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Three-dimensional structure of Dengue virus serotype 1 complexed with HMAb 14c10 Fab
by single particle (icosahedral) reconstruction, at 7 A resolution
#1: Surface view with section colored by density value, Surface level: 2.5, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 2.5, Made by UCSF CHIMERA
#3: Surface view with fitted model, atomic models: PDB-3j05, Surface level: 2.5, Made by UCSF CHIMERA
#4: Simplified surface model with fitted atomic model: PDB-3j05, Made by Jmol
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 5268 |
|---|---|
| Authors | Teoh EP, Kukkaro P, Teo EW, Lim A, Tan TT, Shi PY, Yip A, Schul W, Leo S, Chan SH, Smith KGC, Ooi EE, Kemeny DM, Ng G, Ng ML, Alonso S, Fisher D, Hanson B, Lok SM, MacAry PA |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 2.5, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 2.5, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-3j05, Surface level: 2.5, Made by UCSF CHIMERA #4: Simplified surface model with fitted atomic model: PDB-3j05, 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 | Sci Transl Med, Vol. 4, Issue 139, Page 139ra83, Year 2012 |
|---|---|
| Title | The structural basis for serotype-specific neutralization of dengue virus by a human antibody. |
| Authors | Ee Ping Teoh, Petra Kukkaro, En Wei Teo, Angeline P C Lim, Tze Tong Tan, Andy Yip, Wouter Schul, Myint Aung, Victor A Kostyuchenko, Yee Sin Leo, Soh Ha Chan, Kenneth G C Smith, Annie Hoi Yi Chan, Gang Zou, Eng Eong Ooi, D Michael Kemeny, Grace K Tan, Jowin K W Ng, Mah Lee Ng, Sylvie Alonso, Dale Fisher, Pei-Yong Shi, Brendon J Hanson, Shee-Mei Lok, Paul A MacAry Department of Microbiology and Life Sciences Institute Immunology Programme, National University of Singapore, Singapore 117597, Singapore. |
| Keywords |  Animals, Antibodies, Neutralizing (pharmacology), Antiviral Agents (pharmacology), Cryoelectron Microscopy, Dengue (drug therapy), Dengue Virus (drug effects), Epitopes (immunology), Humans, Mice |
| Links | DOI: 10.1126/scitranslmed.3003888, PubMed: 22723463 |
 Map | |||||||||||||||||||||||||
| File |  EMD-5268.map ( map file in CCP4 format, 500002 KB ) | ||||||||||||||||||||||||
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| 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 = 950.0 A , B = 950.0 A , C = 950.0 A , alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 1.9 A , Y = 1.9 A , Z = 1.9 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | cryo-EM reconstruction of a complex of Dengue serotype 1 with 14C10 antibodies | ||||||||||||||||||||||||
 Supplement |
 Sample | |
| Name | Dengue virus serotype 1 with Fab fragment of human monoclonal antibody 14c10 |
|---|---|
| Number of Components | 2 |
| Oligomeric State | 120 Fab molecules bind to one dengue virion |
| Component #1: virus - Dengue 1 | |
| Scientific name | Dengue virus 1 |
| Common Name | Dengue 1 |
| Details | strain PVP 159 |
| Scientific Name of Species | Dengue virus 1 (NCBI Taxonomy: 11053) |
| Common Name of Species | Dengue 1 |
| Enveloped | Yes |
| Empty | No |
| Class | VIRION |
| Isolate | STRAIN |
| Natural Source | Host Category: INVERTEBRATES Host Species: Aedes albopictus (NCBI Taxonomy: 7160) |
| Shell | T Number: 3 Diameter: 240 A |
| Component #2: protein - Fab | |
| Scientific name | antibody Fab fragment |
| Common Name | Fab |
| Experimental Mass | 50 MDa |
| Oligomeric Details | monomer |
| Scientific Name of Species | Homo sapiens (NCBI Taxonomy: 9606) |
| Common Name of Species | Human |
| Recombinant expression | Yes |
| Natural Source | Cell: CD22plus B cells Cell Location: secreted Organ Or Tissue: blood |
| Engineered Source | Vector: pTT5 Exp System: Homo sapiens (NCBI Taxonomy: 9606) |
 Experiment | |
| Sample Preparation | |
| Specimen Support Details | lacey carbon copper grid |
|---|---|
| Specimen State | particle |
| Buffer | Details: 120 mM NaCl, 12 mM Tris-HCl, pH 8.0, 1mM EDTA pH: 8.0 |
| Vitrification | |
| Method | 1 second blotting |
| Cryogen Name | ETHANE |
| Details | Vitrification instrument: Vitrobot |
| Humidity | 100 |
| Instrument | FEI VITROBOT |
| Imaging | |
| Microscope | FEI TITAN KRIOS |
| Date | 27-SEP-2010 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 300 kV |
| Electron Dose | 16 e/A**2 |
| Illumination Mode | SPOT SCAN |
| Lens | |
| Magnification | Nominal: 47000 X, |
| Nominal Cs | 2.7 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 760 nm - 4900 nm |
| Specimen Holder | |
| Holder | ( OTHER ) |
| Temperature | 100 Kelvin |
| Camera | |
| Detector | Gatan CCD |
| Image Acquisition | |
| Number of Digital Images | 341 |
| Sampling Size | 15 microns |
| Quant Bit Number | 16 |
| Details | 4k x 4k Gatan CCD |
 Processing | |
| Method | single particle (icosahedral) reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | Cross-common lines |
| Software | EMAN, MPSA |
| CTF Correction | Each particle |
| Resolution By Author | 7 |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Details | The particles were selected manually. |
| Number of Projections | 2129 |
| Applied Symmetry | I (icosahedral) |
| Atomic Model Fitting | |
| Model #0 | |
| Target Criteria | correlation |
| Details | Protocol: rigid body. The domains were fitted separately using Fit In Map feature in Chimera |
| Software | Chimera |
| Refinement Protocol | rigid body |
| Refinement Space | REAL |
| Fitted Coordinate | |
| PDB entry ID | |
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