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- EMDB-0620: Full length HIV-1 Envelope glycoprotein clone AMC011 in complex w... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0620 | ||||||||||||
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Title | Full length HIV-1 Envelope glycoprotein clone AMC011 in complex with PGT151 Fab and PGZL1 Fab | ||||||||||||
![]() | AMC011 FL in complex with PGT151 and PGZL1 Fabs | ||||||||||||
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Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.9 Å | ||||||||||||
![]() | Rantalainen KR | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: An MPER antibody neutralizes HIV-1 using germline features shared among donors. Authors: Lei Zhang / Adriana Irimia / Lingling He / Elise Landais / Kimmo Rantalainen / Daniel P Leaman / Thomas Vollbrecht / Armando Stano / Daniel I Sands / Arthur S Kim / / Pascal Poignard / ...Authors: Lei Zhang / Adriana Irimia / Lingling He / Elise Landais / Kimmo Rantalainen / Daniel P Leaman / Thomas Vollbrecht / Armando Stano / Daniel I Sands / Arthur S Kim / / Pascal Poignard / Dennis R Burton / Ben Murrell / Andrew B Ward / Jiang Zhu / Ian A Wilson / Michael B Zwick / ![]() ![]() ![]() Abstract: The membrane-proximal external region (MPER) of HIV-1 envelope glycoprotein (Env) can be targeted by neutralizing antibodies of exceptional breadth. MPER antibodies usually have long, hydrophobic ...The membrane-proximal external region (MPER) of HIV-1 envelope glycoprotein (Env) can be targeted by neutralizing antibodies of exceptional breadth. MPER antibodies usually have long, hydrophobic CDRH3s, lack activity as inferred germline precursors, are often from the minor IgG3 subclass, and some are polyreactive, such as 4E10. Here we describe an MPER broadly neutralizing antibody from the major IgG1 subclass, PGZL1, which shares germline V/D-region genes with 4E10, has a shorter CDRH3, and is less polyreactive. A recombinant sublineage variant pan-neutralizes a 130-isolate panel at 1.4 μg/ml (IC). Notably, a germline revertant with mature CDR3s neutralizes 12% of viruses and still binds MPER after DJ reversion. Crystal structures of lipid-bound PGZL1 variants and cryo-EM reconstruction of an Env-PGZL1 complex reveal how these antibodies recognize MPER and viral membrane. Discovery of common genetic and structural elements among MPER antibodies from different patients suggests that such antibodies could be elicited using carefully designed immunogens. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 115 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.8 KB 13.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.4 KB | Display | ![]() |
Images | ![]() | 119 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Others | ![]() ![]() | 98.4 MB 98.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.2 KB | Display | ![]() |
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Full document | ![]() | 77.3 KB | Display | |
Data in XML | ![]() | 493 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6o3dC ![]() 6o3gC ![]() 6o3jC ![]() 6o3kC ![]() 6o3lC ![]() 6o3uC ![]() 6o41C ![]() 6o42C C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | AMC011 FL in complex with PGT151 and PGZL1 Fabs | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map 2- AMC011 FL in complex with PGT151 and PGZL1 Fabs
File | emd_0620_half_map_1.map | ||||||||||||
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Annotation | Half map 2- AMC011 FL in complex with PGT151 and PGZL1 Fabs | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1- AMC011 FL in complex with PGT151 and PGZL1 Fabs
File | emd_0620_half_map_2.map | ||||||||||||
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Annotation | Half map 1- AMC011 FL in complex with PGT151 and PGZL1 Fabs | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : HIV-1 Envelope glycoprotein in complex with human antibody Fab fr...
Entire | Name: HIV-1 Envelope glycoprotein in complex with human antibody Fab fragments PGT151 and PGZL1 |
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Components |
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-Supramolecule #1: HIV-1 Envelope glycoprotein in complex with human antibody Fab fr...
Supramolecule | Name: HIV-1 Envelope glycoprotein in complex with human antibody Fab fragments PGT151 and PGZL1 type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 5.6 mg/mL |
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Buffer | pH: 7.4 |
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 11.5 sec. / Average electron dose: 4.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |