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- EMDB-75340: Cryo-EM structure of Sudan Ebolavirus GP bound by three neutraliz... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-75340
TitleCryo-EM structure of Sudan Ebolavirus GP bound by three neutralizing antibodies 316L, 523S and 294S
Map data
Sample
  • Complex: Sudan ebolavirus GP bound by three neutralizing antibodies
    • Protein or peptide: Envelope glycoprotein 1
    • Protein or peptide: Envelope glycoprotein 2
    • Protein or peptide: 316L Heavy Chain
    • Protein or peptide: 316L Light Chain
    • Protein or peptide: 523S Heavy Chain
    • Protein or peptide: 523S Light Chain
    • Protein or peptide: 294S Heavy Chain
    • Protein or peptide: 294S Light Chain
KeywordsSUDV / neutralizing mAbs / 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
Similarity search - Function
: / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human) / Sudan ebolavirus / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.46 Å
AuthorsCheng J / Zhao B / Misasi J / Pierson TC / Sullivan NJ / Zhou T / Kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of Sudan Ebolavirus GP bound by three neutralizing antibodies 316L, 523S and 294S
Authors: Cheng J / Zhao B / Misasi J / Pierson TC / Sullivan NJ / Zhou T / Kwong PD
History
DepositionJan 29, 2026-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75340.png

Downloads & links

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Map

FileDownload / File: emd_75340.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 460 pix.
= 381.8 Å		0.83 Å/pix.
x 460 pix.
= 381.8 Å		0.83 Å/pix.
x 460 pix.
= 381.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.21289659 - 0.6145749
Average (Standard dev.)0.00014305627 (±0.012467622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 381.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_75340_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_75340_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 : Sudan ebolavirus GP bound by three neutralizing antibodies

EntireName: Sudan ebolavirus GP bound by three neutralizing antibodies
Components
  • Complex: Sudan ebolavirus GP bound by three neutralizing antibodies
    • Protein or peptide: Envelope glycoprotein 1
    • Protein or peptide: Envelope glycoprotein 2
    • Protein or peptide: 316L Heavy Chain
    • Protein or peptide: 316L Light Chain
    • Protein or peptide: 523S Heavy Chain
    • Protein or peptide: 523S Light Chain
    • Protein or peptide: 294S Heavy Chain
    • Protein or peptide: 294S Light Chain

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Supramolecule #1: Sudan ebolavirus GP bound by three neutralizing antibodies

SupramoleculeName: Sudan ebolavirus GP bound by three neutralizing antibodies
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Envelope glycoprotein 1

MacromoleculeName: Envelope glycoprotein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sudan ebolavirus
Molecular weightTheoretical: 22.49424 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SMPLGVVTNS TLEVTEIDQL VCKDHLASTD QLKSVGLNLE GSGVSTDIPS ATKRWGFRSG VPPKVVSYEA GEWAENCYNL EIKKPDGSE CLPPPPDGVR GFPRCRYVHK AQGTGPCPGD YAFHKDGAFF LYDRLASTVI YRGVNFAEGV IAFLILAKPK E TFLQSPPI ...String:
SMPLGVVTNS TLEVTEIDQL VCKDHLASTD QLKSVGLNLE GSGVSTDIPS ATKRWGFRSG VPPKVVSYEA GEWAENCYNL EIKKPDGSE CLPPPPDGVR GFPRCRYVHK AQGTGPCPGD YAFHKDGAFF LYDRLASTVI YRGVNFAEGV IAFLILAKPK E TFLQSPPI REAVNYTENT SSYYATSYLE YEIENFGAQH STTLFK

UniProtKB: Envelope glycoprotein

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Macromolecule #2: Envelope glycoprotein 2

MacromoleculeName: Envelope glycoprotein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sudan ebolavirus
Molecular weightTheoretical: 13.982947 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
KCNPNLHYWT AQEQHNAAGI AWIPYFGPGA EGIYTEGLMH NQNALVCGLR QLANETTQAL QLFLRATTEL RTYTILNRKA IDFLLRRWG GTCRILGPDC CIEPHDWTKN ITDKINQIIH DFI

UniProtKB: Envelope glycoprotein

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Macromolecule #3: 316L Heavy Chain

MacromoleculeName: 316L Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 13.299984 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EERLVESGGG LVQPGGSLRL SCAASGFTFG DYAMHWVRQV PGKSLEWLSG ISWSGYTTYS ADSVKGRFTI SRDNAKNSLY LQMNRLRPE DTGLYYCVTL IGAIGIKDSL DVWGRGVLVT VSS

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Macromolecule #4: 316L Light Chain

MacromoleculeName: 316L Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 11.779799 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVLTQPPSV SGAPGQRVTV SCSGSSSNIG AGNYVQWYQQ LPGTAPKVLI YQTEKRPSGT SDRFSGSKSD TSASLTINGL QSEDEADYY CQVYDSNLNG WVFGGGTRLT VL

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Macromolecule #5: 523S Heavy Chain

MacromoleculeName: 523S Heavy Chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.711205 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE LKKPGASVKV SCKASGYTFS DHYVHWVRQA PGQGLEWMGR INPNSGGTNY AQRFLGRVTM TRDASISTAY LDLSSLRSD DTAVYYCARS SSSWSGHYYY YMDVWGKGTT VTVSS

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Macromolecule #6: 523S Light Chain

MacromoleculeName: 523S Light Chain / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.366523 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVLTQPPSV SAAPGQRVTI SCSGSTSNIA SNFVSWYQQL PGTAPKLLIY DNHKRPSGIP DRFSGSKSGT SATLGITGLQ TGDEADYYC GTWDSSLSAG VFGGGTKVTV L

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Macromolecule #7: 294S Heavy Chain

MacromoleculeName: 294S Heavy Chain / type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.835411 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSQTLSL TCTVSGGSIS SGGYHWSWIR QHPGKGLEWI GNIYYNGRTY YNPSLKSRVT ISVDTSENEF SLKLSSVTA ADTAVYYCAR DRRRPRIGHD YGMDVWGQGT KVIVSS

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Macromolecule #8: 294S Light Chain

MacromoleculeName: 294S Light Chain / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.787044 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDRVT ISCRASQSIS NFLNWYQQKP GQAPKLLIYT ASNLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QIYNTGMYSF GQGTKLEIK

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3ve0

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 467000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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