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- EMDB-6372: JRFL Env SOSIP.664 in complex with CD4-binding site broadly neutr... -

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Basic information

Entry
Database: EMDB / ID: EMD-6372
TitleJRFL Env SOSIP.664 in complex with CD4-binding site broadly neutralizing antibody DRVIA7
Map dataHIV-1 soluble Env SOSIP trimer in complex with broadly neutralizing antibody DRVIA7 Fab
Sample
  • Sample: Fab of broadly neutralizing antibody DRVIA7 in complex with HIV-1 JRFL Env SOSIP.664 trimer
  • Protein or peptide: HIV-1 Env SOSIP gp140
  • Protein or peptide: DRVIA7 anti-HIV antibody Fab
KeywordsHIV-1 / Env / broadly-neutralizing antibody / CD4 binding site / SOSIP
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 21.0 Å
AuthorsOzorowski G / Ward AB
CitationJournal: Immunity / Year: 2016
Title: Key gp120 Glycans Pose Roadblocks to the Rapid Development of VRC01-Class Antibodies in an HIV-1-Infected Chinese Donor.
Authors: Leopold Kong / Bin Ju / Yajing Chen / Linling He / Li Ren / Jiandong Liu / Kunxue Hong / Bin Su / Zheng Wang / Gabriel Ozorowski / Xiaolin Ji / Yuanzi Hua / Yanli Chen / Marc C Deller / ...Authors: Leopold Kong / Bin Ju / Yajing Chen / Linling He / Li Ren / Jiandong Liu / Kunxue Hong / Bin Su / Zheng Wang / Gabriel Ozorowski / Xiaolin Ji / Yuanzi Hua / Yanli Chen / Marc C Deller / Yanling Hao / Yi Feng / Fernando Garces / Richard Wilson / Kaifan Dai / Sijy O'Dell / Krisha McKee / John R Mascola / Andrew B Ward / Richard T Wyatt / Yuxing Li / Ian A Wilson / Jiang Zhu / Yiming Shao /
Abstract: VRC01-class antibodies neutralize diverse HIV-1 strains by targeting the conserved CD4-binding site. Despite extensive investigations, crucial events in the early stage of VRC01 development remain ...VRC01-class antibodies neutralize diverse HIV-1 strains by targeting the conserved CD4-binding site. Despite extensive investigations, crucial events in the early stage of VRC01 development remain elusive. We demonstrated how VRC01-class antibodies emerged in a Chinese donor by antigen-specific single B cell sorting, structural and functional studies, and longitudinal antibody and virus repertoire analyses. A monoclonal antibody DRVIA7 with modest neutralizing breadth was isolated that displayed a subset of VRC01 signatures. X-ray and EM structures revealed a VRC01-like angle of approach, but less favorable interactions between the DRVIA7 light-chain CDR1 and the N terminus with N276 and V5 glycans of gp120. Although the DRVIA7 lineage was unable to acquire broad neutralization, longitudinal analysis revealed a repertoire-encoded VRC01 light-chain CDR3 signature and VRC01-like neutralizing heavy-chain precursors that rapidly matured within 2 years. Thus, light chain accommodation of the glycan shield should be taken into account in vaccine design targeting this conserved site of vulnerability.
History
DepositionJul 2, 2015-
Header (metadata) releaseAug 19, 2015-
Map releaseApr 27, 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: 12.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 12.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6372.png

Downloads & links

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Map

FileDownload / File: emd_6372.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-1 soluble Env SOSIP trimer in complex with broadly neutralizing antibody DRVIA7 Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.98 Å/pix.
x 160 pix.
= 316.8 Å		1.98 Å/pix.
x 160 pix.
= 316.8 Å		1.98 Å/pix.
x 160 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.98 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 12.300000000000001 / Movie #1: 12.3
Minimum - Maximum-17.831092829999999 - 54.103721620000002
Average (Standard dev.)0.46472159 (±4.16127872)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.981.981.98
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z316.800316.800316.800
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/NS160160160
D min/max/mean-17.83154.1040.465

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Supplemental data

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Sample components

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Entire : Fab of broadly neutralizing antibody DRVIA7 in complex with HIV-1...

EntireName: Fab of broadly neutralizing antibody DRVIA7 in complex with HIV-1 JRFL Env SOSIP.664 trimer
Components
  • Sample: Fab of broadly neutralizing antibody DRVIA7 in complex with HIV-1 JRFL Env SOSIP.664 trimer
  • Protein or peptide: HIV-1 Env SOSIP gp140
  • Protein or peptide: DRVIA7 anti-HIV antibody Fab

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Supramolecule #1000: Fab of broadly neutralizing antibody DRVIA7 in complex with HIV-1...

SupramoleculeName: Fab of broadly neutralizing antibody DRVIA7 in complex with HIV-1 JRFL Env SOSIP.664 trimer
type: sample / ID: 1000
Details: Incubated Fab with trimer overnight at room temperature prior to placing on grid.
Oligomeric state: Trimer of JRFL SOSIP.664 with one Fab bound to each protomer
Number unique components: 2
Molecular weightTheoretical: 570 KDa

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Macromolecule #1: HIV-1 Env SOSIP gp140

MacromoleculeName: HIV-1 Env SOSIP gp140 / type: protein_or_peptide / ID: 1 / Name.synonym: SOSIP.664 / Number of copies: 1 / Oligomeric state: Trimer / Recombinant expression: Yes
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: JRFL / synonym: HIV-1
Molecular weightTheoretical: 420 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Macromolecule #2: DRVIA7 anti-HIV antibody Fab

MacromoleculeName: DRVIA7 anti-HIV antibody Fab / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 50 KDa
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

Concentration0.05 mg/mL
BufferpH: 7.4 / Details: 50 mM Tris-HCl, pH 7.4, 150 mM NaCl
StainingType: NEGATIVE
Details: Grids containing adsorbed protein were treated with 3 uL of 2% w/v uranyl formate for 60 seconds. Uranyl formate was then removed with blotting paper.
GridDetails: Glow-discharged CU400 copper grids with carbon support
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeOTHER
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 73,000 magnification.
Specialist opticsEnergy filter - Name: FEI
DetailsA series of tilts from 0 to 50 degrees in 10 degree increments was collected to increase side views.
DateApr 6, 2015
Image recordingCategory: CCD / Film or detector model: FEI CETA (4k x 4k) / Number real images: 142 / Average electron dose: 25.05 e/Å2
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -1.5 µm / Nominal defocus min: -1.5 µm / Nominal magnification: 73000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle min: -50

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Image processing

DetailsParticles were selected automatically using DogPicker. Initial 2D class averages were inspected; those displaying complexes of trimer with Fab were subjected another round of classification. Only classes that clearly showed two or three Fabs per trimer were used for reconstruction.
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: OTHER / Software - Name: EMAN2, Sparx / Number images used: 10685

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