|Entry||Database: EMDB / ID: 5268|
|Title||Three-dimensional structure of Dengue virus serotype 1 complexed with HMAb 14c10 Fab|
|Keywords||virus / dengue / serotype 1 / mature virus / human antibody / neutralizing / serotype specific / Fab|
|Sample||Dengue virus serotype 1 with Fab fragment of human monoclonal antibody 14c10|
|Source||Dengue virus 1 / virus / Dengue 1|
Homo sapiens / human
|Map data||cryo-EM reconstruction of a complex of Dengue serotype 1 with 14C10 antibodies|
|Method||single particle (icosahedral) reconstruction, at 7 Å resolution|
|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|
|Citation||Sci Transl Med, 2012, 4, 139ra83-139ra83|
Sci Transl Med, 2012, 4, 139ra83-139ra83 Yorodumi Papers
|Validation Report||PDB-ID: 3j05|
About validation report
|Date||Deposition: Mar 15, 2011 / Header (metadata) release: Mar 23, 2011 / Map release: Jun 27, 2012 / Last update: Jun 27, 2012|
Downloads & links
|File||emd_5268.map.gz (map file in CCP4 format, 488283 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.9 Å|
CCP4 map header:
-Entire Dengue virus serotype 1 with Fab fragment of human monoclonal ant...
|Entire||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 virus 1
|Virus||Name: Dengue virus 1 / a.k.a: Dengue 1 / Class: VIRION / Details: strain PVP 159 / Enveloped: Yes / Empty: No / Isolate: STRAIN|
|Species||Species: Dengue virus 1 / virus / Dengue 1|
|Source (natural)||Host Species: Aedes albopictus / arthropod / image: Aedes aegypti|
Host category: INVERTEBRATES
-Component #2: protein, antibody Fab fragment
|Protein||Name: antibody Fab fragment / a.k.a: Fab / Oligomeric Details: monomer / Recombinant expression: Yes|
|Mass||Experimental: 50 MDa|
|Source||Species: Homo sapiens / human|
|Source (engineered)||Expression System: Homo sapiens / human / Vector: pTT5|
|Source (natural)||Location in cell: secreted / Cell: CD22plus B cells / Organ or tissue: blood|
|Sample solution||Buffer solution: 120 mM NaCl, 12 mM Tris-HCl, pH 8.0, 1mM EDTA|
|Support film||lacey carbon copper grid|
|Vitrification||Instrument: FEI VITROBOT / Cryogen name: ETHANE / Humidity: 100 % / Method: 1 second blotting / Details: Vitrification instrument: Vitrobot|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS / Date: Sep 27, 2010|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 16 e/Å2 / Illumination mode: SPOT SCAN|
|Lens||Magnification: 47000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 760 - 4900 nm|
|Specimen Holder||Model: OTHER / Temperature: 100 K|
|Camera||Detector: GENERIC GATAN|
|Image acquisition||Number of digital images: 341 / Sampling size: 15 microns / Bit depth: 16 / Details: 4k x 4k Gatan CCD|
|Processing||Method: single particle (icosahedral) reconstruction / Details: The particles were selected manually. / Number of projections: 2129 / Applied symmetry: I (icosahedral)|
|3D reconstruction||Algorithm: Cross-common lines / Software: EMAN, MPSA / CTF correction: Each particle / Resolution: 7 Å / Resolution method: FSC 0.5|
-Atomic model buiding
-Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
- Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
- Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.
External links: The 2017 Nobel Prize in Chemistry - Press Release
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- All the functionalities will be ported from the levgacy version.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi