3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Mapping the structure and function of the E1 and E2 glycoproteins in alphaviruses.
by single particle (icosahedral) reconstruction, at 9.0 A resolution
#1: Surface view with section colored by density value, Surface level: 75, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 75, Made by UCSF CHIMERA
#3: Surface view with fitted model, atomic models: PDB-1z8y, Surface level: 100, Made by UCSF CHIMERA
#4: Surface view with fitted model, atomic models: PDB-2xfb, Surface level: 100, Made by UCSF CHIMERA
#5: Surface view with fitted model, atomic models: PDB-3muw, Surface level: 100, Made by UCSF CHIMERA
#6: Simplified surface model with fitted atomic model: PDB-1z8y, Made by Jmol
#7: Simplified surface model with fitted atomic model: PDB-2xfb, Made by Jmol
#8: Simplified surface model with fitted atomic model: PDB-3muw, Made by Jmol
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 1121 |
|---|---|
| Authors | Mukhopadhyay S, Zhang W, Gabler S, Chipman PR, Strauss EG, Strauss JH, Baker TS, Kuhn RJ, Rossmann MG |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 75, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 75, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-1z8y, Surface level: 100, Made by UCSF CHIMERA #4: Surface view with fitted model, atomic models: PDB-2xfb, Surface level: 100, Made by UCSF CHIMERA #5: Surface view with fitted model, atomic models: PDB-3muw, Surface level: 100, Made by UCSF CHIMERA #6: Simplified surface model with fitted atomic model: PDB-1z8y, Made by Jmol #7: Simplified surface model with fitted atomic model: PDB-2xfb, Made by Jmol #8: Simplified surface model with fitted atomic model: PDB-3muw, Made by Jmol |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article Fit: output model of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | Structure, Vol. 14, Issue 1, Page 63-73, Year 2006 |
|---|---|
| Title | Mapping the structure and function of the E1 and E2 glycoproteins in alphaviruses. |
| Authors | Suchetana Mukhopadhyay, Wei Zhang, Stefan Gabler, Paul R Chipman, Ellen G Strauss, James H Strauss, Timothy S Baker, Richard J Kuhn, Michael G Rossmann Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA. |
| Keywords |  Cryoelectron Microscopy, Crystallography, X-Ray, Membrane Glycoproteins (chemistry), Nucleocapsid Proteins (chemistry), Protein Interaction Mapping, Protein Structure, Tertiary, Sindbis Virus (chemistry), Viral Envelope Proteins (chemistry), Viral Fusion Proteins (chemistry), glycoprotein E1, Sindbis virus, glycoprotein E2, Sindbis virus |
| Links | PII: S0969-2126(05)00393-X, DOI: 10.1016/j.str.2005.07.025, PubMed: 16407066, PMC: PMC2757649 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1121.map ( map file in CCP4 format, 72844 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | float (32-bit) | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A = 787.18 A , B = 787.18 A , C = 787.18 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 1.78499 A , Y = 1.78499 A , Z = 1.78499 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | center of virus is where z=0 | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Sindbis TE12 E2-N318Q |
|---|---|
| Number of Components | 1 |
| Details | Sample is a single deglycosylated virus. For mutagenesis and purification, please see Pletnev et al. (2001) Cell. Virus contains 3 proteins (E1, E2, capsid), a lipid bilyer, and a positive-strand RNA genome. |
| Component #1: virus - Sindbis strain TE12 | |
| Scientific name | Sindbis virus |
| Common Name | Sindbis strain TE12 |
| Experimental Mass | 52 MDa |
| Details | deglycosylated virus |
| Scientific Name of Species | Sindbis virus (NCBI Taxonomy: 11034) |
| Common Name of Species | Sindbis strain TE12 |
| Empty | No |
| Enveloped | Yes |
| Isolate | STRAIN |
| Class | VIRION |
| Natural Source | Host Species: Homo sapiens (NCBI Taxonomy: 9606) Host Category: INVERTEBRATES |
| Shell | Diameter: 710 A Name Element: glycoprotein T Number: 4 |
| Shell | Diameter: 480 A T Number: 4 Name Element: lipid bilayer |
| Shell | T Number: 4 Diameter: 410 A Name Element: capsid |
 Experiment | |
| Sample Preparation | |
| Specimen Conc | 6 mg/ml |
|---|---|
| Staining | no staining |
| Specimen Support Details | holey carbon 400 mesh copper grid |
| Specimen State | particle |
| Buffer | Details: 20 mM Tris-Cl, 200 mM NaCl, 0.1 mM EDTA pH: 7.4 |
| Vitrification | |
| Cryogen Name | ETHANE |
| Instrument | HOMEMADE PLUNGER |
| Method | standard methods |
| Time Resolved State | Vitrified immediately after blotting. |
| Details | Vitrification instrument: Purdue manufactured, gravity driven device. Vitrification carried out in hood. |
| Imaging | |
| Microscope | FEI/PHILIPS CM200T |
| Date | 2000-06-21 |
| Details | Low dose |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 18 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 38000 X, Calibrated: 39220 X |
| Astigmatism | objective lens astigmatism was corrected at 100,000 times magnification |
| Nominal Cs | 2.0 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 1100 nm - 2580 nm |
| Specimen Holder | |
| Holder | Side entry liquid nitrogen-cooled cryo specimen holder ( GATAN LIQUID NITROGEN ) |
| Tilt Angle | 0 degrees - 0 degrees |
| Temperature | ( 87 Kelvin - 100 Kelvin ) |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Number of Digital Images | 27 |
| Sampling Size | 7 microns |
| Od Range | 1.0 |
| Quant Bit Number | 8 |
| Scanner | ZEISS SCAI |
| Details | optical density range is 0.33-1.35 |
 Processing | |
| Method | single particle (icosahedral) reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | model-based common lines |
| Software | Purdue Suite |
| CTF Correction | CTF correction of each particle. |
| Resolution By Author | 9.0 |
| Resolution Method | FSC at 0.5 cut-off |
| Euler Angles Details | Euler angles (theta, phi, omega) are defined as three successive rotations in a right hand coordinate system. First, the viewer is rotated counterclockwise around the z-axis (angle 'phi') and then rotated counterclockwise around the new y-axis (angle 'theta') and rotate clockwise around the new z-axis (angle 'omega'). |
| Details | resolution determined by splitting data set into two groups. |
| Single Particle | |
| Number of Projections | 7085 |
| Number of Class Averages | 3 |
| Details | The particles were selected interactively at the computer terminal. |
| Applied Symmetry | I (icosahedral) |
| Atomic Model Fitting | |
| Model #0 | |
| Details | Protocol: Rigid body. each protein in the asymmetric unit was fitting individually. |
| Refinement Protocol | rigid body |
| Refinement Space | REAL |
| Target Criteria | sumf |
| Software | EMFIT |
| Model #1 | |
| Refinement Space | REAL |
| Target Criteria | sumf |
| Refinement Protocol | rigid body |
| Details | Protocol: Rigid body. each protein in the asymmetric unit was fitting individually. |
| Software | EMFIT |
| Fitted Coordinate | |
| PDB entry ID | |
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