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Electron crystallography reveals the asymmetry of the trimeric glycine betaine transporter BetP from Corynebacterium glutamicum

by electron crystallography, at 8.0 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.077, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.077, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1756
AuthorsTsai C-J, Khafizov KF, Hakulinen J, Forrest LR, Kraemer R, Kuehlbrandt W, Ziegler C
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.077, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.077, Made by UCSF CHIMERA

Supplemental images

emd-1765.jpg
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Article
Citation - Primary
ArticleJ. Mol. Biol., Vol. 407, Issue 3, Page 368-81, Year 2011
TitleStructural asymmetry in a trimeric Na+/betaine symporter, BetP, from Corynebacterium glutamicum.
AuthorsChing-Ju Tsai, Kamil Khafizov, Jonna Hakulinen, Lucy R Forrest, Lucy R Forrest, Reinhard Krämer, Werner Kühlbrandt, Christine Ziegler
Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.
KeywordsBacterial Proteins (chemistry), BetP protein, Corynebacterium glutamicum, Betaine (metabolism, 107-43-7), Carrier Proteins (chemistry), Corynebacterium glutamicum (metabolism), Crystallography, X-Ray, Ion Transport, Models, Molecular, Protein Structure, Secondary, Sodium (metabolism, 7440-23-5), Structure-Activity Relationship
LinksPII: S0022-2836(11)00057-X, DOI: 10.1016/j.jmb.2011.01.028, PubMed: 21281647
Map
FileEMD-1756.map ( map file in CCP4 format, 342 KB )
Projections & SlicesSize of images:
AxesY (Sec.)X (Row.)Z (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:0.077 (by author), 0.077 (movie #1):
Minimum - Maximum: -0.31079239 - 0.31979445
Average (Standard dev.): -0.00266912 (0.07689252)
Data TypeImage stored as Reals
Space Group Number4
Map Geometry
Axis Order : Z X Y
Dimensions : 34 50 50
Origin : 0 0 0
Limit : 33 49 49
Spacing : 40 68 64
Unit CellA = 91.6 A , B = 154.0 A , C = 150.0 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Pixel SpacingX = 2.29 A , Y = 2.26471 A , Z = 2.34375 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.292.26470588235292.34375
M x/y/z406864
origin x/y/z0.0000.0000.000
length x/y/z91.600154.000150.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ505034
MAP C/R/S312
start NC/NR/NS000
NC/NR/NS345050
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.3110.320-0.003
Annotation DetailsThis is a 3D volume reconstructed from 2D crystals of BetP.
Supplement
Images
Images

emd-1765.jpg
Sample
NameSodium/betaine symporter BetP with 45 amino acids truncated at the C-terminus
Number of Components1
Oligomeric StateOne assymetric homotrimer of BetP
Theoretical Mass0.18 MDa
Details2D crystals were grown with lipids extracted from Corynebacterium glutamicum
Component #1: protein - BetP
Scientific nameSodium betaine symporter
Common NameBetP
Theoretical Mass0.18 MDa
Oligomeric DetailsTrimer
Number of Copies3
Scientific Name of SpeciesCorynebacterium glutamicum (NCBI Taxonomy: 1718)
Recombinant expressionYes
Natural SourceCell Location: Cell membrane
Engineered SourceExp System: Escherichia coli (NCBI Taxonomy: 562)
Experiment
Sample Preparation
Specimen Conc1 mg/ml
Two D Crystal ParametersGamma: 90 degrees
Beta: 90 degrees
B Length: 155.1 A
A Length: 92.1 A
Plane Group: P 1 21
C Length: 150 A
Alpha: 90 degrees
StainingSamples embedded in 5% glucose
Specimen Support Details400 mesh copper or molybdenum grid
Specimen StatetwoDArray
BufferDetails: 50mM pH 7.5 Tris-HCl, 200mM NaCl, 4mM CaCl2, 5% glycerol, 5% MPD, 3mM NaN3
pH: 7.5
Vitrification
Cryogen NameNITROGEN
DetailsVitrification instrument: Manual freezing
Humidity20
InstrumentHOMEMADE PLUNGER
Temperature77 Kelvin
Imaging
MicroscopeJEOL 3000SFF
Electron Gun
Electron SourceLAB6
Accelerating Voltage300 kV
Electron Dose10 e/A**2
Illumination ModeSPOT SCAN
Lens
MagnificationNominal: 45000 X,
Nominal Cs1.6 mm
Imaging ModeBRIGHT FIELD
Defocus300 nm - 2000 nm
Specimen Holder
HolderCartridges with tilt angles from 0-50 degrees ( JEOL )
Tilt Angle-50 degrees - 50 degrees
Temperature4.2 Kelvin ( 4.2 Kelvin - 20 Kelvin )
Camera
DetectorKodak SO163 film
Image Acquisition
ScannerZEISS SCAI
Number of Digital Images72
Sampling Size7 microns
Quant Bit Number8
DetailsImage size 6000 pixel.
Processing
Methodelectron crystallography
3 D reconstruction
SoftwareImage2000
CTF CorrectionCTF correction of each image
DetailsB factor was set to -300.
Resolution By Author8.0
Two D Crystal
DetailsImages were processed using Image2000 package.
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Data from EMDB
Header (meta data in XML format)emd-1756.xml (8 KB)
Map dataemd_1756.map.gz (248.1 KB)
Imagesemd-1765.jpg (188.5 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1756
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 4.4 MB
Session file for UCSF-Chimera, 26.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 2.9 MB
.webm (WebM/VP8 format), 4 MB
Session file for UCSF-Chimera, 26.7 KB