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- EMDB-49127: Cryo-EM structure of SUDV glycoprotein with modified HR1c (L579P)... -

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Basic information

Entry
Database: EMDB / ID: EMD-49127
TitleCryo-EM structure of SUDV glycoprotein with modified HR1c (L579P) and HR2 stalk bound to CA45 Fab
Map data
Sample
  • Complex: Cryo-EM structure of Sudan Virus glycoprotein with modified HR1c (L579P) and HR2 stalk complex with CA45 Fab
    • Protein or peptide: SUDV Gulu - GP1
    • Protein or peptide: SUDV Gulu - GP2
    • Protein or peptide: CA45 Fab heavy chain
    • Protein or peptide: CA45 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSudan Virus / Glycoproteins / prefusion / viral protein
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 speciesSudan ebolavirus / Sudan ebolavirus (strain Human/Uganda/Gulu/2000) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsLee YZ / Ward AB / Zhu J
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Cryo-EM structure of SUDV glycoprotein with modified HR1c (L579P) and HR2 stalk bound to CA45 Fab
Authors: Lee YZ / Ward AB / Zhu J
History
DepositionFeb 8, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49127.png

Downloads & links

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Map

FileDownload / File: emd_49127.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 300 pix.
= 266.7 Å		0.89 Å/pix.
x 300 pix.
= 266.7 Å		0.89 Å/pix.
x 300 pix.
= 266.7 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.889 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.77536994 - 1.2856547
Average (Standard dev.)0.000119234115 (±0.025736032)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 266.7 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49127_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_49127_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 : Cryo-EM structure of Sudan Virus glycoprotein with modified HR1c ...

EntireName: Cryo-EM structure of Sudan Virus glycoprotein with modified HR1c (L579P) and HR2 stalk complex with CA45 Fab
Components
  • Complex: Cryo-EM structure of Sudan Virus glycoprotein with modified HR1c (L579P) and HR2 stalk complex with CA45 Fab
    • Protein or peptide: SUDV Gulu - GP1
    • Protein or peptide: SUDV Gulu - GP2
    • Protein or peptide: CA45 Fab heavy chain
    • Protein or peptide: CA45 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of Sudan Virus glycoprotein with modified HR1c ...

SupramoleculeName: Cryo-EM structure of Sudan Virus glycoprotein with modified HR1c (L579P) and HR2 stalk complex with CA45 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Sudan ebolavirus

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Macromolecule #1: SUDV Gulu - GP1

MacromoleculeName: SUDV Gulu - GP1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sudan ebolavirus (strain Human/Uganda/Gulu/2000) / Strain: Human/Uganda/Gulu/2000
Molecular weightTheoretical: 51.22177 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 STTLFKIDNN TFVRLDRPHT PQFLFQLNDT IHLHQQLSNT TG RLIWTLD ANINADIGEW AFWENKKNLS EQLRGEELSF EALSLNETED DDAASSRITK GRISDRATRK YSDLVPKNSP GMV PLHIPE GETTLPSQNS TEGRRVGVNT QETITETAAT IIGTNGNHMQ ISTIGIRPSS SQIPSSSPTT APSPEAQTPT THTS GPSVM ATEEPTTPPG SSPGPTTEAP TLTTPENITT AVKTVLPQES TSNGLITSTV TGILGSLGLR KRSRR

UniProtKB: Envelope glycoprotein

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Macromolecule #2: SUDV Gulu - GP2

MacromoleculeName: SUDV Gulu - GP2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sudan ebolavirus (strain Human/Uganda/Gulu/2000) / Strain: Human/Uganda/Gulu/2000
Molecular weightTheoretical: 18.572 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QTNTKATGKC NPNLHYWTAQ EQHNAAGIAW IPYFGPGAEG IYTEGLMHNQ NALVCGLRQL ANETTQALQL FLRATTEPRT YTILNRKAI DFLLRRWGGT CRILGPDCCI EPHDLTKNIT DKINQIIHDF IDNPLPNASG YIPEAPRDGQ AYVRKDGEWV L LSTFL

UniProtKB: Envelope glycoprotein

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Macromolecule #3: CA45 Fab heavy chain

MacromoleculeName: CA45 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.041066 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: VQLQEWGEGL VKPSETLSLT CAVYGGSISG YYHWNWIRLP PGKGLEWIGN IDGNSASTNY NPSLKTRVTI SKDTSKNQIS LKVRSLTAA DTAVYYCARD PGFTIFGVVI TSWSGLDSWG QGAVVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS ...String:
VQLQEWGEGL VKPSETLSLT CAVYGGSISG YYHWNWIRLP PGKGLEWIGN IDGNSASTNY NPSLKTRVTI SKDTSKNQIS LKVRSLTAA DTAVYYCARD PGFTIFGVVI TSWSGLDSWG QGAVVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP KSCDKTHT

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Macromolecule #4: CA45 Fab light chain

MacromoleculeName: CA45 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.29176 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIQMTQSPSS LSASVGDTVT ITCRASQSIS NNLAWYQQRP RRAPQLLIYA ASNLASGVPS RFSGSGSGTD FTLTISSLQA EDFAAYYCQ QHNTLPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDTVT ITCRASQSIS NNLAWYQQRP RRAPQLLIYA ASNLASGVPS RFSGSGSGTD FTLTISSLQA EDFAAYYCQ QHNTLPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGECS

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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:
ConcentrationFormulaName
10.0 mMNa2HPO4disodium phosphate
1.8 mMKH2PO4monopotassium phosphate
2.7 mMKClpotassium chloride
137.0 mMNaClSodium chloride
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 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: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 163924
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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