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- EMDB-7345: An anti-gH/gL antibody that neutralizes dual-tropic infection def... -

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Basic information

Entry
Database: EMDB / ID: EMD-7345
TitleAn anti-gH/gL antibody that neutralizes dual-tropic infection defines a site of vulnerability on Epstein-Barr virus
Map dataAn anti-gH/gL antibody that neutralizes dual-tropic infection defines a site of vulnerability on Epstein-Barr virus
Sample
  • Complex: Epstein-Barr virus glycoproteins H,L,42 in complex with the human antibody Fab fragment AMMO1.
    • Complex: Epstein-Barr viral protein
      • Protein or peptide: Epstein-barr virus glycoprotein H
      • Protein or peptide: Epstein-barr virus glycoprotein L
      • Protein or peptide: Epstein-barr virus glycoprotein 42
    • Complex: Human antibody
      • Protein or peptide: Human antibody AMMO1 heavy chain
      • Protein or peptide: Human antibody AMMO1 light chain
Biological speciesHuman herpesvirus 4 (Epstein-Barr virus) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsSnijder J / Ortego MS
CitationJournal: Immunity / Year: 2018
Title: An Antibody Targeting the Fusion Machinery Neutralizes Dual-Tropic Infection and Defines a Site of Vulnerability on Epstein-Barr Virus.
Authors: Joost Snijder / Michael S Ortego / Connor Weidle / Andrew B Stuart / Matthew D Gray / M Juliana McElrath / Marie Pancera / David Veesler / Andrew T McGuire /
Abstract: Epstein-Barr virus (EBV) is a causative agent of infectious mononucleosis and is associated with 200,000 new cases of cancer and 140,000 deaths annually. Subunit vaccines against this pathogen have ...Epstein-Barr virus (EBV) is a causative agent of infectious mononucleosis and is associated with 200,000 new cases of cancer and 140,000 deaths annually. Subunit vaccines against this pathogen have focused on the gp350 glycoprotein and remain unsuccessful. We isolated human antibodies recognizing the EBV fusion machinery (gH/gL and gB) from rare memory B cells. One anti-gH/gL antibody, AMMO1, potently neutralized infection of B cells and epithelial cells, the two major cell types targeted by EBV. We determined a cryo-electron microscopy reconstruction of the gH/gL-gp42-AMMO1 complex and demonstrated that AMMO1 bound to a discontinuous epitope formed by both gH and gL at the Domain-I/Domain-II interface. Integrating structural, biochemical, and infectivity data, we propose that AMMO1 inhibits fusion of the viral and cellular membranes. This work identifies a crucial epitope that may aid in the design of next-generation subunit vaccines against this major public health burden.
History
DepositionJan 17, 2018-
Header (metadata) releaseMay 2, 2018-
Map releaseMay 2, 2018-
UpdateMay 2, 2018-
Current statusMay 2, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7345.png

Downloads & links

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Map

FileDownload / File: emd_7345.map.gz / Format: CCP4 / Size: 5.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAn anti-gH/gL antibody that neutralizes dual-tropic infection defines a site of vulnerability on Epstein-Barr virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.72 Å/pix.
x 112 pix.
= 304.64 Å		2.72 Å/pix.
x 112 pix.
= 304.64 Å		2.72 Å/pix.
x 112 pix.
= 304.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.053332526 - 0.25414705
Average (Standard dev.)0.00152336 (±0.014326657)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions112112112
Spacing112112112
CellA=B=C: 304.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.722.722.72
M x/y/z112112112
origin x/y/z0.0000.0000.000
length x/y/z304.640304.640304.640
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS112112112
D min/max/mean-0.0530.2540.002

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Supplemental data

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Sample components

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Entire : Epstein-Barr virus glycoproteins H,L,42 in complex with the human...

EntireName: Epstein-Barr virus glycoproteins H,L,42 in complex with the human antibody Fab fragment AMMO1.
Components
  • Complex: Epstein-Barr virus glycoproteins H,L,42 in complex with the human antibody Fab fragment AMMO1.
    • Complex: Epstein-Barr viral protein
      • Protein or peptide: Epstein-barr virus glycoprotein H
      • Protein or peptide: Epstein-barr virus glycoprotein L
      • Protein or peptide: Epstein-barr virus glycoprotein 42
    • Complex: Human antibody
      • Protein or peptide: Human antibody AMMO1 heavy chain
      • Protein or peptide: Human antibody AMMO1 light chain

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Supramolecule #1: Epstein-Barr virus glycoproteins H,L,42 in complex with the human...

SupramoleculeName: Epstein-Barr virus glycoproteins H,L,42 in complex with the human antibody Fab fragment AMMO1.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Epstein-Barr viral protein

SupramoleculeName: Epstein-Barr viral protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Human herpesvirus 4 (Epstein-Barr virus)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293

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Supramolecule #3: Human antibody

SupramoleculeName: Human antibody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293

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Macromolecule #1: Epstein-barr virus glycoprotein H

MacromoleculeName: Epstein-barr virus glycoprotein H / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSASSLSEV KLHLDIEGHA SHYTIPWTEL MAKVPGLSPE ALWREANVTE DLASMLNRYK LIYKTSGTLG IALAEPVDIP AVSEGSMQVD ASKVHPGVIS GLNSPACMLS APLEKQLFYY IGTMLPNTRP HSYVFYQLRC HLSYVALSIN ...String:
MDAMKRGLCC VLLLCGAVFV SPSASSLSEV KLHLDIEGHA SHYTIPWTEL MAKVPGLSPE ALWREANVTE DLASMLNRYK LIYKTSGTLG IALAEPVDIP AVSEGSMQVD ASKVHPGVIS GLNSPACMLS APLEKQLFYY IGTMLPNTRP HSYVFYQLRC HLSYVALSIN GDKFQYTGAM TSKFLMGTYK RVTEKGDEHV LSLVFGKTKD LPDLRGPFSY PSLTSAQSGD YSLVIVTTFV HYANFHNYFV PNLKDMFSRA VTMTAASYAR YVLQKLVLLE MKGGCREPEL DTETLTTMFE VSVAFFKVGH AVGETGNGCV DLRWLAKSFF ELTVLKDIIG ICYGATVKGM QSYGLERLAA MLMATVKMEE LGHLTTEKQE YALRLATVGY PKAGVYSGLI GGATSVLLSA YNRHPLFQPL HTVMRETLFI GSHVVLRELR LNVTTQGPNL ALYQLLSTAL CSALEIGEVL RGLALGTESG LFSPCYLSLR FDLTRDKLLS MAPQEATLDQ AAVSYAVDGF LGRLSLERED RDAWHLPAYK CVDRLDKVLM IIPLINVTFI ISSDREVRGS ALYEASTTYL SSSLFLSPVI MNKCSQGAVA GEPRQIPKIQ NFTRTQKSCI FCGFALLSYD EKEGLETTTY ITSQEVQNSI LSSNYFDFDN LHVHYLLLTT NGTVMEIAGL YEERAHGSGS GHHHHHH

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Macromolecule #2: Epstein-barr virus glycoprotein L

MacromoleculeName: Epstein-barr virus glycoprotein L / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
SequenceString:
MDAMKRGLCC VLLLCGAVFV SPSASWAYPC CHVTQLRAQH LLALENISDI YLVSNQTCDG FSLASLNSPK NGSNQLVISR CANGLNVVSF FISILKRSSS ALTGHLRELL TTLETLYGSF SVEDLFGANL NRYAWHRGG

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Macromolecule #3: Epstein-barr virus glycoprotein 42

MacromoleculeName: Epstein-barr virus glycoprotein 42 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSASGGGRV AAAAITWVPK PNVEVWPVDP PPPVNFNKTA EQEYGDKEVK LPHWTPTLHT FQVPQNYTKA NCTYCNTREY TFSYKGCCFY FTKKKHTWNG CFQACAELYP CTYFYGPTPD ILPVVTRNLN AIESLWVGVY RVGEGNWTSL ...String:
MDAMKRGLCC VLLLCGAVFV SPSASGGGRV AAAAITWVPK PNVEVWPVDP PPPVNFNKTA EQEYGDKEVK LPHWTPTLHT FQVPQNYTKA NCTYCNTREY TFSYKGCCFY FTKKKHTWNG CFQACAELYP CTYFYGPTPD ILPVVTRNLN AIESLWVGVY RVGEGNWTSL DGGTFKVYQI FGSHCTYVSK FSTVPVSHHE CSFLKPCLCV SQRSNSGSGS GHHHHHH

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Macromolecule #4: Human antibody AMMO1 heavy chain

MacromoleculeName: Human antibody AMMO1 heavy chain / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
SequenceString: (PCA)VQLVQSGAD VKKPGASVK V SCKASGYT FI HFGISWV RQA PGQGLE WMGW IDTNN GNTNY AQSL QGRVTM TTD TSTGTAY ME LRSLSTDD T AVYFCARAL EMGHRSGFPF DYWGQGVLV T VSPASTKG PS VFPLAPS SKS TSGGTA ALGC LVKDY ...String:
(PCA)VQLVQSGAD VKKPGASVK V SCKASGYT FI HFGISWV RQA PGQGLE WMGW IDTNN GNTNY AQSL QGRVTM TTD TSTGTAY ME LRSLSTDD T AVYFCARAL EMGHRSGFPF DYWGQGVLV T VSPASTKG PS VFPLAPS SKS TSGGTA ALGC LVKDY FPEPV TVSW NSGALT SGV HTFPAVL QS SGLYSLSS V VTVPSSSLG TQTYICNVNH KPSNTKVDK R VEPKSC

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Macromolecule #5: Human antibody AMMO1 light chain

MacromoleculeName: Human antibody AMMO1 light chain / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
SequenceString: SYELTQPPSV SVAPGQRATI TCGGHNIGAK NVHWYQQKPG QAPVLVIQYD SDRPSGIPER FSGSNSGSTA TLTISRVEAG DEADYYCQVW DSGRGHPLYV FGGGTKVTVL GQPKANPTVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK AGVETTTPSK ...String:
SYELTQPPSV SVAPGQRATI TCGGHNIGAK NVHWYQQKPG QAPVLVIQYD SDRPSGIPER FSGSNSGSTA TLTISRVEAG DEADYYCQVW DSGRGHPLYV FGGGTKVTVL GQPKANPTVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK AGVETTTPSK QSNNKYAASS YLSLTPEQWK SHRSYSCQVT HEGSTVEKTV APTECS

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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

BufferpH: 7.5
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 / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 72000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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