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Download EndnoteVaccine-Induced Developmental Pathways in Rhesus Macaques for Neutralizing Antibodies Targeting the HIV-1 Fusion Peptide
Kong, R., Duan, H., Sheng, Z., Xu, K., Acharya, P., Kwong, P.D., Mascola, J.M.To be published.
6MPH
Cryo-EM structure at 3.8 A resolution of HIV-1 fusion peptide-directed antibody, DF1W-a.01, elicited by vaccination of Rhesus macaques, in complex with stabilized HIV-1 Env BG505 DS-SOSIP, which was also bound to antibodies VRC03 and PGT122
- DOI: 10.2210/pdb6MPH/pdb
- EMDataResource: EMD-9189
- Classification: VIRAL PROTEIN
- Organism(s): Human immunodeficiency virus 1
- Expression System: Homo sapiens
- Deposited: 2018-10-06 Released: 2019-07-24
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.8 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by: Sequence | Structure
Entity ID: 1 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| DF1W-a.01 heavy chain | 1, 3, H | 118 | N/A | Mutation(s): 0 |
| Protein Feature View is not available: No corresponding UniProt sequence found. | ||||
Entity ID: 2 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| DF1W-a.01 Light chain | 2, 4, L | 112 | N/A | Mutation(s): 0 |
| Protein Feature View is not available: No corresponding UniProt sequence found. | ||||
Entity ID: 3 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| Envelope glycoprotein gp41 | 6, D, E | 153 | Human immunodeficiency virus 1 | Mutation(s): 0 Gene Names: env |
Find proteins for Q2N0S7 (Human immunodeficiency virus 1) Go to UniProtKB: Q2N0S7 | ||||
Entity ID: 4 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| Envelope glycoprotein gp120 | A, B, C | 473 | Human immunodeficiency virus 1 | Mutation(s): 0 Gene Names: env |
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Go to UniProtKB: Q2N0S6 | ||||
Entity ID: 5 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| PGT122 heavy chain | M, X, Y | 132 | N/A | Mutation(s): 0 |
| Protein Feature View is not available: No corresponding UniProt sequence found. | ||||
Entity ID: 6 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| PGT122 Light Chain | N, Z, a | 107 | N/A | Mutation(s): 0 |
| Protein Feature View is not available: No corresponding UniProt sequence found. | ||||
Entity ID: 7 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| VRC03 Heavy chain | Q, f, g | 227 | N/A | Mutation(s): 0 |
| Protein Feature View is not available: No corresponding UniProt sequence found. | ||||
Entity ID: 8 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| VRC03 Light Chain | R, h, i | 102 | N/A | Mutation(s): 0 |
| Protein Feature View is not available: No corresponding UniProt sequence found. | ||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MAN Query on MAN | A, B, C, h, i, R | ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N |  | Ligand Interaction | |
| BMA Query on BMA | A, B, C, h, i, R | BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N |  | Ligand Interaction | |
| NAG Query on NAG | 6, A, B, C, D, E, h, i, R | N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.8 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
Entry History
Deposition Data
- Deposited Date: 2018-10-06
- Released Date: 2019-07-24
- Deposition Author(s): Acharya, P., Xu, K., Kwong, P.D.
