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- EMDB-25471: Structure of EBOV GP lacking the mucin-like domain with 1C11 scFv... -

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Basic information

Entry
Database: EMDB / ID: EMD-25471
TitleStructure of EBOV GP lacking the mucin-like domain with 1C11 scFv and 1C3 Fab bound
Map dataEBOV GP lacking the mucin-like domain with 1C11 scFv and 1C3 Fab bound
Sample
  • Complex: Complex of EBOV GP lacking the mucin-like-domain with 1C11 scFv and 1C3 Fab
    • Protein or peptide: Virion spike glycoprotein GP1
    • Protein or peptide: Virion spike glycoprotein GP2
    • Protein or peptide: 1C11 scFv
  • Protein or peptide: 1C3 heavy chain
  • Protein or peptide: 1C3 light chain
KeywordsVIRAL PROTEIN / glycoprotein / immune system / antibody / Ebola virus / VIRAL PROTEIN-Immune System complex
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / extracellular region / membrane
Similarity search - Function
: / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2
Similarity search - Domain/homology
Envelope glycoprotein / Envelope glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human) / Ebola virus - Gabon (1994-1997) / Zaire ebolavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsMilligan JC / Yu X
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5 U19 AI142790 United States
CitationJournal: Cell / Year: 2022
Title: Asymmetric and non-stoichiometric glycoprotein recognition by two distinct antibodies results in broad protection against ebolaviruses.
Authors: Jacob C Milligan / Carl W Davis / Xiaoying Yu / Philipp A Ilinykh / Kai Huang / Peter J Halfmann / Robert W Cross / Viktoriya Borisevich / Krystle N Agans / Joan B Geisbert / Chakravarthy ...Authors: Jacob C Milligan / Carl W Davis / Xiaoying Yu / Philipp A Ilinykh / Kai Huang / Peter J Halfmann / Robert W Cross / Viktoriya Borisevich / Krystle N Agans / Joan B Geisbert / Chakravarthy Chennareddy / Arthur J Goff / Ashley E Piper / Sean Hui / Kelly C L Shaffer / Tierra Buck / Megan L Heinrich / Luis M Branco / Ian Crozier / Michael R Holbrook / Jens H Kuhn / Yoshihiro Kawaoka / Pamela J Glass / Alexander Bukreyev / Thomas W Geisbert / Gabriella Worwa / Rafi Ahmed / Erica Ollmann Saphire /
Abstract: Several ebolaviruses cause outbreaks of severe disease. Vaccines and monoclonal antibody cocktails are available to treat Ebola virus (EBOV) infections, but not Sudan virus (SUDV) or other ...Several ebolaviruses cause outbreaks of severe disease. Vaccines and monoclonal antibody cocktails are available to treat Ebola virus (EBOV) infections, but not Sudan virus (SUDV) or other ebolaviruses. Current cocktails contain antibodies that cross-react with the secreted soluble glycoprotein (sGP) that absorbs virus-neutralizing antibodies. By sorting memory B cells from EBOV infection survivors, we isolated two broadly reactive anti-GP monoclonal antibodies, 1C3 and 1C11, that potently neutralize, protect rodents from disease, and lack sGP cross-reactivity. Both antibodies recognize quaternary epitopes in trimeric ebolavirus GP. 1C11 bridges adjacent protomers via the fusion loop. 1C3 has a tripartite epitope in the center of the trimer apex. One 1C3 antigen-binding fragment anchors simultaneously to the three receptor-binding sites in the GP trimer, and separate 1C3 paratope regions interact differently with identical residues on the three protomers. A cocktail of both antibodies completely protected nonhuman primates from EBOV and SUDV infections, indicating their potential clinical value.
History
DepositionNov 19, 2021-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25471.png

Downloads & links

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Map

FileDownload / File: emd_25471.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEBOV GP lacking the mucin-like domain with 1C11 scFv and 1C3 Fab bound
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: 0.03
Minimum - Maximum-0.09280562 - 0.14911507
Average (Standard dev.)0.000002675334 (±0.004524166)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Sample components

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Entire : Complex of EBOV GP lacking the mucin-like-domain with 1C11 scFv a...

EntireName: Complex of EBOV GP lacking the mucin-like-domain with 1C11 scFv and 1C3 Fab
Components
  • Complex: Complex of EBOV GP lacking the mucin-like-domain with 1C11 scFv and 1C3 Fab
    • Protein or peptide: Virion spike glycoprotein GP1
    • Protein or peptide: Virion spike glycoprotein GP2
    • Protein or peptide: 1C11 scFv
  • Protein or peptide: 1C3 heavy chain
  • Protein or peptide: 1C3 light chain

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Supramolecule #1: Complex of EBOV GP lacking the mucin-like-domain with 1C11 scFv a...

SupramoleculeName: Complex of EBOV GP lacking the mucin-like-domain with 1C11 scFv and 1C3 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: Virion spike glycoprotein GP1

MacromoleculeName: Virion spike glycoprotein GP1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus - Gabon (1994-1997) / Strain: Mayinga-76
Molecular weightTheoretical: 31.297158 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: IPLGVIHNST LQVSDVDKLV CRDKLSSTNQ LRSVGLNLEG NGVATDVPSA TKRWGFRSGV PPKVVNYEAG EWAENCYNLE IKKPDGSEC LPAAPDGIRG FPRCRYVHKV SGTGPCAGDF AFHKEGAFFL YDRLASTVIY RGTTFAEGVV AFLILPQAKK D FFSSHPLR ...String:
IPLGVIHNST LQVSDVDKLV CRDKLSSTNQ LRSVGLNLEG NGVATDVPSA TKRWGFRSGV PPKVVNYEAG EWAENCYNLE IKKPDGSEC LPAAPDGIRG FPRCRYVHKV SGTGPCAGDF AFHKEGAFFL YDRLASTVIY RGTTFAEGVV AFLILPQAKK D FFSSHPLR EPVNATEDPS SGYYSTTIRY QATGFGTNET EYLFEVDNLT YVQLESRFTP QFLLQLNETI YTSGKRSNTT GK LIWKVNP EIDTTIGEWA FWETKKNLTR KIRSEELSFT VVS

UniProtKB: Envelope glycoprotein

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Macromolecule #2: Virion spike glycoprotein GP2

MacromoleculeName: Virion spike glycoprotein GP2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Zaire ebolavirus
Molecular weightTheoretical: 10.756211 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString:
IVNAQPKCNP NLHYWTTQDE GAAIGLAWIP YFGPAAEGIY TEGLMHNQDG LICGLRQLAN ETTQALQLFL RATTELRTFS ILNRKAIDF LLQRWGG

UniProtKB: Envelope glycoprotein

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Macromolecule #3: 1C11 scFv

MacromoleculeName: 1C11 scFv / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.783773 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: QVQLVQSGAE VKKPGASVKV SCRTSGYTFS SYNIHWVRQA PGQGLEWMGV INPYGRSTTL YARRFRDRVT MTRDTSTSTV YMELSSLRS EDTAVYFCGR LYSGAPYGLD VWGQGSTVTV SSGTGGSGGG GSGGGGSGGG ASDIVMTQSP LSLPVTPGEP A SISCRSSQ ...String:
QVQLVQSGAE VKKPGASVKV SCRTSGYTFS SYNIHWVRQA PGQGLEWMGV INPYGRSTTL YARRFRDRVT MTRDTSTSTV YMELSSLRS EDTAVYFCGR LYSGAPYGLD VWGQGSTVTV SSGTGGSGGG GSGGGGSGGG ASDIVMTQSP LSLPVTPGEP A SISCRSSQ SLLHSNGYNY VDWYLQKPGQ SPQLLIYLGS SRASGVPDRF SGSGSGTDFT LKISRVETED VGIYYCMQGL QT PLTFGGG TKVEIK

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Macromolecule #4: 1C3 heavy chain

MacromoleculeName: 1C3 heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.308938 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QVQLVQSGAE VKKPGSSVKV ACKVSGGTFS SYTISWVRQA PGQGLEWMGG IIPSFGVGHY SQKFRDRVTL TADKSTTTAF LELSSVRSE DTALYYCAIL GTFNWKSGGN YFGPWGQGTL VTVSS

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Macromolecule #5: 1C3 light chain

MacromoleculeName: 1C3 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.62405 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
DIVLTQSPDS LAASLGERAT ISCKSSHSVL YSSNNKDFFA WYQQKPGQPP KLLISWASTR ESGVPVRFNG GGSGTHFTLT ISSLQAEDV AVYYCQQYFS SPITFGQGTR LEIKRT

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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: 7.4 / Component - Name: TBS
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average exposure time: 54.95 sec. / Average electron dose: 34.97 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 75948
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7swd:
Structure of EBOV GP lacking the mucin-like domain with 1C11 scFv and 1C3 Fab bound

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