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The RNA polymerase and transcription elongation factor Spt4-5 complex structure

by single particle reconstruction, at 13 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.0005, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.0005, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1840
TitleThe RNA polymerase and transcription elongation factor Spt4-5 complex structure
Mapccp4 density map for PFu RNA polymerase-Spt4-Spt5 complex
SamplePyrococcus furiosus RNA polymerase and transcription elongation factor Spt4/5 complex structure
KeywordsRNA polymerase, transcription elongation, X-ray crystallography, cryo-EM, Spt4/5-DSIF-NusG
AuthorsBose D, Klein B, Baker K, Yusoff Z, Murakami K, Zhang X
DateDeposition: 2010-12-02, Header release: 2010-12-10, Map release: 2011-01-07, Last update: 2011-09-09
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.0005, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.0005, Made by UCSF CHIMERA

Supplemental images

EMD-1840.tif
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-3p8b
Cite

Cite: data citing same article

Similar strucutres (beta)

Diagram

EMDB-1804

EMDB-1803

EMDB-1802

EMDB-1975

EMDB-5127
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 108, Issue 2, Page 546-50, Year 2011
TitleRNA polymerase and transcription elongation factor Spt4/5 complex structure.
AuthorsBrianna J Klein, Daniel Bose, Kevin J Baker, Zahirah M Yusoff, Xiaodong Zhang, Katsuhiko S Murakami
Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
KeywordsAmino Acid Sequence, Animals, Chromosomal Proteins, Non-Histone (physiology), Cryoelectron Microscopy (methods), Crystallography, X-Ray (methods), DNA (genetics, 9007-49-2), DNA-Directed DNA Polymerase (genetics, 2.7.7.7), DNA-Directed RNA Polymerases (metabolism, 2.7.7.6), Humans, Molecular Sequence Data, Nuclear Proteins (physiology), Nucleic Acids (chemistry), Pyrococcus furiosus (genetics), SPT4 protein, S cerevisiae, SPT5 transcriptional elongation factor (138673-72-0), Saccharomyces cerevisiae Proteins (physiology), Sequence Homology, Amino Acid, Transcription, Genetic, Transcriptional Elongation Factors (physiology)
LinksDOI: 10.1073/pnas.1013828108, PubMed: 21187417, PMC: PMC3021056
Map
FileEMD-1840.map ( map file in CCP4 format, 8390 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:0.0005 (by author), 0.0005 (movie #1):
Minimum - Maximum: -0.00357582 - 0.00813123
Average (Standard dev.): 7.78792e-06 (0.000228225)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin-64-64-64
Limit636363
Spacing128128128
Unit CellA= B= C: 450.56 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 3.52 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z3.523.523.52
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z450.560450.560450.560
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-30-24-70
NX/NY/NZ6149141
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0040.0080.000
Annotation Detailsccp4 density map for PFu RNA polymerase-Spt4-Spt5 complex
Supplement
Images
Images

EMD-1840.tif
Sample
NamePyrococcus furiosus RNA polymerase and transcription elongation factor Spt4/5 complex structure
Number of Components3
Oligomeric StateMultisubunit RNAP core bound to heterodimer of Spt4 and Spt 5
Theoretical Mass0.4MDa
Experimental Mass0.4MDa
Component #1: protein - RNAP core
Scientific nameRNA polymerase core
Common NameRNAP core
Theoretical Mass0.38 MDa
Experimental Mass0.38 MDa
Oligomeric Detailsmultisubunit
Scientific Name of SpeciesPyrococcus furiosus
NCBI taxonomy2261
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 2261
Expression system: Pyrococcus furiosus
Component #2: protein - Spt4
Scientific nameSpt4
Theoretical Mass0.011 MDa
Experimental Mass0.011 MDa
Oligomeric DetailsHeterodimer with Spt5
Number of Copies1
Scientific Name of SpeciesPyrococcus furiosus
NCBI taxonomy2261
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Component #3: protein - Spt5
Scientific nameSpt5
Theoretical Mass0.017 MDa
Experimental Mass0.017 MDa
Oligomeric DetailsHeterodimer with Spt4
Number of Copies1
Scientific Name of SpeciesPyrococcus furiosus
NCBI taxonomy2261
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Experiment
Sample Preparation
Specimen Conc0.1 mg/ml
Specimen Support DetailsGlow discharged 300 mesh Quantifoil
Specimen Stateparticle
BufferDetails: 10 mM Tris-HCl (pH 8 at 4C), 0.2M KCl, 0.1 mM EDTA, 2 mM DTT, 5 mM BME
pH: 8
Vitrification
Cryogen NameETHANE
DetailsVitrification instrument: Vitrobot
Humidity100
InstrumentFEI VITROBOT
Temperature90 Kelvin
Imaging
MicroscopeFEI/PHILIPS CM200FEG/ST
DetailsLow dose conditions
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose10 e/A**2
Illumination ModeSPOT SCAN
Lens
MagnificationNominal: 50000
Imaging ModeBRIGHT FIELD
Specimen Holder
HolderSingle Tilt (Gatan)
ModelGATAN LIQUID NITROGEN
Camera
Detector4kx4k CCD (TVIPS)
Image Acquisition
Quant Bit Number16
DetailsCCD images
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmCommon lines
Euler Angles DetailsIMAGIC alpha, beta and gamma
SoftwareIMAGIC V, TIGRIS, EMAN
CTF CorrectionMicrograph
Resolution By Author13 A
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Projections70890
Atomic Model Fitting
Model #0
DetailsProtocol: Rigid body
Refinement Protocolrigid body
Refinement SpaceREAL
Softwarechimera, CNS
PDB Entry ID3HKZ

PDB-3hkz
Model #1
Refinement SpaceREAL
Refinement Protocolrigid body
DetailsProtocol: Rigid body. X-ray structure of P. furiosus Spt4 and Spt5-NGN and Spt5-KOW were manually fitted into these densities. For fitting the Spt4 and Spt5-NGN, a hydrophobic cavity on the Spt5-NGN surface was positioned in front of a tip of the coiled-coil of the RpoA1 subunit as suggested by the site-directed and deletion mutagenesis studies. The model was refined using model-minimize.inp in CNS that carried out the conjugate gradient minimization with no experimental energy terms.
Softwarechimera, CNS
PDB Entry ID3P8B

PDB-3p8b
Download
Data from EMDB
Header (meta data in XML format)emd-1840.xml (9.7 KB)
Map dataemd_1840.map.gz (257.3 KB)
ImagesEMD-1840.tif (807.6 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1840
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 26.3 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.4 MB
Session file for UCSF-Chimera, 26.3 KB