 19, 2017 / Map release: Apr 19, 2017 / Last update: Jun 7, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0341
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0341
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5x0y
  • Surface level: 0.0341
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_6700.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.32 Å/pix.
= 337.92 Å
256 pix
1.32 Å/pix.
= 337.92 Å
256 pix
1.32 Å/pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour Level:0.0341 (by author), 0.0341 (movie #1):
Minimum - Maximum-0.038502302 - 0.092987455
Average (Standard dev.)0.00025256493 (0.002908369)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z337.920337.920337.920
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0390.0930.000

-
Supplemental data

-
Sample components

+
Entire SHL2 complex

EntireName: SHL2 complex / Number of components: 8

+
Component #1: protein, SHL2 complex

ProteinName: SHL2 complex / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #2: protein, Histone H3.2

ProteinName: Histone H3.2 / Recombinant expression: No
MassTheoretical: 15.289904 kDa
Source (engineered)Expression System: Xenopus laevis (African clawed frog)

+
Component #3: protein, Histone H4

ProteinName: Histone H4 / Recombinant expression: No
MassTheoretical: 11.263231 kDa
Source (engineered)Expression System: Xenopus laevis (African clawed frog)

+
Component #4: protein, Histone H2A

ProteinName: Histone H2A / Recombinant expression: No
MassTheoretical: 13.978241 kDa
Source (engineered)Expression System: Xenopus laevis (African clawed frog)

+
Component #5: protein, Histone H2B 1.1

ProteinName: Histone H2B 1.1 / Recombinant expression: No
MassTheoretical: 13.524752 kDa
Source (engineered)Expression System: Xenopus laevis (African clawed frog)

+
Component #6: nucleic-acid, DNA (167-MER)

Nucleic-acidName: DNA (167-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DT)(DC)(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)(DG)(DA)(DT)(DA)(DG)(DC) (DT)(DT)(DG)(DT)(DC)(DG)(DA)(DG)(DA)(DA) (DG)(DT)(DA)(DC)(DG)(DA)(DT)
MassTheoretical: 51.381758 kDa

+
Component #7: nucleic-acid, DNA (167-MER)

Nucleic-acidName: DNA (167-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DT)(DC)(DG)(DT)(DA)(DC)(DT)(DT)(DC) (DT)(DC)(DG)(DA)(DC)(DA)(DA)(DG)(DC)(DT) (DA)(DT)(DC)(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)(DG)(DA)(DT)
MassTheoretical: 51.723949 kDa

+
Component #8: protein, Transcription regulatory protein SNF2

ProteinName: Transcription regulatory protein SNF2 / Recombinant expression: No
MassTheoretical: 85.802805 kDa
Source (engineered)Expression System: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 281 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 90725
3D reconstructionSoftware: Relion / Resolution: 4.69 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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