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- EMDB-7344: An anti-gH/gL antibody that neutralizes dual-tropic infection def... -

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Basic information

Entry
Database: EMDB / ID: EMD-7344
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 virusEpstein–Barr virus
      • Protein or peptide: Envelope glycoprotein H
      • Protein or peptide: Envelope glycoprotein L
      • Protein or peptide: Glycoprotein 42
    • Complex: Human
      • Protein or peptide: Antibody Fab AMMO1 heavy chain
      • Protein or peptide: Antibody Fab AMMO1 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


host cell endosome membrane / host cell Golgi apparatus / carbohydrate binding / membrane => GO:0016020 / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
Envelope glycoprotein H / Glycoprotein 42 / Envelope glycoprotein L
Similarity search - Component
Biological speciesHuman herpesvirus 4 (Epstein-Barr virus) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsSnijder J / Ortego MS / Weidle C / Stuart AB / Gray MA / McElrath MJ / Pancera M / Veesler D / McGuire AT / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120553 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
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 16, 2018-
Header (metadata) releaseFeb 7, 2018-
Map releaseMay 2, 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: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6c5v
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7344.png

Downloads & links

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Map

FileDownload / File: emd_7344.map.gz / Format: CCP4 / Size: 42.9 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
Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.15324071 - 0.30906358
Average (Standard dev.)0.00055957725 (±0.007286191)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 304.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z224224224
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/NS224224224
D min/max/mean-0.1530.3090.001

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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 virusEpstein–Barr virus
      • Protein or peptide: Envelope glycoprotein H
      • Protein or peptide: Envelope glycoprotein L
      • Protein or peptide: Glycoprotein 42
    • Complex: Human
      • Protein or peptide: Antibody Fab AMMO1 heavy chain
      • Protein or peptide: Antibody Fab AMMO1 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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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: #1-#5

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Supramolecule #2: Epstein-Barr virus

SupramoleculeName: Epstein-Barr virus / 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

SupramoleculeName: Human / 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: Envelope glycoprotein H

MacromoleculeName: Envelope glycoprotein H / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 4 (Epstein-Barr virus) / Strain: GD1
Molecular weightTheoretical: 77.091547 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSASSLSEV KLHLDIEGHA SHYTIPWTEL MAKVPGLSPE ALWREANVTE DLASMLNRYK LIYKTSGTL GIALAEPVDI PAVSEGSMQV DASKVHPGVI SGLNSPACML SAPLEKQLFY YIGTMLPNTR PHSYVFYQLR C HLSYVALS ...String:
MDAMKRGLCC VLLLCGAVFV SPSASSLSEV KLHLDIEGHA SHYTIPWTEL MAKVPGLSPE ALWREANVTE DLASMLNRYK LIYKTSGTL GIALAEPVDI PAVSEGSMQV DASKVHPGVI SGLNSPACML SAPLEKQLFY YIGTMLPNTR PHSYVFYQLR C HLSYVALS INGDKFQYTG AMTSKFLMGT YKRVTEKGDE HVLSLVFGKT KDLPDLRGPF SYPSLTSAQS GDYSLVIVTT FV HYANFHN YFVPNLKDMF SRAVTMTAAS YARYVLQKLV LLEMKGGCRE PELDTETLTT MFEVSVAFFK VGHAVGETGN GCV DLRWLA KSFFELTVLK DIIGICYGAT VKGMQSYGLE RLAAMLMATV KMEELGHLTT EKQEYALRLA TVGYPKAGVY SGLI GGATS VLLSAYNRHP LFQPLHTVMR ETLFIGSHVV LRELRLNVTT QGPNLALYQL LSTALCSALE IGEVLRGLAL GTESG LFSP CYLSLRFDLT RDKLLSMAPQ EATLDQAAVS YAVDGFLGRL SLEREDRDAW HLPAYKCVDR LDKVLMIIPL INVTFI ISS DREVRGSALY EASTTYLSSS LFLSPVIMNK CSQGAVAGEP RQIPKIQNFT RTQKSCIFCG FALLSYDEKE GLETTTY IT SQEVQNSILS SNYFDFDNLH VHYLLLTTNG TVMEIAGLYE ERAHGSGSGH HHHHH

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Macromolecule #2: Envelope glycoprotein L

MacromoleculeName: Envelope glycoprotein L / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 4 (Epstein-Barr virus) / Strain: AG876
Molecular weightTheoretical: 15.145395 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MDAMKRGLCC VLLLCGAVFV SPSASWAYPC CHVTQLRAQH LLALENISDI YLVSNQTCDG FSLASLNSPK NGSNQLVISR CANGLNVVS FFISILKRSS SALTGHLREL LTTLETLYGS FSVEDLFGAN LNRYAWHRGG

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Macromolecule #3: Glycoprotein 42

MacromoleculeName: Glycoprotein 42 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 4 (Epstein-Barr virus) / Strain: GD1
Molecular weightTheoretical: 25.356859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSASGGGRV AAAAITWVPK PNVEVWPVDP PPPVNFNKTA EQEYGDKEVK LPHWTPTLHT FQVPQNYTK ANCTYCNTRE YTFSYKGCCF YFTKKKHTWN GCFQACAELY PCTYFYGPTP DILPVVTRNL NAIESLWVGV Y RVGEGNWT ...String:
MDAMKRGLCC VLLLCGAVFV SPSASGGGRV AAAAITWVPK PNVEVWPVDP PPPVNFNKTA EQEYGDKEVK LPHWTPTLHT FQVPQNYTK ANCTYCNTRE YTFSYKGCCF YFTKKKHTWN GCFQACAELY PCTYFYGPTP DILPVVTRNL NAIESLWVGV Y RVGEGNWT SLDGGTFKVY QIFGSHCTYV SKFSTVPVSH HECSFLKPCL CVSQRSNSGS GSGHHHHHH

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Macromolecule #4: Antibody Fab AMMO1 heavy chain

MacromoleculeName: Antibody Fab AMMO1 heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.982885 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: (PCA)VQLVQSGAD VKKPGASVKV SCKASGYTFI HFGISWVRQA PGQGLEWMGW IDTNNGNTNY AQSLQGRVTM TTDTST GTA YMELRSLSTD DTAVYFCARA LEMGHRSGFP FDYWGQGVLV TVSPASTKGP SVFPLAPSSK STSGGTAALG CLVKDYF PE PVTVSWNSGA ...String:
(PCA)VQLVQSGAD VKKPGASVKV SCKASGYTFI HFGISWVRQA PGQGLEWMGW IDTNNGNTNY AQSLQGRVTM TTDTST GTA YMELRSLSTD DTAVYFCARA LEMGHRSGFP FDYWGQGVLV TVSPASTKGP SVFPLAPSSK STSGGTAALG CLVKDYF PE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KRVEPKSC

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Macromolecule #5: Antibody Fab AMMO1 light chain

MacromoleculeName: Antibody Fab AMMO1 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.095514 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SYELTQPPSV SVAPGQRATI TCGGHNIGAK NVHWYQQKPG QAPVLVIQYD SDRPSGIPER FSGSNSGSTA TLTISRVEAG DEADYYCQV WDSGRGHPLY VFGGGTKVTV LGQPKANPTV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
SYELTQPPSV SVAPGQRATI TCGGHNIGAK NVHWYQQKPG QAPVLVIQYD SDRPSGIPER FSGSNSGSTA TLTISRVEAG DEADYYCQV WDSGRGHPLY VFGGGTKVTV LGQPKANPTV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 65.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 72000

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