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- EMDB-2331: Negative stain reconstruction of BG505 SOSIP gp140 HIV-1 trimer i... -

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Basic information

Entry
Database: EMDB / ID: EMD-2331
TitleNegative stain reconstruction of BG505 SOSIP gp140 HIV-1 trimer in complex with PGT135 Fab
Map dataReconstruction of PGT135-BG505 SOSIP complex
Sample
  • Sample: PGT135 Fab fragment bound to HIV-1 clade A BG505 background SOSIP gp140 trimer.
  • Protein or peptide: HIV-1 SOSIP.664 gp140
  • Protein or peptide: PGT135 broadly neutralizing antibody
KeywordsHIV / SOSIP / broadly neutralizing antibodies
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsLee JH / Kong L / Murin CD / Cupo A / Moore JP / Wilson IA / Ward AB
CitationJournal: Nat Struct Mol Biol / Year: 2013
Title: Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120.
Authors: Leopold Kong / Jeong Hyun Lee / Katie J Doores / Charles D Murin / Jean-Philippe Julien / Ryan McBride / Yan Liu / Andre Marozsan / Albert Cupo / Per-Johan Klasse / Simon Hoffenberg / ...Authors: Leopold Kong / Jeong Hyun Lee / Katie J Doores / Charles D Murin / Jean-Philippe Julien / Ryan McBride / Yan Liu / Andre Marozsan / Albert Cupo / Per-Johan Klasse / Simon Hoffenberg / Michael Caulfield / C Richter King / Yuanzi Hua / Khoa M Le / Reza Khayat / Marc C Deller / Thomas Clayton / Henry Tien / Ten Feizi / Rogier W Sanders / James C Paulson / John P Moore / Robyn L Stanfield / Dennis R Burton / Andrew B Ward / Ian A Wilson /
Abstract: A substantial proportion of the broadly neutralizing antibodies (bnAbs) identified in certain HIV-infected donors recognize glycan-dependent epitopes on HIV-1 gp120. Here we elucidate how the bnAb ...A substantial proportion of the broadly neutralizing antibodies (bnAbs) identified in certain HIV-infected donors recognize glycan-dependent epitopes on HIV-1 gp120. Here we elucidate how the bnAb PGT 135 binds its Asn332 glycan-dependent epitope from its 3.1-Å crystal structure with gp120, CD4 and Fab 17b. PGT 135 interacts with glycans at Asn332, Asn392 and Asn386, using long CDR loops H1 and H3 to penetrate the glycan shield and access the gp120 protein surface. EM reveals that PGT 135 can accommodate the conformational and chemical diversity of gp120 glycans by altering its angle of engagement. Combined structural studies of PGT 135, PGT 128 and 2G12 show that this Asn332-dependent antigenic region is highly accessible and much more extensive than initially appreciated, which allows for multiple binding modes and varied angles of approach; thereby it represents a supersite of vulnerability for antibody neutralization.
History
DepositionMar 14, 2013-
Header (metadata) releaseApr 10, 2013-
Map releaseJun 5, 2013-
UpdateJul 17, 2013-
Current statusJul 17, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.96
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.96
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2331.png

Downloads & links

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Map

FileDownload / File: emd_2331.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of PGT135-BG505 SOSIP complex
Voxel sizeX=Y=Z: 2.18 Å
Density
Contour LevelBy AUTHOR: 1.96 / Movie #1: 1.96
Minimum - Maximum-4.59452868 - 8.87144661
Average (Standard dev.)0.0 (±0.64018303)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-37-37-37
Dimensions160160160
Spacing160160160
CellA=B=C: 348.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.182.182.18
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z348.800348.800348.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-27-15-36
NX/NY/NZ553173
MAP C/R/S123
start NC/NR/NS-37-37-37
NC/NR/NS160160160
D min/max/mean-4.5958.871-0.000

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Supplemental data

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Sample components

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Entire : PGT135 Fab fragment bound to HIV-1 clade A BG505 background SOSIP...

EntireName: PGT135 Fab fragment bound to HIV-1 clade A BG505 background SOSIP gp140 trimer.
Components
  • Sample: PGT135 Fab fragment bound to HIV-1 clade A BG505 background SOSIP gp140 trimer.
  • Protein or peptide: HIV-1 SOSIP.664 gp140
  • Protein or peptide: PGT135 broadly neutralizing antibody

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Supramolecule #1000: PGT135 Fab fragment bound to HIV-1 clade A BG505 background SOSIP...

SupramoleculeName: PGT135 Fab fragment bound to HIV-1 clade A BG505 background SOSIP gp140 trimer.
type: sample / ID: 1000 / Oligomeric state: One Fab binds one gp140 monomer / Number unique components: 2
Molecular weightTheoretical: 500 KDa

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Macromolecule #1: HIV-1 SOSIP.664 gp140

MacromoleculeName: HIV-1 SOSIP.664 gp140 / type: protein_or_peptide / ID: 1 / Details: co-expressed with Furin / Number of copies: 3 / Oligomeric state: trimer / Recombinant expression: Yes
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: BG505
Molecular weightTheoretical: 350 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: human / Recombinant cell: HEK293S / Recombinant plasmid: pPPI4

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Macromolecule #2: PGT135 broadly neutralizing antibody

MacromoleculeName: PGT135 broadly neutralizing antibody / type: protein_or_peptide / ID: 2 / Name.synonym: bnAb PGT135 / Number of copies: 3 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: B-Cell
Molecular weightTheoretical: 50 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: SF9

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.03 mg/mL
BufferpH: 7.4 / Details: 1x TBS
StainingType: NEGATIVE / Details: Stained with 2% UF
GridDetails: 400 Cu mesh grid glow discharged at 20 mA
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 0.92 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle min: -50
Alignment procedureLegacy - Astigmatism: objective astigmatism corrected at 100,000 mag
Legacy - Electron beam tilt params: -2
DetailsImages collected in 5 degree increments from 0 to -55
DateJun 12, 2012
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Digitization - Sampling interval: 0.109 µm / Number real images: 1095 / Average electron dose: 20 e/Å2 / Details: Data collected on CCD / Bits/pixel: 16
Tilt angle max0
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Not corrected
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN
Details: Particles picked automatically using DoG-picker and cleaned up with reference free 2D class averaging
Number images used: 8831

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