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dATP-inhibited class Ia ribonucleotide reductase from E. coli: alpha4beta4 open conformation 7

by single particle reconstruction, at 33.1 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 1.88, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.88, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5437
TitledATP-inhibited class Ia ribonucleotide reductase from E. coli: alpha4beta4 open conformation 7
Mapalpha4beta4 open conformation 7
SampleE. coli Class Ia ribonucleotide reductase
Keywordsribonucleotide reductase, allostery, inhibition, nucleotide metabolism
AuthorsZimanyi CM, Ando N, Brignole E, Asturias FJ, Stubbe J, Drennan CL
DateDeposition: 2012-06-13, Header release: 2012-07-13, Map release: 2012-07-25, Last update: 2012-10-24
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 1.88, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.88, Made by UCSF CHIMERA

Supplemental images

EMDB figure
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Cite: data citing same article

Article
Citation - Primary
ArticleStructure, Vol. 20, Issue 8, Page 1374-83, Year 2012
TitleTangled up in knots: structures of inactivated forms of E. coli class Ia ribonucleotide reductase.
AuthorsChristina M Zimanyi, Nozomi Ando, Edward J Brignole, Francisco J Asturias, Joanne Stubbe, Catherine L Drennan
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Keywords2'-deoxyadenosine triphosphate (1927-31-7), Crystallography, X-Ray, Cytidine Diphosphate (analogs & derivatives, 63-38-7), Deoxyadenine Nucleotides (chemistry), Escherichia coli Proteins (antagonists & inhibitors), Exoribonucleases (antagonists & inhibitors, 3.1.-), Microscopy, Electron, Models, Molecular, Protein Binding, Protein Structure, Quaternary, Protein Subunits (antagonists & inhibitors), Scattering, Small Angle, X-Ray Diffraction, gemcitabine-5'-diphosphate, rnr protein, E coli
LinksPII: S0969-2126(12)00211-0, DOI: 10.1016/j.str.2012.05.009, PubMed: 22727814, PMC: PMC3459064
Map
FileEMD-5437.map ( map file in CCP4 format, 1495 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.

(generated in cubic-lattice coordinate)

Density

Histogram

Histogram (log scale)
Contour Level:1.88 (by author), 1.88 (movie #1):
Minimum - Maximum: -4.68228865 - 8.78501797
Average (Standard dev.): 0.02093046 (0.66588986)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions727272
Origin000
Limit717171
Spacing727272
Unit CellA: 313.92 A, B: 313.92 A, C: 470.88 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX: 4.36 A, Y: 4.36 A, Z: 6.54 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z4.364.366.54
M x/y/z727272
origin x/y/z0.0000.0000.000
length x/y/z313.920313.920470.880
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-150-1500
NX/NY/NZ301301151
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS727272
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-4.6828.7850.021
Annotation Detailsalpha4beta4 open conformation 7
Supplement
Sample
NameE. coli Class Ia ribonucleotide reductase
Number of Components1
Oligomeric Statetwo alpha2 subunits in complex with two beta2 subunits
Theoretical Mass0.517MDa
Mass-estimation MethodCalculated from amino acid sequence of subunits
Experimental Mass0.517MDa
Component #1: protein - RNR
Scientific nameE. coli Class Ia ribonucleotide reductase
Common NameRNR
Theoretical Mass0.517 MDa
Experimental Mass0.517 MDa
Detailsalpha4beta4 open conformation
Oligomeric Detailshetero-octamer
Number of Copies1
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
LinksGene Ontology: GO:0005971
Experiment
Sample Preparation
Staining5ul protein, washed immediately 3x [2% uranyl acetate, 0.2% trehalose], carbon sandwich
Specimen Support Detailsthin carbon support on 300 mesh Cu/Rh grid, glow discharge in amylamine
Specimen Stateparticle
BufferDetails: 50 mM HEPES, 15 mM MgCl2, 1 mM EDTA, 1 mM CDP, 0.05 mM dATP
pH: 7.6
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI F20
Date31-JUL-2010
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage120 kV
Electron Dose25 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus275 nm - 1801 nm
Specimen Holder
Holderroom temperature
ModelSIDE ENTRY, EUCENTRIC
Tilt Angle-59.1 degrees - -54.3 degrees
Camera
DetectorGatan Ultrascan 4000
Image Acquisition
Number of Digital Images89
Quant Bit Number16
Detailsimages acquired as tilt-pairs
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmrandom conical tilt
SoftwareSPIDER
CTF Correctioneach particle
Resolution By Author33.1 A
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Projections257
DetailsSemi-automated particle selection from untilted images with EMAN2. Particles matched in tilted images using modified TiltPicker. Processed in SPIDER.
Atomic Model Fitting
Model #0
DetailsProtocol: rigid body. Subunits iteratively fit with Chimera
Refinement Protocolrigid body
Refinement SpaceREAL
Target Criteriacorrelation
SoftwareChimera
PDB Entry ID4R1R

PDB-4r1r
PDB Chain IDA, B, D, E
Model #1
Refinement SpaceREAL
Target Criteriacorrelation
Refinement Protocolrigid body
DetailsProtocol: rigid body. Subunits iteratively fit with Chimera
SoftwareChimera
PDB Entry ID1RIB

PDB-1rib
PDB Chain IDA, B
Download
Data from EMDB
Header (meta data in XML format)emd-5437.xml (8.5 KB)
Map dataemd_5437.map.gz (1.3 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5437
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 26.4 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.6 MB
Session file for UCSF-Chimera, 26.5 KB