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- PDB-6vo0: BG505 SOSIP.v5.2 in complex with rabbit Fab 43A2 -

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Basic information

Entry
Database: PDB / ID: 6vo0
TitleBG505 SOSIP.v5.2 in complex with rabbit Fab 43A2
Components
  • (Envelope glycoprotein ...) x 2
  • 43A2 heavy chain
  • 43A2 light chain
KeywordsVIRAL PROTEIN / HIV / Env / antibody
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of receptor clustering / host cell endosome membrane / actin filament reorganization / mitigation of host immune response by virus / viral protein processing / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane ...positive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of receptor clustering / host cell endosome membrane / actin filament reorganization / mitigation of host immune response by virus / viral protein processing / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host plasma membrane / 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
Retroviral envelope protein GP41-like / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Gp120 core superfamily / Envelope glycoprotein Gp160
Envelope glycoprotein gp160
Biological speciesOryctolagus cuniculus (rabbit)
Human immunodeficiency virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsNogal, B. / Cottrell, C.A. / Ward, A.B.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI100663 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F31 AI131873 United States
CitationJournal: Sci Adv / Year: 2020
Title: HIV envelope trimer-elicited autologous neutralizing antibodies bind a region overlapping the N332 glycan supersite.
Authors: Bartek Nogal / Laura E McCoy / Marit J van Gils / Christopher A Cottrell / James E Voss / Raiees Andrabi / Matthias Pauthner / Chi-Hui Liang / Terrence Messmer / Rebecca Nedellec / Mia Shin ...Authors: Bartek Nogal / Laura E McCoy / Marit J van Gils / Christopher A Cottrell / James E Voss / Raiees Andrabi / Matthias Pauthner / Chi-Hui Liang / Terrence Messmer / Rebecca Nedellec / Mia Shin / Hannah L Turner / Gabriel Ozorowski / Rogier W Sanders / Dennis R Burton / Andrew B Ward /
Abstract: To date, immunization studies of rabbits with the BG505 SOSIP.664 HIV envelope glycoprotein trimers have revealed the 241/289 glycan hole as the dominant neutralizing antibody epitope. Here, we ...To date, immunization studies of rabbits with the BG505 SOSIP.664 HIV envelope glycoprotein trimers have revealed the 241/289 glycan hole as the dominant neutralizing antibody epitope. Here, we isolated monoclonal antibodies from a rabbit that did not exhibit glycan hole-dependent autologous serum neutralization. The antibodies did not compete with a previously isolated glycan hole-specific antibody but did compete with N332 glycan supersite broadly neutralizing antibodies. A 3.5-Å cryoEM structure of one of the antibodies in complex with the BG505 SOSIP.v5.2 trimer demonstrated that while the epitope recognized overlapped the N332 glycan supersite by contacting the GDIR motif at the base of V3, primary contacts were located in the variable V1 loop. These data suggest that strain-specific responses to V1 may interfere with broadly neutralizing responses to the N332 glycan supersite and vaccine immunogens may require engineering to minimize these off-target responses or steer them toward a more desirable pathway.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJan 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release

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Structure viewerMolecule:
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Assembly

Deposited unit
L: 43A2 light chain
H: 43A2 heavy chain
A: Envelope glycoprotein gp120
B: Envelope glycoprotein gp41
J: 43A2 light chain
G: 43A2 heavy chain
C: Envelope glycoprotein gp120
E: Envelope glycoprotein gp41
K: 43A2 light chain
I: 43A2 heavy chain
D: Envelope glycoprotein gp120
F: Envelope glycoprotein gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,45684
Polymers286,65212
Non-polymers15,80472
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Envelope glycoprotein ... , 2 types, 6 molecules ACDBEF

#3: Protein Envelope glycoprotein gp120 / / BG505 SOSIP.v5.2 gp120


Mass: 53268.371 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6
#4: Protein Envelope glycoprotein gp41 / BG505 SOSIP.v5.2 gp41


Mass: 17178.549 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6

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Antibody / Protein , 2 types, 6 molecules LJKHGI

#1: Antibody 43A2 light chain


Mass: 12078.307 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Protein 43A2 heavy chain


Mass: 13025.553 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)

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Sugars , 2 types, 72 molecules

#5: Sugar...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 69
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
#6: Sugar ChemComp-BMA / BETA-D-MANNOSE / Mannose


Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1BG505 SOSIP.v5.2 in complex with rabbit Fab 43A2COMPLEX1, 2, 3, 40MULTIPLE SOURCES
2Fab 43A2COMPLEX1, 21RECOMBINANT
3BG505 SOSIP.v5.2COMPLEX3, 41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Oryctolagus cuniculus (rabbit)9986
23Human immunodeficiency virus 111676
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderModel: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 49.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2Leginonimage acquisition
7Cootmodel fitting
8UCSF Chimeramodel fitting
13cryoSPARC13D reconstruction
14RosettaEMmodel refinement
15Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 85841 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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