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- EMDB-38899: Ebola virus glycoprotein in complex with a broadly neutralizing a... -

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Basic information

Entry
Database: EMDB / ID: EMD-38899
TitleEbola virus glycoprotein in complex with a broadly neutralizing antibody 2G1
Map data
Sample
  • Complex: Ebola virus glycoprotein in complex with a broadly neutralizing antibody 2G1
    • Complex: Ebola virus glycoprotein
      • Protein or peptide: Virion spike glycoprotein
      • Protein or peptide: SGP
    • Complex: 2G1 Fab
      • Protein or peptide: 2G1 VH
      • Protein or peptide: 2G1 VL
KeywordsANTIVIRAL PROTEIN
Function / homologyFiloviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / extracellular region / membrane / SGP / Virion spike glycoprotein
Function and homology information
Biological speciesHenipavirus nipahense / Ebola virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsFan PF / Yu CM / Chen W
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82204260 China
CitationJournal: To Be Published
Title: Ebola virus glycoprotein in complex with a broadly neutralizing antibody 2G1
Authors: Fan PF / Yu CM / Chen W
History
DepositionJan 29, 2024-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38899.png

Downloads & links

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Map

FileDownload / File: emd_38899.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 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: 0.25
Minimum - Maximum-0.6701415 - 1.4473783
Average (Standard dev.)-0.00017585265 (±0.023662347)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38899_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38899_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ebola virus glycoprotein in complex with a broadly neutralizing a...

EntireName: Ebola virus glycoprotein in complex with a broadly neutralizing antibody 2G1
Components
  • Complex: Ebola virus glycoprotein in complex with a broadly neutralizing antibody 2G1
    • Complex: Ebola virus glycoprotein
      • Protein or peptide: Virion spike glycoprotein
      • Protein or peptide: SGP
    • Complex: 2G1 Fab
      • Protein or peptide: 2G1 VH
      • Protein or peptide: 2G1 VL

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Supramolecule #1: Ebola virus glycoprotein in complex with a broadly neutralizing a...

SupramoleculeName: Ebola virus glycoprotein in complex with a broadly neutralizing antibody 2G1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Henipavirus nipahense

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Supramolecule #2: Ebola virus glycoprotein

SupramoleculeName: Ebola virus glycoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Ebola virus

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Supramolecule #3: 2G1 Fab

SupramoleculeName: 2G1 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 2G1 VH

MacromoleculeName: 2G1 VH / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.535075 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LVKRGGSLRL SCVVSGYTFG GYSMHWVRQA PGKGLEWVSG ISSSSYYKYY ADSVKGRFTI SRDNAKNSLY LQMNSLRAE DTAVYYCARD MGYCSGGSCP NFDFWGQGTT VTVSS

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Macromolecule #2: 2G1 VL

MacromoleculeName: 2G1 VL / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.342541 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
IQMTQSPSSL SASVGDRVTI TCRTSQSISN YLNWYQQIPG KAPKLLISTA SNLHSGVSSR FSGSGSGTHF TLTISSLQPE DFATYYCQQ SYSTPSFGQG TKVEIK

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Macromolecule #3: Virion spike glycoprotein

MacromoleculeName: Virion spike glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus
Molecular weightTheoretical: 10.883393 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VIVNAQPKCN PNLHYWTTQD EGAAIGLAWI PYFGPAAEGI YTEGLMHNQD GLICGLRQLA NETTQALQLF LRATTELRTF SILNRKAID FLLQRWAA

UniProtKB: Virion spike glycoprotein

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Macromolecule #4: SGP

MacromoleculeName: SGP / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus
Molecular weightTheoretical: 16.984287 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SIPLGVIHNS TLQVSDVDKL VCRDKLSSTN QLRSVGLNLE GNGVATDVPS VTKRWGFRSG VPPKVVNYEA GEWAENCYNL EIKKPDGSE CLPAAPDGIR GFPRCRYVHK VSGTGPCAGD FAFHKEGAFF LYDRLASTVI YRGTTFAEGV VAFLILAA

UniProtKB: SGP

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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

Concentration1.0 mg/mL
BufferpH: 7.4 / Details: 137 mM NaCl, 2.7mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 8926 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7kej

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 326558
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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