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- EMDB-41849: Structure of 310-18A5 Fab in complex with A/Solomon Islands/3/200... -

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Entry
Database: EMDB / ID: EMD-41849
TitleStructure of 310-18A5 Fab in complex with A/Solomon Islands/3/2006(H1N1) influenza virus hemagglutinin
Map dataA/Solomon Islands/3/2006(H1N1) hemagglutinin in complex with 18A5 Fab
Sample
  • Complex: Structure of 310-18A5 Fab in complex with A/Solomon Islands/3/2006(H1N1) influenza virus hemagglutinin
Keywordsantibody / hemagglutinin / influenza / ANTIVIRAL PROTEIN
Biological speciesInfluenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.81 Å
AuthorsLei R / Wu NC
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI167910 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AT011966 United States
Michelson Medical Research FoundationPrize for Human Immunology and Vaccine Research United States
Searle Scholars Program United States
CitationJournal: To Be Published
Title: An explainable language model for antibody epitope prediction using curated influenza hemagglutinin antibodies
Authors: Wang Y / Lv H / Lei R / Yeung Y / Shen IR / Choi D / Teo Q / Tan TJC / Gopal AB / Chen X / Graham CS / Wu NC
History
DepositionSep 6, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

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Map

FileDownload / File: emd_41849.map.gz / Format: CCP4 / Size: 775.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA/Solomon Islands/3/2006(H1N1) hemagglutinin in complex with 18A5 Fab
Voxel sizeX=Y=Z: 0.48 Å
Density
Contour LevelBy AUTHOR: 0.0143
Minimum - Maximum-0.015918152 - 0.062690504
Average (Standard dev.)0.00025473768 (±0.0030406888)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions588588588
Spacing588588588
CellA=B=C: 282.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Structure of 310-18A5 Fab in complex with A/Solomon Islands/3/200...

EntireName: Structure of 310-18A5 Fab in complex with A/Solomon Islands/3/2006(H1N1) influenza virus hemagglutinin
Components
  • Complex: Structure of 310-18A5 Fab in complex with A/Solomon Islands/3/2006(H1N1) influenza virus hemagglutinin

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Supramolecule #1: Structure of 310-18A5 Fab in complex with A/Solomon Islands/3/200...

SupramoleculeName: Structure of 310-18A5 Fab in complex with A/Solomon Islands/3/2006(H1N1) influenza virus hemagglutinin
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Influenza A virus / Strain: A/Solomon Islands/3/2006(H1N1)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.05 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris-HCl
100.0 mMsodium chlorideNaCl

Details: 20 mM Tris-HCl, 100 mM NaCl, pH 8.0
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Detailswith 7.5 uM LMNG

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.76 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39446
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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