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- EMDB-6379: Electron Microscopy of Bg505 in complex with 9H3L antibody -

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Basic information

Entry
Database: EMDB / ID: EMD-6379
TitleElectron Microscopy of Bg505 in complex with 9H3L antibody
Map dataBg505 SOSIP in complex with 9H3L
Sample
  • Sample: Bg505 SOSIP in complex with 9H3L
  • Protein or peptide: Bg505 SOSIP
  • Protein or peptide: 9H3L antibody
Biological speciesSimian-Human immunodeficiency virus / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 21.0 Å
AuthorsGarces F / de Val N / Ward AB / Wilson IA
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 6, 2015-
Header (metadata) releaseAug 19, 2015-
Map releaseMay 4, 2016-
UpdateMay 4, 2016-
Current statusMay 4, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8.94
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 8.94
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_6379.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBg505 SOSIP in complex with 9H3L
Voxel sizeX=Y=Z: 4.1 Å
Density
Contour LevelBy AUTHOR: 8.94 / Movie #1: 8.94
Minimum - Maximum-26.618736269999999 - 51.571224209999997
Average (Standard dev.)-0.33304694 (±4.35876703)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z328.000328.000328.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-31-64
NX/NY/NZ6963129
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-26.61951.571-0.333

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Supplemental data

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Sample components

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Entire : Bg505 SOSIP in complex with 9H3L

EntireName: Bg505 SOSIP in complex with 9H3L
Components
  • Sample: Bg505 SOSIP in complex with 9H3L
  • Protein or peptide: Bg505 SOSIP
  • Protein or peptide: 9H3L antibody

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Supramolecule #1000: Bg505 SOSIP in complex with 9H3L

SupramoleculeName: Bg505 SOSIP in complex with 9H3L / type: sample / ID: 1000 / Oligomeric state: one trimer of Bg505 bound to three Fabs / Number unique components: 2
Molecular weightExperimental: 570 KDa / Theoretical: 570 KDa / Method: Size exclusion chromatography

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Macromolecule #1: Bg505 SOSIP

MacromoleculeName: Bg505 SOSIP / type: protein_or_peptide / ID: 1 / Oligomeric state: trimer / Recombinant expression: Yes
Source (natural)Organism: Simian-Human immunodeficiency virus / synonym: HIV
Molecular weightExperimental: 570 KDa / Theoretical: 570 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Macromolecule #2: 9H3L antibody

MacromoleculeName: 9H3L antibody / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human
Recombinant expressionOrganism: Homo sapiens (human) / 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

Concentration0.03 mg/mL
BufferpH: 7.4 / Details: 50 mM Tris-HCl, 150 mM NaCl
StainingType: NEGATIVE
Details: Grids were stained for 30 seconds using 2% uranyl formate.
GridDetails: 400 Cu mesh grids were negatively glow discharged for 30 seconds at 20 mA.
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 46000
Sample stageSpecimen holder model: OTHER / Tilt angle max: 50
DateMay 8, 2015
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 126 / Average electron dose: 30.43 e/Å2
Tilt angle min0
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Final two d classificationNumber classes: 147
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: OTHER / Software - Name: sparx, EMAN2 / Number images used: 16946
DetailsThe particles were selected and processed using Appion.

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Atomic model buiding 1

Initial modelPDB ID:
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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