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- EMDB-7459: Cryo-EM structure at 3.8 A resolution of vaccine-elicited antibod... -

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Basic information

Entry
Database: EMDB / ID: EMD-7459
TitleCryo-EM structure at 3.8 A resolution of vaccine-elicited antibody vFP20.01 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122
Map dataprimary map
Sample
  • Complex: vFP20.01-BG505 DS-SOSIP-VRC03-PGT122
    • Complex: PGT122
      • Protein or peptide: PGT122 Heavy chain
      • Protein or peptide: PGT122 Light Chain
    • Complex: VRC03
      • Protein or peptide: VRC03 Light Chain
      • Protein or peptide: VRC03 Heavy Chain
    • Complex: Glycoprotein
      • Protein or peptide: Glycoprotein 41
      • Protein or peptide: Glycoprotein 120
    • Complex: vFP20.01
      • Protein or peptide: vFP20.01 Heavy Chain
      • Protein or peptide: vFP20.01 Light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-mannopyranose
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsAcharya P / Carragher B / Potter CS / Kwong PD
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)OD019994 United States
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
DepositionFeb 8, 2018-
Header (metadata) releaseMar 14, 2018-
Map releaseMay 16, 2018-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.544
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.544
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6cde
  • Surface level: 0.544
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6cde
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7459.png

Downloads & links

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Map

FileDownload / File: emd_7459.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 384 pix.
= 407.04 Å		1.06 Å/pix.
x 384 pix.
= 407.04 Å		1.06 Å/pix.
x 384 pix.
= 407.04 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.544 / Movie #1: 0.544
Minimum - Maximum-1.3979257 - 3.0661054
Average (Standard dev.)0.0038648555 (±0.093476325)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 407.03998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z407.040407.040407.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-1.3983.0660.004

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Supplemental data

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Mask #1

Fileemd_7459_msk_1.map
Projections & Slices
AxesZYX

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Mask #2

Fileemd_7459_msk_2.map
Projections & Slices
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Additional map: additional map #1

Fileemd_7459_additional_1.map
Annotationadditional map #1
Projections & Slices
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Additional map: additional map #2

Fileemd_7459_additional_2.map
Annotationadditional map #2
Projections & Slices
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Histogram

Histogram (log scale)

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Additional map: additional map #3

Fileemd_7459_additional_3.map
Annotationadditional map #3
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: additional map #4

Fileemd_7459_additional_4.map
Annotationadditional map #4
Projections & Slices
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Sample components

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Entire : vFP20.01-BG505 DS-SOSIP-VRC03-PGT122

EntireName: vFP20.01-BG505 DS-SOSIP-VRC03-PGT122
Components
  • Complex: vFP20.01-BG505 DS-SOSIP-VRC03-PGT122
    • Complex: PGT122
      • Protein or peptide: PGT122 Heavy chain
      • Protein or peptide: PGT122 Light Chain
    • Complex: VRC03
      • Protein or peptide: VRC03 Light Chain
      • Protein or peptide: VRC03 Heavy Chain
    • Complex: Glycoprotein
      • Protein or peptide: Glycoprotein 41
      • Protein or peptide: Glycoprotein 120
    • Complex: vFP20.01
      • Protein or peptide: vFP20.01 Heavy Chain
      • Protein or peptide: vFP20.01 Light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: vFP20.01-BG505 DS-SOSIP-VRC03-PGT122

SupramoleculeName: vFP20.01-BG505 DS-SOSIP-VRC03-PGT122 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#8, #1-#2

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Supramolecule #2: PGT122

SupramoleculeName: PGT122 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: VRC03

SupramoleculeName: VRC03 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #4: Glycoprotein

SupramoleculeName: Glycoprotein / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #5: vFP20.01

SupramoleculeName: vFP20.01 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: vFP20.01 Heavy Chain

MacromoleculeName: vFP20.01 Heavy Chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.673586 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQQSGAD LVRPGASVTL SCKASGYTFT DYEMHWMKQT PVHGLEWIGA IVPETGYTAY NQKFKGKAIL TADKSSNTVY MQFRSLTSE DSAVYYCSRL KLLGYFDVWG TGTTVTVSPA STKGPSVFPL APGTAALGCL VKDYFPEPVT VSWNSGALTS G VHTFPAVL ...String:
QVQLQQSGAD LVRPGASVTL SCKASGYTFT DYEMHWMKQT PVHGLEWIGA IVPETGYTAY NQKFKGKAIL TADKSSNTVY MQFRSLTSE DSAVYYCSRL KLLGYFDVWG TGTTVTVSPA STKGPSVFPL APGTAALGCL VKDYFPEPVT VSWNSGALTS G VHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK AEP

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Macromolecule #2: vFP20.01 Light chain

MacromoleculeName: vFP20.01 Light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.826666 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVLMTQTPLS LPVSLGDQAS ISCKSSQSIV YKDGNSYLEW YLQKVGQSPK LLIYRVSNRF SGVPDRFSGS GSGTDFTLKI SRVEAEDLG VYYCFQGTHL PYTFGGGTKL EMKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
DVLMTQTPLS LPVSLGDQAS ISCKSSQSIV YKDGNSYLEW YLQKVGQSPK LLIYRVSNRF SGVPDRFSGS GSGTDFTLKI SRVEAEDLG VYYCFQGTHL PYTFGGGTKL EMKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNR

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Macromolecule #3: PGT122 Heavy chain

MacromoleculeName: PGT122 Heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.710848 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVHLQESGPG LVKPSETLSL TCNVSGTLVR DNYWSWIRQP LGKQPEWIGY VHDSGDTNYN PSLKSRVHLS LDKSKNLVSL RLTGVTAAD SAIYYCATTK HGRRIYGVVA FKEWFTYFYM DVWGKGTSVT VSSASTKGPS VFPLAPSSGG TAALGCLVKD Y FPEPVTVS ...String:
QVHLQESGPG LVKPSETLSL TCNVSGTLVR DNYWSWIRQP LGKQPEWIGY VHDSGDTNYN PSLKSRVHLS LDKSKNLVSL RLTGVTAAD SAIYYCATTK HGRRIYGVVA FKEWFTYFYM DVWGKGTSVT VSSASTKGPS VFPLAPSSGG TAALGCLVKD Y FPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP

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Macromolecule #4: PGT122 Light Chain

MacromoleculeName: PGT122 Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.560941 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: APTFVSVAPG QTARITCGEE SLGSRSVIWY QQRPGQAPSL IIYNNNDRPS GIPDRFSGSP GSTFGTTATL TITSVEAGDE ADYYCHIWD SRRPTNWVFG EGTTLIVLSQ PKAAPSVTLF PPSSEELQAN KATLVCLISD FYPGAVTVAW KADSSPVKAG V ETTTPSKQ ...String:
APTFVSVAPG QTARITCGEE SLGSRSVIWY QQRPGQAPSL IIYNNNDRPS GIPDRFSGSP GSTFGTTATL TITSVEAGDE ADYYCHIWD SRRPTNWVFG EGTTLIVLSQ PKAAPSVTLF PPSSEELQAN KATLVCLISD FYPGAVTVAW KADSSPVKAG V ETTTPSKQ SNNKYAASSY LSLTPEQWKS HKSYSCQVTH EGSTVEKTVA PT

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Macromolecule #5: VRC03 Light Chain

MacromoleculeName: VRC03 Light Chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.043652 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPGI LSLSPGETAT LFCKASQGGN AMTWYQKRRG QVPRLLIYDT SRRASGVPDR FVGSGSGTDF FLTINKLDRE DFAVYYCQQ FEFFGLGSEL EVHRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL QSGNSQESVT E QDSKDSTY ...String:
EIVLTQSPGI LSLSPGETAT LFCKASQGGN AMTWYQKRRG QVPRLLIYDT SRRASGVPDR FVGSGSGTDF FLTINKLDRE DFAVYYCQQ FEFFGLGSEL EVHRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL QSGNSQESVT E QDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE

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Macromolecule #6: VRC03 Heavy Chain

MacromoleculeName: VRC03 Heavy Chain / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.653771 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAV IKTPGSSVKI SCRASGYNFR DYSIHWVRLI PDKGFEWIGW IKPLWGAVSY ARQLQGRVSM TRQLSQDPDD PDWGVAYME FSGLTPADTA EYFCVRRGSC DYCGDFPWQY WGQGTVVVVS SASTKGPSVF PLAPSSGGTA ALGCLVKDYF P EPVTVSWN ...String:
QVQLVQSGAV IKTPGSSVKI SCRASGYNFR DYSIHWVRLI PDKGFEWIGW IKPLWGAVSY ARQLQGRVSM TRQLSQDPDD PDWGVAYME FSGLTPADTA EYFCVRRGSC DYCGDFPWQY WGQGTVVVVS SASTKGPSVF PLAPSSGGTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEPK

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Macromolecule #7: Glycoprotein 41

MacromoleculeName: Glycoprotein 41 / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.162525 KDa
Recombinant expressionOrganism: Human immunodeficiency virus 1
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAIEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

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Macromolecule #8: Glycoprotein 120

MacromoleculeName: Glycoprotein 120 / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 52.986969 KDa
Recombinant expressionOrganism: Human immunodeficiency virus 1
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT ...String:
AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT SACTQACPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CPSVSTVQCT HGIKPVVSTQ LLLNGSLAEE EV MIRSENI TNNAKNILVQ FNTPVQINCT RPNNNTRKSI RIGPGQAFYA TGDIIGDIRQ AHCNVSKATW NETLGKVVKQ LRK HFGNNT IIRFANSSGG DLEVTTHSFN CGGEFFYCNT SGLFNSTWIS NTSVQGSNST GSNDSITLPC RIKQIINMWQ RIGQ CMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRV

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Macromolecule #18: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 18 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #19: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 19 / Number of copies: 3 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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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

Concentration0.5 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 723 / Average electron dose: 70.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: -2.8 µm / Calibrated defocus min: -1.8 µm / Calibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 108962
CTF correctionSoftware - Name: Gctf
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 48248
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: OTHER / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 4
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 107 / Target criteria: Correlation Coefficient
Output model

PDB-6cde:
Cryo-EM structure at 3.8 A resolution of vaccine-elicited antibody vFP20.01 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122

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