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- EMDB-43170: Cryo-EM structure of antibody T5-1E11 in complex with stabilized ... -

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Basic information

Entry
Database: EMDB / ID: EMD-43170
TitleCryo-EM structure of antibody T5-1E11 in complex with stabilized H1N1 Influenza Hemagglutinin Trimer (A/Kiev/1/57)
Map data
Sample
  • Complex: Antibody T5-1E11 Fab in complex with influenza hemagglutinin trimer
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: T5-1E11 Fab heavy chain
    • Protein or peptide: T5-1E11 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsBroadly neutralizing antibody / group 1 / influenza / cryo-EM / Fab / hemagglutinin / trimer / spike / IMMUNE SYSTEM / viral protein / IMMUNE SYSTEM-VIRAL PROTEIN complex
Biological speciesInfluenza A virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsCerutti G / Shapiro L
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: Structure / Year: 2025
Title: Distinct binding modes drive the broad neutralization profile of two persistent influenza hemagglutinin stem-specific antibody lineages.
Authors: Grace E Mantus / Gabriele Cerutti / Michael Chambers / Rebecca A Gillespie / Geoffrey D Shimberg / Abby Spangler / Jason Gorman / Tongqing Zhou / Chen-Hsiang Shen / Masaru Kanekiyo / Peter D ...Authors: Grace E Mantus / Gabriele Cerutti / Michael Chambers / Rebecca A Gillespie / Geoffrey D Shimberg / Abby Spangler / Jason Gorman / Tongqing Zhou / Chen-Hsiang Shen / Masaru Kanekiyo / Peter D Kwong / Lawrence Shapiro / Sarah F Andrews /
Abstract: Elicitation of antibodies to the influenza hemagglutinin stem is a critical part of universal influenza vaccine strategies. While numerous broadly reactive stem antibodies have been isolated, our ...Elicitation of antibodies to the influenza hemagglutinin stem is a critical part of universal influenza vaccine strategies. While numerous broadly reactive stem antibodies have been isolated, our understanding of how these antibodies mature within the human B cell repertoire is limited. Here, we isolated and tracked two stem-specific antibody lineages over a decade in a single participant that received multiple seasonal and pandemic influenza vaccinations. Despite similar binding and neutralization profiles, antibodies from these lineages utilized fundamentally different interactions to engage the central epitope on the influenza stem. Structural analysis of an unmutated common ancestor from one lineage identified critical residues that were the main drivers of increased affinity and breadth to group 1 influenza subtypes. These observations demonstrate the heterogeneous pathways by which stem-specific antibodies can mature within the human B cell repertoire.
History
DepositionDec 18, 2023-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43170.png

Downloads & links

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Map

FileDownload / File: emd_43170.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324.9 Å		1.08 Å/pix.
x 300 pix.
= 324.9 Å		1.08 Å/pix.
x 300 pix.
= 324.9 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-3.0816445 - 3.927929
Average (Standard dev.)0.0012051954 (±0.073413454)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_43170_additional_1.map
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Half map: #2

Fileemd_43170_half_map_1.map
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Half map: #1

Fileemd_43170_half_map_2.map
Projections & Slices
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Sample components

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Entire : Antibody T5-1E11 Fab in complex with influenza hemagglutinin trimer

EntireName: Antibody T5-1E11 Fab in complex with influenza hemagglutinin trimer
Components
  • Complex: Antibody T5-1E11 Fab in complex with influenza hemagglutinin trimer
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: T5-1E11 Fab heavy chain
    • Protein or peptide: T5-1E11 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Antibody T5-1E11 Fab in complex with influenza hemagglutinin trimer

SupramoleculeName: Antibody T5-1E11 Fab in complex with influenza hemagglutinin trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 64.431961 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKAKLLILLC ALSATDADTI CIGYHANNST DTVDTVCEKN VTVTHSVNLL EDSHNGKLCR LKGKAPLQLG NCNIAGWVLG NPECESLLS NRSWSYIAET PNSENGTCFP GDFADYEELR EQLSSVSSFE RFEIFPKERS WPNHTTRGVT AACPHAMKSS F YKNLVWLT ...String:
MKAKLLILLC ALSATDADTI CIGYHANNST DTVDTVCEKN VTVTHSVNLL EDSHNGKLCR LKGKAPLQLG NCNIAGWVLG NPECESLLS NRSWSYIAET PNSENGTCFP GDFADYEELR EQLSSVSSFE RFEIFPKERS WPNHTTRGVT AACPHAMKSS F YKNLVWLT EANGSYPNLS RSYVNNQEKE VLVLWGVHHP SNIEDQRTLY RKDNAYVSVV SSNYNRRFTP EIAKRPKVRG QS GRINYYW TLLEPGDTII FEATGNLIAP WYAFALSRGP GSGIITSNAP LDECDTKCQT PQGAINSSLP FQNIHPVTIG ECP KYVRST KLRMVTGLRN IPSFQSRGLF GAIAGFIEGG WTGMMDGWYG YHHQNEQGSG YAADQKSTQN AINCITNKVN SVIE KMNTQ FTAVGKEFNK LEKRMENLNK KVDDGFLDIW TYNAELLVLL ENERTLDFHD SNVKNLYEKV KNQLRNNAKE LGNGC FEFY HKCDNECMES VKNGTYDYPK YSEESKLNRE KIDGSGYIPE APRDGQAYVR KDGEWVLLST FLGSGLNDIF EAQKIE WHE GHHHHHH

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Macromolecule #2: T5-1E11 Fab heavy chain

MacromoleculeName: T5-1E11 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.777717 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKPSETLSL TCTVSGASVS SYFWSWIRQP AGKALEWIGR IYTSGNTKSN PSLESRVTMS LDASKDQFSL KLTSVTAAD TAVYYCAAGR LDYSDTTGYY KPPPLDYWGQ GALVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
QVQLQESGPG LVKPSETLSL TCTVSGASVS SYFWSWIRQP AGKALEWIGR IYTSGNTKSN PSLESRVTMS LDASKDQFSL KLTSVTAAD TAVYYCAAGR LDYSDTTGYY KPPPLDYWGQ GALVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCDKTH

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Macromolecule #3: T5-1E11 Fab light chain

MacromoleculeName: T5-1E11 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.091902 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVVMTQSPLS LPVTLGQPAS ISCRSSQGLA FLDGNTYLSW FQQRPGQSPR RLIYKVSNRD SGVPDRFSGS GSRTDFTLKI SRVEAEDVG VYYCMQGTHW PLTFGGGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
DVVMTQSPLS LPVTLGQPAS ISCRSSQGLA FLDGNTYLSW FQQRPGQSPR RLIYKVSNRD SGVPDRFSGS GSRTDFTLKI SRVEAEDVG VYYCMQGTHW PLTFGGGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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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: 16 / 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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.21 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 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: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 463321
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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