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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: Immunity / Year: 2024
Title: An explainable language model for antibody specificity prediction using curated influenza hemagglutinin antibodies.
Authors: Yiquan Wang / Huibin Lv / Qi Wen Teo / Ruipeng Lei / Akshita B Gopal / Wenhao O Ouyang / Yuen-Hei Yeung / Timothy J C Tan / Danbi Choi / Ivana R Shen / Xin Chen / Claire S Graham / Nicholas C Wu /
Abstract: Despite decades of antibody research, it remains challenging to predict the specificity of an antibody solely based on its sequence. Two major obstacles are the lack of appropriate models and the ...Despite decades of antibody research, it remains challenging to predict the specificity of an antibody solely based on its sequence. Two major obstacles are the lack of appropriate models and the inaccessibility of datasets for model training. In this study, we curated >5,000 influenza hemagglutinin (HA) antibodies by mining research publications and patents, which revealed many distinct sequence features between antibodies to HA head and stem domains. We then leveraged this dataset to develop a lightweight memory B cell language model (mBLM) for sequence-based antibody specificity prediction. Model explainability analysis showed that mBLM could identify key sequence features of HA stem antibodies. Additionally, by applying mBLM to HA antibodies with unknown epitopes, we discovered and experimentally validated many HA stem antibodies. Overall, this study not only advances our molecular understanding of the antibody response to the influenza virus but also provides a valuable resource for applying deep learning to antibody research.
History
DepositionSep 6, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41849.png

Downloads & links

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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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.48 Å/pix.
x 588 pix.
= 282.24 Å		0.48 Å/pix.
x 588 pix.
= 282.24 Å		0.48 Å/pix.
x 588 pix.
= 282.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.48 Å
Density

Histogram

Histogram (log scale)
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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Half map: Half map A

Fileemd_41849_half_map_1.map
AnnotationHalf_map_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_41849_half_map_2.map
AnnotationHalf_map_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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