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Structural Basis of Membrane Bending by the N-BAR Protein Endophilin
by helical reconstruction, at 16 A resolution
#1: Surface view with section colored by density value, Surface level: 1.94, Made by UCSF CHIMERA
#2: Surface view colored by cylindrical radius, Surface level: 1.94, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 2007 |
|---|---|
| Title | Structural Basis of Membrane Bending by the N-BAR Protein Endophilin |
| Map | This a reconstruction of the endophilin A1 N-BAR domain bound to a membrane tubule with a diameter of 25 nm. |
| Sample | N-BAR domain (1-247) of rat endophilinA1 |
| Authors | Mim C, Cui H, Gawronski-Salerno JA, Frost A, Lyman E, Voth GA, Unger VM |
| Date | Deposition: 2011-12-09, Header release: 2012-04-27, Map release: 2012-04-27, Last update: 2012-04-27 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 1.94, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 1.94, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | Cell, Vol. 149, Issue 1, Page 137-45, Year 2012 |
|---|---|
| Title | Structural basis of membrane bending by the N-BAR protein endophilin. |
| Authors | Carsten Mim, Haosheng Cui, Joseph A Gawronski-Salerno, Adam Frost, Edward Lyman, Gregory A Voth, Vinzenz M Unger Department of Molecular Biosciences, Northwestern University, 2205 Campus Drive, Evanston, IL 60208, USA. |
| Keywords |  2-acylglycerophosphate acyltransferase (2.3.1.52), Acyltransferases (chemistry, 2.3.-), Animals, Cell Membrane (chemistry), Cryoelectron Microscopy, Models, Molecular, Nerve Tissue Proteins (chemistry), Protein Interaction Domains and Motifs, Protein Structure, Tertiary, Rats, amphiphysin (147954-52-7) |
| Links | PII: S0092-8674(12)00207-3, DOI: 10.1016/j.cell.2012.01.048, PubMed: 22464326, PMC: PMC3319357 |
 Map | |||||||||||||||||||||||||
| File |  EMD-2007.map ( map file in CCP4 format, 23330 KB ) | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
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| Unit Cell | A= B= C: 491.4 A Alpha=beta=gamma: 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X= Y= Z: 2.73 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | This a reconstruction of the endophilin A1 N-BAR domain bound to a membrane tubule with a diameter of 25 nm. | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | N-BAR domain (1-247) of rat endophilinA1 |
|---|---|
| Number of Components | 1 |
| Oligomeric State | Dimer of the N-BAR domain of endophilin binds to bilayer |
| Experimental Mass | 25MDa |
| Component #1: protein - N-BAR domain | |
| Scientific name | rat endophilinA1 N-BAR domain |
| Common Name | N-BAR domain |
| Experimental Mass | 25 MDa |
| Oligomeric Details | Dimer |
| Number of Copies | 2 |
| Scientific Name of Species | Rattus norvegicus
|
| Common Name of Species | Norway rat |
| NCBI taxonomy | 10116 |
| Recombinant expression | Yes |
| Natural Source | Cell Location: Plasma membrane |
| Engineered Source | Vector: pGEX-6 PI NCBI taxonomy: 562 Expression system: Escherichia coli |
 Experiment | |
| Sample Preparation | |
| Helical Parameters | Axial Symmetry: C2 Delta Z: 25.13 A Delta Phi: 83.57 degrees Hand: RIGHT HANDED |
|---|---|
| Specimen Conc | 0.25 mg/ml |
| Specimen Support Details | C-Flat, 2-2, 400nm mesh |
| Specimen State | helicalArray |
| Crystal Grow Details | protein and liposomes added in solution before freezing |
| Buffer | pH: 7.5 Details: 50mM K-Aspartate, 10mM Tris, 1mM EGTA |
| Vitrification | |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: FEI Vitrobot |
| Humidity | 100 |
| Instrument | FEI VITROBOT |
| Temperature | 105 Kelvin |
| Imaging | |
| Microscope | FEI TECNAI 20 |
| Details | Low Dose Imaging |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 10 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 30000 |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 1.4 nm - 2 nm |
| Specimen Holder | |
| Holder | eucentric, single tilt |
| Model | GATAN LIQUID NITROGEN |
| Camera | |
 Processing | |
| Method | helical reconstruction |
|---|---|
| 3D reconstruction | |
| Algorithm | IHRSR |
| Software | SPIDER,XMIPP,IHRSR |
| CTF Correction | ACE,MATLAB |
| Resolution By Author | 16 A |
| Resolution Method | RMEASURE |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-2007.xml (7.1 KB) | ||
|---|---|---|---|
| Map data | emd_2007.map.gz (6 MB) | ||
| Images | emd-2007.tif (732.8 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2007 | ||
| Movie files | |||
| movie #1 |
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| movie #2 |
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