+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3059 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | ZM197 SOSIP.664 trimer in complex with VRC01 Fab | |||||||||
Map data | Single particle reconstruction of the ZM197 SOSIP + VRC01 Fab complex. | |||||||||
Sample |
| |||||||||
Keywords | HIV-1 / Env / antibody / broadly neutralizing antibodies | |||||||||
Function / homology | Function and homology information positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.32 Å | |||||||||
Authors | Lee JH / Ward AB | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2015 Title: Design and structure of two HIV-1 clade C SOSIP.664 trimers that increase the arsenal of native-like Env immunogens. Authors: Jean-Philippe Julien / Jeong Hyun Lee / Gabriel Ozorowski / Yuanzi Hua / Alba Torrents de la Peña / Steven W de Taeye / Travis Nieusma / Albert Cupo / Anila Yasmeen / Michael Golabek / ...Authors: Jean-Philippe Julien / Jeong Hyun Lee / Gabriel Ozorowski / Yuanzi Hua / Alba Torrents de la Peña / Steven W de Taeye / Travis Nieusma / Albert Cupo / Anila Yasmeen / Michael Golabek / Pavel Pugach / P J Klasse / John P Moore / Rogier W Sanders / Andrew B Ward / Ian A Wilson / Abstract: A key challenge in the quest toward an HIV-1 vaccine is design of immunogens that can generate a broadly neutralizing antibody (bnAb) response against the enormous sequence diversity of the HIV-1 ...A key challenge in the quest toward an HIV-1 vaccine is design of immunogens that can generate a broadly neutralizing antibody (bnAb) response against the enormous sequence diversity of the HIV-1 envelope glycoprotein (Env). We previously demonstrated that a recombinant, soluble, fully cleaved SOSIP.664 trimer based on the clade A BG505 sequence is a faithful antigenic and structural mimic of the native trimer in its prefusion conformation. Here, we sought clade C native-like trimers with comparable properties. We identified DU422 and ZM197M SOSIP.664 trimers as being appropriately thermostable (Tm of 63.4 °C and 62.7 °C, respectively) and predominantly native-like, as determined by negative-stain electron microscopy (EM). Size exclusion chromatography, ELISA, and surface plasmon resonance further showed that these trimers properly display epitopes for all of the major bnAb classes, including quaternary-dependent, trimer-apex (e.g., PGT145) and gp120/gp41 interface (e.g., PGT151) epitopes. A cryo-EM reconstruction of the ZM197M SOSIP.664 trimer complexed with VRC01 Fab against the CD4 binding site at subnanometer resolution revealed a striking overall similarity to its BG505 counterpart with expected local conformational differences in the gp120 V1, V2, and V4 loops. These stable clade C trimers contribute additional diversity to the pool of native-like Env immunogens as key components of strategies to induce bnAbs to HIV-1. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3059.map.gz | 59.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-3059-v30.xml emd-3059.xml | 10.8 KB 10.8 KB | Display Display | EMDB header |
Images | EMD-3059.png emd_3059.png | 1.1 MB 1.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3059 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3059 | HTTPS FTP |
-Validation report
Summary document | emd_3059_validation.pdf.gz | 244.5 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_3059_full_validation.pdf.gz | 243.6 KB | Display | |
Data in XML | emd_3059_validation.xml.gz | 6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3059 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3059 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_3059.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Single particle reconstruction of the ZM197 SOSIP + VRC01 Fab complex. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Fab of VRC01 antibody bound to a clade C ZM176 SOSIP.664 trimer
Entire | Name: Fab of VRC01 antibody bound to a clade C ZM176 SOSIP.664 trimer |
---|---|
Components |
|
-Supramolecule #1000: Fab of VRC01 antibody bound to a clade C ZM176 SOSIP.664 trimer
Supramolecule | Name: Fab of VRC01 antibody bound to a clade C ZM176 SOSIP.664 trimer type: sample / ID: 1000 Oligomeric state: Each VRC01 Fab binds a gp120 on the trimer Number unique components: 2 |
---|---|
Molecular weight | Theoretical: 570 KDa |
-Macromolecule #1: HIV-1 Env
Macromolecule | Name: HIV-1 Env / type: protein_or_peptide / ID: 1 / Name.synonym: SOSIP Details: A SOSIP trimer with the ZM197M isolate sequence with the following mutations: D156N, E295N, V297T and D332N. Number of copies: 1 / Oligomeric state: Trimer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Human immunodeficiency virus 1 / Strain: ZM197M / synonym: HIV-1 |
Molecular weight | Theoretical: 420 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293F / Recombinant plasmid: pPPI4 |
-Macromolecule #2: VRC01 Antibody
Macromolecule | Name: VRC01 Antibody / type: protein_or_peptide / ID: 2 / Name.synonym: VRC01 Details: Each Fab consists of a heavy chain-light chain dimer Number of copies: 3 / Oligomeric state: heterodimer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma |
Molecular weight | Theoretical: 500 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293F |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.00 mg/mL |
---|---|
Buffer | pH: 7.4 / Details: 20 mM Tris, 150 mM NaCl |
Grid | Details: 400 mesh carbon support C-flat holey grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: HOMEMADE PLUNGER Method: Added DDM to 0.01% (w/v) to the sample immediately prior to applying sample on grid. Manually blotted and plunged into liquid ethane. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Temperature | Min: 180 K / Max: 180 K |
Alignment procedure | Legacy - Astigmatism: Objective astigmatism was corrected |
Date | Dec 6, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 1914 / Average electron dose: 30.51 e/Å2 Details: Each image is an aligned sum of 32 frames recorded on the K2. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 25500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Whole micrograph |
---|---|
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.32 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 4903 |