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- PDB-5v8m: BG505 SOSIP.664 trimer in complex with broadly neutralizing HIV a... -

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Basic information

Entry
Database: PDB / ID: 5v8m
TitleBG505 SOSIP.664 trimer in complex with broadly neutralizing HIV antibody 3BNC117
Components
  • (antibody 3BNC117, ...) x 2
  • gp120Envelope glycoprotein GP120
  • gp41
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV / broadly neutralizing antibody / 3BNC117 / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function/homologypositive 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 sourceHuman immunodeficiency virus 1 / HIV / virus
Homo sapiens / / human
MethodElectron microscopy (4.4 Å resolution / Particle / Single particle) / Transmission electron microscopy
AuthorsLee, J.H. / Cottrell, C.A. / Ward, A.B.
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 22, 2017 / Release: May 3, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 3, 2017Structure modelrepositoryInitial release
1.1Jul 26, 2017Structure modelAuthor supporting evidence / Data collection / Structure summaryem_image_scans / pdbx_audit_support / struct_pdbx_audit_support.funding_organization / _struct.title

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Assembly

Deposited unit
A: gp120
B: gp41
H: antibody 3BNC117, heavy chain
L: antibody 3BNC117, light chain
F: gp120
I: gp41
R: antibody 3BNC117, heavy chain
T: antibody 3BNC117, light chain
G: gp120
J: gp41
S: antibody 3BNC117, heavy chain
U: antibody 3BNC117, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)388,298165
Polyers356,67012
Non-polymers31,628153
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)71360
ΔGint (kcal/M)314
Surface area (Å2)118300

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Components

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Protein/peptide , 2 types, 6 molecules AFGBIJ

#1: Protein/peptide gp120 / Envelope glycoprotein GP120 / envelope glycoprotein gp120


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
#2: Protein/peptide gp41 / / envelope glycoprotein gp41


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

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Antibody 3BNC117, ... , 2 types, 6 molecules HRSLTU

#3: Protein/peptide antibody 3BNC117, heavy chain


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
#4: Protein/peptide antibody 3BNC117, light chain


Mass: 23022.658 Da / Num. of mol.: 3 / Fragment: Fab / Source: (gene. exp.) Homo sapiens / Cell line (production host): HEK293F / Production host: Homo sapiens

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Non-polymers , 3 types, 153 molecules

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


Mass: 221.208 Da / Num. of mol.: 99 / Formula: C8H15NO6 / : N-Acetylglucosamine
#6: Chemical
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 15 / Formula: C6H12O6 / : Mannose
#7: Chemical...
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 39 / Formula: C6H12O6 / : Mannose

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: BG505 SOSIP.664 soluble Env trimer in complex with 3BNC117 Fab
Type: COMPLEX / Entity ID: 1,2,3,4 / Source: RECOMBINANT
Molecular weightValue: 0.51 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Homo sapiens
Source (recombinant)Cell: HEK293F / Organism: Homo sapiens
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 32 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 22625 / Symmetry type: POINT

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