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- EMDB-9138: HIV-1 vaccine elicited Fab BDA1 in complex with the HIV Env trime... -

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Basic information

Entry
Database: EMDB / ID: EMD-9138
TitleHIV-1 vaccine elicited Fab BDA1 in complex with the HIV Env trimer BG505 SOSIPv5.2
Map dataHIV-1 vaccine elicited Fab BDA1 in complex with the HIV Env trimer BG505 SOSIPv5.2
Sample
  • Complex: HIV-1 vaccine elicited Fab BDA1 in complex with the HIV Env trimer BG505 SOSIPv5.2
    • Complex: SOSIP trimer
      • Protein or peptide: BG505 SOSIPv5.2 gp120
      • Protein or peptide: BG505 SOSIPv5.2 gp41
    • Complex: BDA1 Fab
      • Protein or peptide: BDA1 Fab heavy chain
      • Protein or peptide: BDA1 Fab light chain
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human) / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / negative staining / Resolution: 21.0 Å
AuthorsCottrell CA / Ward AB
CitationJournal: Cell / Year: 2019
Title: Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance.
Authors: Kimberly M Cirelli / Diane G Carnathan / Bartek Nogal / Jacob T Martin / Oscar L Rodriguez / Amit A Upadhyay / Chiamaka A Enemuo / Etse H Gebru / Yury Choe / Federico Viviano / Catherine ...Authors: Kimberly M Cirelli / Diane G Carnathan / Bartek Nogal / Jacob T Martin / Oscar L Rodriguez / Amit A Upadhyay / Chiamaka A Enemuo / Etse H Gebru / Yury Choe / Federico Viviano / Catherine Nakao / Matthias G Pauthner / Samantha Reiss / Christopher A Cottrell / Melissa L Smith / Raiza Bastidas / William Gibson / Amber N Wolabaugh / Mariane B Melo / Benjamin Cossette / Venkatesh Kumar / Nirav B Patel / Talar Tokatlian / Sergey Menis / Daniel W Kulp / Dennis R Burton / Ben Murrell / William R Schief / Steven E Bosinger / Andrew B Ward / Corey T Watson / Guido Silvestri / Darrell J Irvine / Shane Crotty /
Abstract: Conventional immunization strategies will likely be insufficient for the development of a broadly neutralizing antibody (bnAb) vaccine for HIV or other difficult pathogens because of the ...Conventional immunization strategies will likely be insufficient for the development of a broadly neutralizing antibody (bnAb) vaccine for HIV or other difficult pathogens because of the immunological hurdles posed, including B cell immunodominance and germinal center (GC) quantity and quality. We found that two independent methods of slow delivery immunization of rhesus monkeys (RMs) resulted in more robust T follicular helper (T) cell responses and GC B cells with improved Env-binding, tracked by longitudinal fine needle aspirates. Improved GCs correlated with the development of >20-fold higher titers of autologous nAbs. Using a new RM genomic immunoglobulin locus reference, we identified differential IgV gene use between immunization modalities. Ab mapping demonstrated targeting of immunodominant non-neutralizing epitopes by conventional bolus-immunized animals, whereas slow delivery-immunized animals targeted a more diverse set of epitopes. Thus, alternative immunization strategies can enhance nAb development by altering GCs and modulating the immunodominance of non-neutralizing epitopes.
History
DepositionSep 27, 2018-
Header (metadata) releaseOct 31, 2018-
Map releaseMay 29, 2019-
UpdateMay 29, 2019-
Current statusMay 29, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01669377
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.01669377
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9138.png

Downloads & links

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Map

FileDownload / File: emd_9138.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-1 vaccine elicited Fab BDA1 in complex with the HIV Env trimer BG505 SOSIPv5.2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.98 Å/pix.
x 192 pix.
= 380.16 Å		1.98 Å/pix.
x 192 pix.
= 380.16 Å		1.98 Å/pix.
x 192 pix.
= 380.16 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: 0.012 / Movie #1: 0.0166938
Minimum - Maximum-0.04054257 - 0.14626986
Average (Standard dev.)-0.00003215719 (±0.004640977)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 380.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.981.981.98
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z380.160380.160380.160
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0410.146-0.000

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Supplemental data

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Sample components

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Entire : HIV-1 vaccine elicited Fab BDA1 in complex with the HIV Env trime...

EntireName: HIV-1 vaccine elicited Fab BDA1 in complex with the HIV Env trimer BG505 SOSIPv5.2
Components
  • Complex: HIV-1 vaccine elicited Fab BDA1 in complex with the HIV Env trimer BG505 SOSIPv5.2
    • Complex: SOSIP trimer
      • Protein or peptide: BG505 SOSIPv5.2 gp120
      • Protein or peptide: BG505 SOSIPv5.2 gp41
    • Complex: BDA1 Fab
      • Protein or peptide: BDA1 Fab heavy chain
      • Protein or peptide: BDA1 Fab light chain

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Supramolecule #1: HIV-1 vaccine elicited Fab BDA1 in complex with the HIV Env trime...

SupramoleculeName: HIV-1 vaccine elicited Fab BDA1 in complex with the HIV Env trimer BG505 SOSIPv5.2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: SOSIP trimer

SupramoleculeName: SOSIP trimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1

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Supramolecule #3: BDA1 Fab

SupramoleculeName: BDA1 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: BG505 SOSIPv5.2 gp120

MacromoleculeName: BG505 SOSIPv5.2 gp120 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETKKHNVWA THCCVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPCV KLTPLCVTLQ CTNVTNNITD DMRGELKNCS FNMTTELRDK KQKVYSLFYR LDVVQINENQ GNRSNNSNKE YRLINCNTSA ...String:
AENLWVTVYY GVPVWKDAET TLFCASDAKA YETKKHNVWA THCCVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPCV KLTPLCVTLQ CTNVTNNITD DMRGELKNCS FNMTTELRDK KQKVYSLFYR LDVVQINENQ GNRSNNSNKE YRLINCNTSA ITQACPKVSF EPIPIHYCAP AGFAILKCKD KKFNGTGPCP SVSTVQCTHG IKPVVSTQLL LNGSLAEEEV MIRSENITNN AKNILVQFNT PVQINCTRPN NNTRKSIRIG PGQWFYATGD IIGDIRQAHC NVSKATWNET LGKVVKQLRK HFGNNTIIRF ANSSGGDLEV TTHSFNCGGE FFYCNTSGLF NSTWISNTSV QGSNSTGSND SITLPCRIKQ IINMWQRIGQ AMYAPPIQGV IRCVSNITGL ILTRDGGSTN STTETFRPGG GDMRDNWRSE LYKYKVVKIE PLGVAPTRCK RRVVGRRRRR R

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Macromolecule #2: BG505 SOSIPv5.2 gp41

MacromoleculeName: BG505 SOSIPv5.2 gp41 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEC QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSGK LICCTNVPWN SSWSNRNLSE IWDNMTWLQW DKEISNYTQI IYGLLEESQN QQEKNEQDLL ALD

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Macromolecule #3: BDA1 Fab heavy chain

MacromoleculeName: BDA1 Fab heavy chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSETLSL TCAVSGASIS IYWWGWIRQP PGKGLEWIGE IIGSSGSTNS NPSFKSRVTI SKDASKNQFS LNLNSVTAAD TAVYYCVRVG AAISLPFDYW GQGVLVTVSS

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Macromolecule #4: BDA1 Fab light chain

MacromoleculeName: BDA1 Fab light chain / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SYELTQPPSV SVSPGQTARI TCSGDALPKK YAYWFQQKPG QSPVLIIYED NKRPSGIPER FSGSSSGTVA TLTISGAQVE DEGDYYCYSR HSSGNHGLFG GGTRLTVL

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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

BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Formate
GridMaterial: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 122593
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0b0) / Number images used: 15024
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 2 / Avg.num./class: 15000 / Software - Name: RELION (ver. 3.0b0)

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