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- PDB-9n8f: Cryo-EM structure of SUDV glycoprotein with modified HR1c (L579P)... -

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Basic information

Entry
Database: PDB / ID: 9n8f
TitleCryo-EM structure of SUDV glycoprotein with modified HR1c (L579P) and HR2 stalk bound to CA45 Fab
Components
  • CA45 Fab heavy chain
  • CA45 Fab light chain
  • SUDV Gulu - GP1
  • SUDV Gulu - GP2
KeywordsVIRAL PROTEIN / Sudan Virus / Glycoproteins / prefusion
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
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsLee, Y.Z. / Ward, A.B. / Zhu, J.
Funding support1items
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, Y.Z. / Ward, A.B. / Zhu, J.
History
DepositionFeb 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUDV Gulu - GP1
D: SUDV Gulu - GP2
H: CA45 Fab heavy chain
L: CA45 Fab light chain
E: SUDV Gulu - GP2
I: CA45 Fab heavy chain
M: CA45 Fab light chain
C: SUDV Gulu - GP1
F: SUDV Gulu - GP2
J: CA45 Fab heavy chain
N: CA45 Fab light chain
B: SUDV Gulu - GP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)356,31718
Polymers354,38012
Non-polymers1,9376
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 6 molecules ACBDEF

#1: Protein SUDV Gulu - GP1 / GP1 / 2 / GP


Mass: 51221.770 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sudan ebolavirus (strain Human/Uganda/Gulu/2000)
Strain: Human/Uganda/Gulu/2000 / Gene: GP / Production host: Homo sapiens (human) / References: UniProt: Q7T9D9
#2: Protein SUDV Gulu - GP2 / GP1 / 2-delta


Mass: 18572.000 Da / Num. of mol.: 3 / Mutation: L579P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sudan ebolavirus (strain Human/Uganda/Gulu/2000)
Strain: Human/Uganda/Gulu/2000 / Gene: GP / Production host: Homo sapiens (human) / References: UniProt: Q7T9D9

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Antibody , 2 types, 6 molecules HIJLMN

#3: Antibody CA45 Fab heavy chain


Mass: 25041.066 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody CA45 Fab light chain


Mass: 23291.760 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Sugars , 2 types, 6 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of Sudan Virus glycoprotein with modified HR1c (L579P) and HR2 stalk complex with CA45 Fab
Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Source (natural)Organism: Sudan ebolavirus
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMdisodium phosphateNa2HPO41
21.8 mMmonopotassium phosphateKH2PO41
32.7 mMpotassium chlorideKCl1
4137 mMSodium chlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 163924 / Symmetry type: POINT
RefinementHighest resolution: 3.13 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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