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- EMDB-3093: BG505 SOSIP.664 N137A trimer in complex with PGT124 Fab with 3H h... -

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Basic information

Entry
Database: EMDB / ID: EMD-3093
TitleBG505 SOSIP.664 N137A trimer in complex with PGT124 Fab with 3H heavy chain
Map dataReconstruction of PGT124 H3 Fab in complex with BG505 SOSIP.664 N137A
Sample
  • Sample: PGT124 3H+3L Fab in complex with BG505 SOSIP.664 N137A
  • Protein or peptide: BG505 SOSIP.664 Env trimer
  • Protein or peptide: PGT124 Antibody
KeywordsPGT124 / HIV-1 / broadly neutralizing antibody / Env
Biological speciesHuman Immunodeficiency Virus-1 / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 17.0 Å
AuthorsLee JH / Garces F / Wilson IA / Ward AB
CitationJournal: Immunity / Year: 2015
Title: Affinity Maturation of a Potent Family of HIV Antibodies Is Primarily Focused on Accommodating or Avoiding Glycans.
Authors: Fernando Garces / Jeong Hyun Lee / Natalia de Val / Alba Torrents de la Pena / Leopold Kong / Cristina Puchades / Yuanzi Hua / Robyn L Stanfield / Dennis R Burton / John P Moore / Rogier W ...Authors: Fernando Garces / Jeong Hyun Lee / Natalia de Val / Alba Torrents de la Pena / Leopold Kong / Cristina Puchades / Yuanzi Hua / Robyn L Stanfield / Dennis R Burton / John P Moore / Rogier W Sanders / Andrew B Ward / Ian A Wilson /
Abstract: The high-mannose patch on the HIV-1 envelope (Env) glycoprotein is the epicenter for binding of the potent broadly neutralizing PGT121 family of antibodies, but strategies for generating such ...The high-mannose patch on the HIV-1 envelope (Env) glycoprotein is the epicenter for binding of the potent broadly neutralizing PGT121 family of antibodies, but strategies for generating such antibodies by vaccination have not been defined. We generated structures of inferred antibody intermediates by X-ray crystallography and electron microscopy to elucidate the molecular events that occurred during evolution of this family. Binding analyses revealed that affinity maturation was primarily focused on avoiding, accommodating, or binding the N137 glycan. The overall antibody approach angle to Env was defined very early in the maturation process, yet some variation evolved in the PGT121 family branches that led to differences in glycan specificities in their respective epitopes. Furthermore, we determined a crystal structure of the recombinant BG505 SOSIP.664 HIV-1 trimer with a PGT121 family member at 3.0 Å that, in concert with these antibody intermediate structures, provides insights to advance design of HIV vaccine candidates.
History
DepositionJul 9, 2015-
Header (metadata) releaseAug 12, 2015-
Map releaseAug 24, 2016-
UpdateAug 24, 2016-
Current statusAug 24, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0153
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0153
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3093.png

Downloads & links

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Map

FileDownload / File: emd_3093.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of PGT124 H3 Fab in complex with BG505 SOSIP.664 N137A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 160 pix.
= 328. Å		2.05 Å/pix.
x 160 pix.
= 328. Å		2.05 Å/pix.
x 160 pix.
= 328. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0153 / Movie #1: 0.0153
Minimum - Maximum-0.02878539 - 0.0560587
Average (Standard dev.)-0.00019382 (±0.00493135)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z328.000328.000328.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0290.056-0.000

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Supplemental data

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Sample components

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Entire : PGT124 3H+3L Fab in complex with BG505 SOSIP.664 N137A

EntireName: PGT124 3H+3L Fab in complex with BG505 SOSIP.664 N137A
Components
  • Sample: PGT124 3H+3L Fab in complex with BG505 SOSIP.664 N137A
  • Protein or peptide: BG505 SOSIP.664 Env trimer
  • Protein or peptide: PGT124 Antibody

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Supramolecule #1000: PGT124 3H+3L Fab in complex with BG505 SOSIP.664 N137A

SupramoleculeName: PGT124 3H+3L Fab in complex with BG505 SOSIP.664 N137A
type: sample / ID: 1000 / Oligomeric state: 3 Fabs bind one SOSIP trimer / Number unique components: 2
Molecular weightTheoretical: 570 MDa

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Macromolecule #1: BG505 SOSIP.664 Env trimer

MacromoleculeName: BG505 SOSIP.664 Env trimer / type: protein_or_peptide / ID: 1 / Name.synonym: BG505 SOSIP.664 / Details: Has N137A mutation / Number of copies: 1 / Oligomeric state: Trimer / Recombinant expression: Yes
Source (natural)Organism: Human Immunodeficiency Virus-1 / Strain: BG505 / synonym: HIV-1
Molecular weightTheoretical: 420 MDa
Recombinant expressionOrganism: Mammalian (mammals) / Recombinant cell: HEK293S

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Macromolecule #2: PGT124 Antibody

MacromoleculeName: PGT124 Antibody / type: protein_or_peptide / ID: 2 / Name.synonym: PGT124
Details: The Fab has a heavy chain (H3) and light chain (L3) pairing, from the PGT124 lineage.
Number of copies: 3 / Oligomeric state: heterodimer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 50 MDa
Recombinant expressionOrganism: Mammalian (mammals) / Recombinant cell: HEK293F

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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

Concentration0.01 mg/mL
BufferpH: 7.4 / Details: 20 mM Tris, 150 mM NaCl
StainingType: NEGATIVE
Details: Grids adsorbed with protein then stained with 2% w/v uranyl formate
GridDetails: 400 mesh Cu grid with carbon support, plasma cleaned
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
TemperatureAverage: 298 K
Alignment procedureLegacy - Astigmatism: Corrected at 52,000x mag
DateAug 31, 2014
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 343 / Average electron dose: 25 e/Å2
Tilt angle min0
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: OTHER / Software - Name: Sparx / Number images used: 27577

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Atomic model buiding 1

Initial modelPDB ID:

5cez

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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