|Entry||Database: EMDB / ID: 8578|
|Title||Negative Stain EM of C05 mutant Fab (VPGSGW) and CR9114 Fab in complex with H1 HA Trimer|
|Map data||EM negative stain map of CR9114 and VPGSGW fabs in complex with H1 hemagglutinin trimer.|
|Sample||Negative stain EM map of C05 Mutant Fab (VPGSGW) and CR9114 fabs in complex with H1 HA trimer.|
Function and homology information
|Source||Influenza A virus (A/Solomon Islands/3/2006(H1N1)) / virus|
|Method||Negative stain / single particle reconstruction / 18 Å resolution|
|Authors||Turner HL / Ward AB|
|Citation||Journal: Nat Commun / Year: 2017|
Title: In vitro evolution of an influenza broadly neutralizing antibody is modulated by hemagglutinin receptor specificity.
Authors: Nicholas C Wu / Geramie Grande / Hannah L Turner / Andrew B Ward / Jia Xie / Richard A Lerner / Ian A Wilson
Abstract: The relatively recent discovery and characterization of human broadly neutralizing antibodies (bnAbs) against influenza virus provide valuable insights into antiviral and vaccine development. ...The relatively recent discovery and characterization of human broadly neutralizing antibodies (bnAbs) against influenza virus provide valuable insights into antiviral and vaccine development. However, the factors that influence the evolution of high-affinity bnAbs remain elusive. We therefore explore the functional sequence space of bnAb C05, which targets the receptor-binding site (RBS) of influenza haemagglutinin (HA) via a long CDR H3. We combine saturation mutagenesis with yeast display to enrich for C05 variants of CDR H3 that bind to H1 and H3 HAs. The C05 variants evolve up to 20-fold higher affinity but increase specificity to each HA subtype used in the selection. Structural analysis reveals that the fine specificity is strongly influenced by a highly conserved substitution that regulates receptor binding in different subtypes. Overall, this study suggests that subtle natural variations in the HA RBS between subtypes and species may differentially influence the evolution of high-affinity bnAbs.
|Date||Deposition: Feb 1, 2017 / Header (metadata) release: Feb 15, 2017 / Map release: May 31, 2017 / Last update: Feb 14, 2018|
Downloads & links
|File||emd_8578.map.gz (map file in CCP4 format, 11944 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 2.05 Å|
CCP4 map header:
-Entire Negative stain EM map of C05 Mutant Fab (VPGSGW) and CR9114 fabs ...
|Entire||Name: Negative stain EM map of C05 Mutant Fab (VPGSGW) and CR9114 fabs in complex with H1 HA trimer.|
Number of components: 1
-Component #1: protein, Negative stain EM map of C05 Mutant Fab (VPGSGW) and CR9...
|Protein||Name: Negative stain EM map of C05 Mutant Fab (VPGSGW) and CR9114 fabs in complex with H1 HA trimer.|
Recombinant expression: No
|Source||Species: Influenza A virus (A/Solomon Islands/3/2006(H1N1)) / virus|
Strain: A/Solomon Islands/3/2006(H1N1)
|Source (engineered)||Expression System: Drosophila / / arthropod / image: Drosophila melanogaster|
|Specimen||Specimen state: particle / Method: Negative stain|
|Sample solution||Specimen conc.: 0.019 mg/ml|
Buffer solution: Solution was made fresh using 0.2um filter.
|Staining||0.2% Uranyl Formate. Samples were placed on 400 mesh copper grids covered with nitrocellulose. Samples were blotted off and UF was added for a total of 30 seconds before being blotted off.|
|Vitrification||Cryogen name: NONE|
-Electron microscopy imaging
Model: Tecnai Spirit / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI SPIRIT|
|Electron gun||Electron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: TVIPS TEMCAM-F416 (4k x 4k)|
|Image acquisition||Number of digital images: 93|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 18874|
|3D reconstruction||Algorithm: BACK PROJECTION / Software: sxali3d.py / Resolution: 18 Å / Resolution method: FSC 0.5 CUT-OFF|
-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)
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
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 / Function and homology information / Changes in new EM Navigator and Yorodumi