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- EMDB-8420: Cryo-EM structure of BG505 DS-SOSIP HIV-1 Env trimer in complex w... -

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Basic information

Entry
Database: EMDB / ID: EMD-8420
TitleCryo-EM structure of BG505 DS-SOSIP HIV-1 Env trimer in complex with vaccine elicited, fusion peptide-directed antibody vFP1.01
Map dataSingle particle cryo-EM reconstruction of stabilized BG505 SOSIP in complex with vaccine elicited fusion peptide directed antibody FP1
Sample
  • Complex: HIV-1 Env trimer
    • Complex: HIV-1 Env trimer in complex with antibody
    • Protein or peptide: BG505 DS-SOSIP
    • Protein or peptide: vFP1.01 Heavy Chain
    • Protein or peptide: vFP1.01 Light chain
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.58 Å
AuthorsAcharya P / Kwong PD / Potter CS / Carragher B
CitationJournal: Nat Med / Year: 2018
Title: Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1.
Authors: Kai Xu / Priyamvada Acharya / Rui Kong / Cheng Cheng / Gwo-Yu Chuang / Kevin Liu / Mark K Louder / Sijy O'Dell / Reda Rawi / Mallika Sastry / Chen-Hsiang Shen / Baoshan Zhang / Tongqing Zhou ...Authors: Kai Xu / Priyamvada Acharya / Rui Kong / Cheng Cheng / Gwo-Yu Chuang / Kevin Liu / Mark K Louder / Sijy O'Dell / Reda Rawi / Mallika Sastry / Chen-Hsiang Shen / Baoshan Zhang / Tongqing Zhou / Mangaiarkarasi Asokan / Robert T Bailer / Michael Chambers / Xuejun Chen / Chang W Choi / Venkata P Dandey / Nicole A Doria-Rose / Aliaksandr Druz / Edward T Eng / S Katie Farney / Kathryn E Foulds / Hui Geng / Ivelin S Georgiev / Jason Gorman / Kurt R Hill / Alexander J Jafari / Young D Kwon / Yen-Ting Lai / Thomas Lemmin / Krisha McKee / Tiffany Y Ohr / Li Ou / Dongjun Peng / Ariana P Rowshan / Zizhang Sheng / John-Paul Todd / Yaroslav Tsybovsky / Elise G Viox / Yiran Wang / Hui Wei / Yongping Yang / Amy F Zhou / Rui Chen / Lu Yang / Diana G Scorpio / Adrian B McDermott / Lawrence Shapiro / Bridget Carragher / Clinton S Potter / John R Mascola / Peter D Kwong /
Abstract: A central goal of HIV-1 vaccine research is the elicitation of antibodies capable of neutralizing diverse primary isolates of HIV-1. Here we show that focusing the immune response to exposed N- ...A central goal of HIV-1 vaccine research is the elicitation of antibodies capable of neutralizing diverse primary isolates of HIV-1. Here we show that focusing the immune response to exposed N-terminal residues of the fusion peptide, a critical component of the viral entry machinery and the epitope of antibodies elicited by HIV-1 infection, through immunization with fusion peptide-coupled carriers and prefusion stabilized envelope trimers, induces cross-clade neutralizing responses. In mice, these immunogens elicited monoclonal antibodies capable of neutralizing up to 31% of a cross-clade panel of 208 HIV-1 strains. Crystal and cryoelectron microscopy structures of these antibodies revealed fusion peptide conformational diversity as a molecular explanation for the cross-clade neutralization. Immunization of guinea pigs and rhesus macaques induced similarly broad fusion peptide-directed neutralizing responses, suggesting translatability. The N terminus of the HIV-1 fusion peptide is thus a promising target of vaccine efforts aimed at eliciting broadly neutralizing antibodies.
History
DepositionOct 5, 2016-
Header (metadata) releaseOct 26, 2016-
Map releaseJan 24, 2018-
UpdateJul 18, 2018-
Current statusJul 18, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8420.png

Downloads & links

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Map

FileDownload / File: emd_8420.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSingle particle cryo-EM reconstruction of stabilized BG505 SOSIP in complex with vaccine elicited fusion peptide directed antibody FP1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.016
Minimum - Maximum-0.042561606 - 0.065297596
Average (Standard dev.)0.00019344286 (±0.0027625593)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z352.000352.000352.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0430.0650.000

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Supplemental data

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Sample components

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Entire : HIV-1 Env trimer

EntireName: HIV-1 Env trimer
Components
  • Complex: HIV-1 Env trimer
    • Complex: HIV-1 Env trimer in complex with antibody
    • Protein or peptide: BG505 DS-SOSIP
    • Protein or peptide: vFP1.01 Heavy Chain
    • Protein or peptide: vFP1.01 Light chain

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Supramolecule #1: HIV-1 Env trimer

SupramoleculeName: HIV-1 Env trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant plasmid: pVRC8400

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Supramolecule #2: HIV-1 Env trimer in complex with antibody

SupramoleculeName: HIV-1 Env trimer in complex with antibody / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant plasmid: pVRC8400

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Macromolecule #1: BG505 DS-SOSIP

MacromoleculeName: BG505 DS-SOSIP / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SRATMPMGSL QPLATLYLLG MLVASVLAAE NLWVTVYYGV PVWKDAETTL FCASDAKAYE TEKHNVWATH ACVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHTDIISLW DQSLKPCVKL TPLCVTLQCT NVTNNITDDM RGELKNCSFN MTTELRDKKQ KVYSLFYRLD ...String:
SRATMPMGSL QPLATLYLLG MLVASVLAAE NLWVTVYYGV PVWKDAETTL FCASDAKAYE TEKHNVWATH ACVPTDPNPQ EIHLENVTEE FNMWKNNMVE QMHTDIISLW DQSLKPCVKL TPLCVTLQCT NVTNNITDDM RGELKNCSFN MTTELRDKKQ KVYSLFYRLD VVQINENQGN RSNNSNKEYR LINCNTSAcT QACPKVSFEP IPIHYCAPAG FAILKCKDKK FNGTGPCPSV STVQCTHGIK PVVSTQLLLN GSLAEEEVMI RSENITNNAK NILVQFNTPV QINCTRPNNN TRKSIRIGPG QAFYATGDII GDIRQAHCNV SKATWNETLG KVVKQLRKHF GNNTIIRFAN SSGGDLEVTT HSFNCGGEFF YCNTSGLFNS TWISNTSVQG SNSTGSNDSI TLPCRIKQII NMWQRIGQcM YAPPIQGVIR CVSNITGLIL TRDGGSTNST TETFRPGGGD MRDNWRSELY KYKVVKIEPL GVAPTRCKRR VVGRRRRRRA VGIGAVFLGF LGAAGSTMGA ASMTLTVQAR NLLSGIVQQQ SNLLRAPEAQ QHLLKLTVWG IKQLQARVLA VERYLRDQQL LGIWGCSGKL ICCTNVPWNS SWSNRNLSEI WDNMTWLQWD KEISNYTQII YGLLEESQNQ QEKNEQDLLA LD

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Macromolecule #2: vFP1.01 Heavy Chain

MacromoleculeName: vFP1.01 Heavy Chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
QVQLQQSGTE LVWPGTSVTL SCKASGYTFT DYEIHWVKQT PVHGLEWIGA IVPKTGYTAY NQKFRGKAIL TADKSSSTAY MDLRRLTSE DSAVYYCTRL RNYWYFDVWG TGTTVTVSPA STKGPSVFPL AP

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Macromolecule #3: vFP1.01 Light chain

MacromoleculeName: vFP1.01 Light chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: DFLMAQTPLS LPVSLGDQAS ISCRSSQSIV YSDGNTYLEW YLQRPGQSPK LLIYKVSNRF SGVPDRFSGS GSGTDFTLRI SRVEAEDLG IYYCFQGSHV PYTFGGGTKL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
DFLMAQTPLS LPVSLGDQAS ISCRSSQSIV YSDGNTYLEW YLQRPGQSPK LLIYKVSNRF SGVPDRFSGS GSGTDFTLRI SRVEAEDLG IYYCFQGSHV PYTFGGGTKL EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNR

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.2 / Component - Name: HEPES
GridModel: EMS C-flat / Material: COPPER / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 10.0 sec. / Average electron dose: 8.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.0)
Startup modelType of model: EMDB MAP
EMDB ID:

5782

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 8.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 14500
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation Coefficient

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