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Structure of an RNA polymerase II-DSIF transcription elongation complex, DSIF-EC4

by single particle reconstruction, at 3.7 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.022, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.022, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 3818
TitleStructure of an RNA polymerase II-DSIF transcription elongation complex, DSIF-EC4
MapLocally filtered map, B-factor 0
SampleRNA polymerase II-DSIF elongation complex
AuthorsBernecky C, Plitzko JM, Cramer P
DateDeposition: 2017-07-18, Header release: 2017-08-23, Map release: 2017-09-13, Last update: 2017-09-13
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.022, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.022, Imaged by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleNat. Struct. Mol. Biol., Year 2017
TitleStructure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp.
AuthorsCarrie Bernecky, Jürgen M Plitzko, Patrick Cramer
Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
Department of Molecular Structural Biology, Max Planck Institute for Biochemistry, Martinsried, Germany.
LinksPubMed: 28892040, DOI: 10.1038/nsmb.3465
Map
Fileemd_3818.map.gz ( map file in CCP4 format, 67109 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.35 A/pix
= 345.6 A
256 pix
1.35 A/pix
= 345.6 A
256 pix
1.35 A/pix
= 345.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.022 (by author), 0.022 (movie #1):
Minimum - Maximum: -0.046392817 - 0.13966373
Average (Standard dev.): -1.41452165E-5 (0.0050458345)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
Unit CellA= B= C: 345.6 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.35 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.351.351.35
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0460.140-0.000
Annotation DetailsLocally filtered map, B-factor 0
Supplement
Mask Set
Mask: #0
Fileemd_3818_msk_1.map ( map file in CCP4 format, 67109 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data TypeImage stored as Reals
DimensionsNumber of Rows: 256 , Number of Columns: 256 , Number of Sections: 256
SpacingSpacing Row: 256 , Spacing Col: 256 , Spacing Sec: 256
OriginOrigin Row: 0 , Origin Col: 0 , Origin Sec: 0
LimitLimit Row: 255 , Limit Col: 255 , Limit Sec: 255
Unit CellA: 345.6 A, B: 345.6 A, C: 345.6 A, alpha: 90 degrees, beta: 90 degrees, gamma: 90 degrees
Axis Order1: X , 2: Y , 3: Z
Statisticsmin.: 0 , max.: 1 , avg.: 0.03366548 , std.: 0.17137234
Pixel SpacingX: 1.35 A, Y: 1.35 A, Z: 1.35 A
Annotation DetailsNone
Space Group Number1
Mask: #1
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Images
Images
Sample
NameRNA polymerase II-DSIF elongation complex
Number of Components4
Theoretical Mass0.13MDa
Component #1: protein - RNA polymerase II-DSIF elongation complex
Scientific nameRNA polymerase II-DSIF elongation complex
Theoretical Mass0.13 MDa
Scientific Name of SpeciesHomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 469008
Expression system: Escherichia coli BL21(DE3)
Component #2: protein - RNA polymerase II
Scientific nameRNA polymerase II
Scientific Name of SpeciesBos taurus

NCBI taxonomy9913
Recombinant expressionNo
Component #3: protein - DSIF
Scientific nameDSIF
Scientific Name of SpeciesHomo sapiens
NCBI taxonomy9606
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 469008
Expression system: Escherichia coli BL21(DE3)
Component #4: protein - DNA-RNA synthetic construct
Scientific nameDNA-RNA synthetic construct
Scientific Name of Speciessynthetic construct
NCBI taxonomy32630
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 32630
Expression system: synthetic construct
Experiment
Sample Preparation
Specimen Stateparticle
Specimen Conc0.25 mg/ml
BufferpH: 7.25
Details: pH was adjusted at 25 degrees Celsius
Vitrification
Cryogen NameETHANE
Humidity100
Temperature277 Kelvin
InstrumentFEI VITROBOT MARK IV
DetailsSample (four microliters) was applied to glow-discharged Quantifoil R 2/1 holey carbon grids, which were then blotted for 8.5s and plunge-frozen in liquid ethane.
Imaging
MicroscopeFEI TITAN KRIOS
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose33 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 37000, Calibrated: 37037
Nominal Cs2.7 mm
Imaging ModeBRIGHT FIELD
Defocus600 nm - 3600 nm
Energy FilterEnergy Filter: GIF Quantum , Energy Window: 0-20 eV
Specimen Holder
ModelFEI TITAN KRIOS AUTOGRID HOLDER
Camera
DetectorGATAN K2 (4k x 4k)
Image Acquisition
#1
Number of Digital Images2549
DetailsMovies were aligned and binned to the physical pixel size of 1.35 angstroms.
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmFOURIER SPACE
SoftwareRELION
Resolution By Author3.7 A
Resolution MethodFSC 0.143 CUT-OFF
Single Particle
Applied SymmetryC1 (asymmetric)
Number of Projections76394
Download
Data from EMDB
Header (meta data in XML format)emd-3818-v19.xml (10.1 KB)
emd-3818-v20.xml (24.4 KB)
emd-3818.xml (10.1 KB)
Map dataemd_3818.map.gz (58.8 MB)
Imagesemd_3818.png (102.5 KB)
Masks (Map data of sub-region, etc)emd_3818_msk_1.map (64 MB)
Othersemd_3818_additional_1.map.gz (59.9 MB)
emd_3818_additional_2.map.gz (59.7 MB)
emd_3818_half_map_1.map.gz (49.7 MB)
emd_3818_half_map_2.map.gz (49.8 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-3818
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.7 MB
Session file for UCSF-Chimera, 26.9 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.7 MB
Session file for UCSF-Chimera, 26.8 KB