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- EMDB-43171: Cryo-EM structure of antibody T5-1E08 in complex with H7N9 Influe... -

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Basic information

Entry
Database: EMDB / ID: EMD-43171
TitleCryo-EM structure of antibody T5-1E08 in complex with H7N9 Influenza Hemagglutinin Trimer (A/Shanghai/2/13)
Map data
Sample
  • Complex: Antibody T5-1E08 Fab in complex with influenza hemagglutinin trimer
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: T5-1E08 Fab heavy chain
    • Protein or peptide: T5-1E08 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsGroup 2 / influenza / antibody maturation / cryo-EM / Fab / trimer / spike / hemagglutinin / IMMUNE SYSTEM / viral protein / IMMUNE SYSTEM-VIRAL PROTEIN complex
Biological speciesInfluenza A virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsCerutti G / Casner RG / 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_43171.png

Downloads & links

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Map

FileDownload / File: emd_43171.map.gz / Format: CCP4 / Size: 91.1 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.)
1.07 Å/pix.
x 288 pix.
= 308.16 Å		1.07 Å/pix.
x 288 pix.
= 308.16 Å		1.07 Å/pix.
x 288 pix.
= 308.16 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.369225 - 2.7352142
Average (Standard dev.)0.0032541614 (±0.047011547)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 308.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_43171_additional_1.map
AnnotationUnsharpened map
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Half map: #2

Fileemd_43171_half_map_1.map
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Half map: #1

Fileemd_43171_half_map_2.map
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Sample components

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Entire : Antibody T5-1E08 Fab in complex with influenza hemagglutinin trimer

EntireName: Antibody T5-1E08 Fab in complex with influenza hemagglutinin trimer
Components
  • Complex: Antibody T5-1E08 Fab in complex with influenza hemagglutinin trimer
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: T5-1E08 Fab heavy chain
    • Protein or peptide: T5-1E08 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Antibody T5-1E08 Fab in complex with influenza hemagglutinin trimer

SupramoleculeName: Antibody T5-1E08 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: 62.181043 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNTQILVFAL IAIIPTNADK ICLGHHAVSN GTKVNTLTER GVEVVNATET VERTNIPRIC SKGKRTVDLG QCGLLGTITG PPQCDQFLE FSADLIIERR EGSDVCYPGK FVNEEALRQI LRESGGIDKE AMGFTYSGIR TNGATSSCRR SGSSFYAEMK W LLSNTDNA ...String:
MNTQILVFAL IAIIPTNADK ICLGHHAVSN GTKVNTLTER GVEVVNATET VERTNIPRIC SKGKRTVDLG QCGLLGTITG PPQCDQFLE FSADLIIERR EGSDVCYPGK FVNEEALRQI LRESGGIDKE AMGFTYSGIR TNGATSSCRR SGSSFYAEMK W LLSNTDNA AFPQMTKSYK NTRKNPALIV WGIHHSGSTA EQTKLYGSGN KLVTVGSSNY QQSFVPSPGA RTQVNGQSGR ID FHWLMLN PNDTVTFSFN GAFIAPDRAS FLRGKSMGIQ SGVQVDADCE GDCYYSGGTI ISNLPFQNID SRAVGKCPRY VKQ RSLLLA TGMKNVPEIP KGRGLFGAIA GFIENGWEGL IDGWYGFRHQ NAQGEGTAAD YKSTQSAIDQ ITGKLNRLIE KTNQ QFELI DNEFTEVEKQ IGNVINWTRD SITEVWSYNA ELLVAMENQH TIDLADSEMD KLYERVKRQL RENAEEDGTG CFEIF HKCD DDCMASIRNN TYDHSKYREE AMQNRIQIDP VKLSSGYKDV ILWFSFGASC FILLAIAMGL VFICVKNGNM RCTICI

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Macromolecule #2: T5-1E08 Fab heavy chain

MacromoleculeName: T5-1E08 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.378469 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLLESGPG LVKPSQTLSL TCTVSGGSVS RGGYYWTWIR QHPGKGLEWI AYVTYSGDTS YNPSLRGRVT ISLETSMNQF SLKVTSVTV ADTALYFCAR VPFYYDTRGV FYGNAEGGFE IWGQGTMATV SSASTKGPSV FPLAPSSKST SGGTAALGCL V KDYFPEPV ...String:
QVQLLESGPG LVKPSQTLSL TCTVSGGSVS RGGYYWTWIR QHPGKGLEWI AYVTYSGDTS YNPSLRGRVT ISLETSMNQF SLKVTSVTV ADTALYFCAR VPFYYDTRGV FYGNAEGGFE IWGQGTMATV SSASTKGPSV FPLAPSSKST SGGTAALGCL V KDYFPEPV TVSWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKSCDKTH

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Macromolecule #3: T5-1E08 Fab light chain

MacromoleculeName: T5-1E08 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.461947 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQGIT NDLRWYQQKP GKAPQCLISS ASRLQSGVSS RFSGSGSGTE FTLTISSLQP EDFATYYCL QHNSYQWTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQGIT NDLRWYQQKP GKAPQCLISS ASRLQSGVSS RFSGSGSGTE FTLTISSLQP EDFATYYCL QHNSYQWTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / 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: 7.2
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: 41.92 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: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69542
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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