|Entry||Database: PDB / ID: 5v8m|
|Title||BG505 SOSIP.664 trimer in complex with broadly neutralizing HIV antibody 3BNC117|
|Keywords||VIRAL PROTEIN/IMMUNE SYSTEM / HIV / broadly neutralizing antibody / 3BNC117 / VIRAL PROTEIN-IMMUNE SYSTEM complex|
|Function/homology||positive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of receptor clustering / actin filament reorganization / Envelope glycoprotein Gp160 / Retroviral envelope protein GP41-like / Retroviral envelope protein / Gp120 core superfamily / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / host cell endosome membrane ...positive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of receptor clustering / actin filament reorganization / Envelope glycoprotein Gp160 / Retroviral envelope protein GP41-like / Retroviral envelope protein / Gp120 core superfamily / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / host cell endosome membrane / evasion or tolerance by virus of host immune response / Envelope glycoprotein GP120 / viral protein processing / fusion of virus membrane with host plasma membrane / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / integral component of membrane / identical protein binding / Envelope glycoprotein gp160|
Function and homology information
|Specimen source||Human immunodeficiency virus 1 / HIV / virus|
Homo sapiens / / human
|Method||Electron microscopy (4.4 Å resolution / Particle / Single particle) / Transmission electron microscopy|
|Authors||Lee, J.H. / Cottrell, C.A. / Ward, A.B.|
|Citation||Journal: Immunity / Year: 2017|
Title: A Broadly Neutralizing Antibody Targets the Dynamic HIV Envelope Trimer Apex via a Long, Rigidified, and Anionic β-Hairpin Structure.
Authors: Jeong Hyun Lee / Raiees Andrabi / Ching-Yao Su / Anila Yasmeen / Jean-Philippe Julien / Leopold Kong / Nicholas C Wu / Ryan McBride / Devin Sok / Matthias Pauthner / Christopher A Cottrell / Travis Nieusma / Claudia Blattner / James C Paulson / Per Johan Klasse / Ian A Wilson / Dennis R Burton / Andrew B Ward
Abstract: Broadly neutralizing antibodies (bnAbs) to HIV delineate vaccine targets and are prophylactic and therapeutic agents. Some of the most potent bnAbs target a quaternary epitope at the apex of the ...Broadly neutralizing antibodies (bnAbs) to HIV delineate vaccine targets and are prophylactic and therapeutic agents. Some of the most potent bnAbs target a quaternary epitope at the apex of the surface HIV envelope (Env) trimer. Using cryo-electron microscopy, we solved the atomic structure of an apex bnAb, PGT145, in complex with Env. We showed that the long anionic HCDR3 of PGT145 penetrated between glycans at the trimer 3-fold axis, to contact peptide residues from all three Env protomers, and thus explains its highly trimer-specific nature. Somatic hypermutation in the other CDRs of PGT145 were crucially involved in stabilizing the structure of the HCDR3, similar to bovine antibodies, to aid in recognition of a cluster of conserved basic residues hypothesized to facilitate trimer disassembly during viral entry. Overall, the findings exemplify the creative solutions that the human immune system can evolve to recognize a conserved motif buried under a canopy of glycans.
Copyright: 2017 The Author(s). Published by Elsevier Inc. All rights reserved.
SummaryFull reportAbout validation report
|Date||Deposition: Mar 22, 2017 / Release: May 3, 2017|
Downloads & links
H: antibody 3BNC117, heavy chain
L: antibody 3BNC117, light chain
R: antibody 3BNC117, heavy chain
T: antibody 3BNC117, light chain
S: antibody 3BNC117, heavy chain
U: antibody 3BNC117, light chain
-Protein/peptide , 2 types, 6 molecules A
F G B I J
Mass: 54064.277 Da / Num. of mol.: 3 / Fragment: UNP residues 30-505 / Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: BG505 / Gene: env / Cell line (production host): HEK293F / Production host: Homo sapiens / References: UniProt:Q2N0S6
Mass: 17146.482 Da / Num. of mol.: 3 / Fragment: UNP residues 509-661 / Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: BG505 / Gene: env / Cell line (production host): HEK293F / Production host: Homo sapiens / References: UniProt:Q2N0S6
-Antibody 3BNC117, ... , 2 types, 6 molecules H
R S L T U
Mass: 24656.484 Da / Num. of mol.: 3 / Fragment: Fab / Source: (gene. exp.) Homo sapiens / Cell: B cell / Cell line (production host): HEK293F / Production host: Homo sapiens
Mass: 23022.658 Da / Num. of mol.: 3 / Fragment: Fab / Source: (gene. exp.) Homo sapiens / Cell line (production host): HEK293F / Production host: Homo sapiens
-Non-polymers , 3 types, 153 molecules
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE|
|Component||Name: BG505 SOSIP.664 soluble Env trimer in complex with 3BNC117 Fab|
Type: COMPLEX / Entity ID: 1,
|Molecular weight||Value: 0.51 deg. / Units: MEGADALTONS / Experimental value: NO||Source (natural)||Organism: Homo sapiens||Source (recombinant)||Cell: HEK293F / Organism: Homo sapiens||Buffer solution||pH: 7.4||Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES||Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD|
|Image recording||Electron dose: 32 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Symmetry||Point symmetry: C3|
|3D reconstruction||Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 22625 / Symmetry type: POINT|
-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