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- EMDB-5856: Negative stain reconstruction of HIV envelope glycoprotein BG505 ... -

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Entry
Database: EMDB / ID: EMD-5856
TitleNegative stain reconstruction of HIV envelope glycoprotein BG505 SOSIP.664 in complex with CAP256-VRC26.09 Fab
Map dataNegative stain reconstruction of HIV-1 BG505 SOSIP.664 in complex with CAP256-VRC26.09 Fab
Sample
  • Sample: HIV-1 BG505 SOSIP.664 in complex with CAP256-VRC26.09 Fab
  • Protein or peptide: envelope glycoprotein BG505 SOSIP.664
  • Protein or peptide: CAP256-VRC26.09 Fab
KeywordsHIV / envelope glycoprotein trimer / CAP256 / VRC.26 / V1/V2 directed antibody
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 28.0 Å
AuthorsWard AB / Kim HJ
CitationJournal: Nature / Year: 2014
Title: Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies.
Authors: Nicole A Doria-Rose / Chaim A Schramm / Jason Gorman / Penny L Moore / Jinal N Bhiman / Brandon J DeKosky / Michael J Ernandes / Ivelin S Georgiev / Helen J Kim / Marie Pancera / Ryan P ...Authors: Nicole A Doria-Rose / Chaim A Schramm / Jason Gorman / Penny L Moore / Jinal N Bhiman / Brandon J DeKosky / Michael J Ernandes / Ivelin S Georgiev / Helen J Kim / Marie Pancera / Ryan P Staupe / Han R Altae-Tran / Robert T Bailer / Ema T Crooks / Albert Cupo / Aliaksandr Druz / Nigel J Garrett / Kam H Hoi / Rui Kong / Mark K Louder / Nancy S Longo / Krisha McKee / Molati Nonyane / Sijy O'Dell / Ryan S Roark / Rebecca S Rudicell / Stephen D Schmidt / Daniel J Sheward / Cinque Soto / Constantinos Kurt Wibmer / Yongping Yang / Zhenhai Zhang / / James C Mullikin / James M Binley / Rogier W Sanders / Ian A Wilson / John P Moore / Andrew B Ward / George Georgiou / Carolyn Williamson / Salim S Abdool Karim / Lynn Morris / Peter D Kwong / Lawrence Shapiro / John R Mascola /
Abstract: Antibodies capable of neutralizing HIV-1 often target variable regions 1 and 2 (V1V2) of the HIV-1 envelope, but the mechanism of their elicitation has been unclear. Here we define the developmental ...Antibodies capable of neutralizing HIV-1 often target variable regions 1 and 2 (V1V2) of the HIV-1 envelope, but the mechanism of their elicitation has been unclear. Here we define the developmental pathway by which such antibodies are generated and acquire the requisite molecular characteristics for neutralization. Twelve somatically related neutralizing antibodies (CAP256-VRC26.01-12) were isolated from donor CAP256 (from the Centre for the AIDS Programme of Research in South Africa (CAPRISA)); each antibody contained the protruding tyrosine-sulphated, anionic antigen-binding loop (complementarity-determining region (CDR) H3) characteristic of this category of antibodies. Their unmutated ancestor emerged between weeks 30-38 post-infection with a 35-residue CDR H3, and neutralized the virus that superinfected this individual 15 weeks after initial infection. Improved neutralization breadth and potency occurred by week 59 with modest affinity maturation, and was preceded by extensive diversification of the virus population. HIV-1 V1V2-directed neutralizing antibodies can thus develop relatively rapidly through initial selection of B cells with a long CDR H3, and limited subsequent somatic hypermutation. These data provide important insights relevant to HIV-1 vaccine development.
History
DepositionJan 6, 2014-
Header (metadata) releaseFeb 12, 2014-
Map releaseMar 19, 2014-
UpdateMay 7, 2014-
Current statusMay 7, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.33
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.33
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_5856.gif

Downloads & links

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Map

FileDownload / File: emd_5856.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain reconstruction of HIV-1 BG505 SOSIP.664 in complex with CAP256-VRC26.09 Fab
Voxel sizeX=Y=Z: 2.05 Å
Density
Contour LevelBy AUTHOR: 2.33 / Movie #1: 2.33
Minimum - Maximum-2.4231379 - 13.975288389999999
Average (Standard dev.)0.0 (±0.8505826)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-39-39-39
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
start NX/NY/NZ-95-75153
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-39-39-39
NC/NR/NS160160160
D min/max/mean-2.42313.9750.000

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Supplemental data

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Sample components

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Entire : HIV-1 BG505 SOSIP.664 in complex with CAP256-VRC26.09 Fab

EntireName: HIV-1 BG505 SOSIP.664 in complex with CAP256-VRC26.09 Fab
Components
  • Sample: HIV-1 BG505 SOSIP.664 in complex with CAP256-VRC26.09 Fab
  • Protein or peptide: envelope glycoprotein BG505 SOSIP.664
  • Protein or peptide: CAP256-VRC26.09 Fab

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Supramolecule #1000: HIV-1 BG505 SOSIP.664 in complex with CAP256-VRC26.09 Fab

SupramoleculeName: HIV-1 BG505 SOSIP.664 in complex with CAP256-VRC26.09 Fab
type: sample / ID: 1000 / Details: Sample was monodisperse / Oligomeric state: One HIV trimer binds one Fab / Number unique components: 2
Molecular weightTheoretical: 410 KDa

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Macromolecule #1: envelope glycoprotein BG505 SOSIP.664

MacromoleculeName: envelope glycoprotein BG505 SOSIP.664 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: Trimer / Recombinant expression: Yes
Source (natural)Organism: Human immunodeficiency virus 1 / synonym: HIV-1 / Location in cell: Membrane
Molecular weightTheoretical: 360 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK 293S / Recombinant plasmid: pPI4

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Macromolecule #2: CAP256-VRC26.09 Fab

MacromoleculeName: CAP256-VRC26.09 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: heterodimer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: B cells
Molecular weightTheoretical: 50 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK 293F / Recombinant plasmid: IgG1, kappa, lambda

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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

Concentration0.08 mg/mL
BufferpH: 7.4 / Details: 50 mM Tris, 150 mM NaCl
StainingType: NEGATIVE
Details: Grids were adsorbed with protein, blotted, and stained with 2% uranyl formate for 20 seconds.
GridDetails: 400 Cu mesh grid with thin carbon support, glow discharged in natural atmosphere
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
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: 1.0 µm / Nominal magnification: 52000
Specialist opticsEnergy filter - Name: FEI
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle max: 50
TemperatureMin: 292 K / Max: 294 K / Average: 293 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
DateOct 18, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 174 / Average electron dose: 25 e/Å2
Tilt angle min0

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Image processing

Final two d classificationNumber classes: 64
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: OTHER / Software - Name: EMAN, EMAN2, Xmipp, IMAGIC / Details: Map was calculated from a single dataset. / Number images used: 6763
DetailsThe particles were picked using the automated DoG Picker and put into a stack using the Appion software package. Initial reference free 2D class averages were calculated using particles binned by 2 via Xmipp Clustering 2D Alignment and sorted into classes. A template stack of 44 class averages was used to generate an ab initio model, which was refined using EMAN.

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