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- EMDB-42528: CryoEM structure of A/Perth/16/2009 H3 in complex with flu HA cen... -

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Basic information

Entry
Database: EMDB / ID: EMD-42528
TitleCryoEM structure of A/Perth/16/2009 H3 in complex with flu HA central stem VH1-18 antibody UCA6
Map dataPerth09H3 UCA6_sharp
Sample
  • Complex: An UCA6 Fab complex with one protomer of a H3 trimer
    • Protein or peptide: UCA6 HC Fv
    • Protein or peptide: UCA6 LC Fv
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsFlu Hemagglutinin / Central stem epitope / VH1-18 / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Influenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsHuang J / Han J / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Immunity / Year: 2024
Title: Eliciting a single amino acid change by vaccination generates antibody protection against group 1 and group 2 influenza A viruses.
Authors: Rashmi Ray / Faez Amokrane Nait Mohamed / Daniel P Maurer / Jiachen Huang / Berk A Alpay / Larance Ronsard / Zhenfei Xie / Julianna Han / Monica Fernandez-Quintero / Quynh Anh Phan / Rebecca ...Authors: Rashmi Ray / Faez Amokrane Nait Mohamed / Daniel P Maurer / Jiachen Huang / Berk A Alpay / Larance Ronsard / Zhenfei Xie / Julianna Han / Monica Fernandez-Quintero / Quynh Anh Phan / Rebecca L Ursin / Mya Vu / Kathrin H Kirsch / Thavaleak Prum / Victoria C Rosado / Thalia Bracamonte-Moreno / Vintus Okonkwo / Julia Bals / Caitlin McCarthy / Usha Nair / Masaru Kanekiyo / Andrew B Ward / Aaron G Schmidt / Facundo D Batista / Daniel Lingwood /
Abstract: Broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem of influenza A viruses (IAVs) tend to be effective against either group 1 or group 2 viral diversity. In rarer cases, ...Broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem of influenza A viruses (IAVs) tend to be effective against either group 1 or group 2 viral diversity. In rarer cases, intergroup protective bnAbs can be generated by human antibody paratopes that accommodate the conserved glycan differences between the group 1 and group 2 stems. We applied germline-engaging nanoparticle immunogens to elicit a class of cross-group bnAbs from physiological precursor frequency within a humanized mouse model. Cross-group protection depended on the presence of the human bnAb precursors within the B cell repertoire, and the vaccine-expanded antibodies enriched for an N55T substitution in the CDRH2 loop, a hallmark of the bnAb class. Structurally, this single mutation introduced a flexible fulcrum to accommodate glycosylation differences and could alone enable cross-group protection. Thus, broad IAV immunity can be expanded from the germline repertoire via minimal antigenic input and an exceptionally simple antibody development pathway.
History
DepositionOct 30, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42528.png

Downloads & links

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Map

FileDownload / File: emd_42528.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPerth09H3 UCA6_sharp
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 384 pix.
= 377.088 Å		0.98 Å/pix.
x 384 pix.
= 377.088 Å		0.98 Å/pix.
x 384 pix.
= 377.088 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.982 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.1901147 - 1.8841715
Average (Standard dev.)-0.00009146465 (±0.03646436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 377.088 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Perth09H3 UCA6 halfB

Fileemd_42528_half_map_1.map
AnnotationPerth09H3 UCA6_halfB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Perth09H3 UCA6 halfA

Fileemd_42528_half_map_2.map
AnnotationPerth09H3 UCA6_halfA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : An UCA6 Fab complex with one protomer of a H3 trimer

EntireName: An UCA6 Fab complex with one protomer of a H3 trimer
Components
  • Complex: An UCA6 Fab complex with one protomer of a H3 trimer
    • Protein or peptide: UCA6 HC Fv
    • Protein or peptide: UCA6 LC Fv
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: An UCA6 Fab complex with one protomer of a H3 trimer

SupramoleculeName: An UCA6 Fab complex with one protomer of a H3 trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: UCA6 HC Fv

MacromoleculeName: UCA6 HC Fv / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.906533 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKKPGASVKV SCKASGYTFT SYGISWVRQA PGQGLEWMGW ISAYNGNTNY AQKLQGRVTM TTDTSTSTAY MELRSLRSD DTAVYYCARG LLQGVVILDS YYYTMDVWGQ GTTVTVSS

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Macromolecule #2: UCA6 LC Fv

MacromoleculeName: UCA6 LC Fv / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.858149 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGSSPRWT FGQGTKLEIK

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Macromolecule #3: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 3 / Details: A/Perth/16/2009 H3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 62.717074 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QKLPGNDNST ATLCLGHHAV PNGTIVKTIT NDQIEVTNAT ELVQSSSTGE ICDSPHQILD GKNCTLIDAL LGDPQCDGFQ NKKWDLFVE RSKAYSNCYP YDVPDYASLR SLVASSGTLE FNNESFNWTG VTQNGTSSAC IRRSKNSFFS RLNWLTHLNF K YPALNVTM ...String:
QKLPGNDNST ATLCLGHHAV PNGTIVKTIT NDQIEVTNAT ELVQSSSTGE ICDSPHQILD GKNCTLIDAL LGDPQCDGFQ NKKWDLFVE RSKAYSNCYP YDVPDYASLR SLVASSGTLE FNNESFNWTG VTQNGTSSAC IRRSKNSFFS RLNWLTHLNF K YPALNVTM PNNEQFDKLY IWGVHHPGTD KDQIFLYAQA SGRITVSTKR SQQTVSPNIG SRPRVRNIPS RISIYWTIVK PG DILLINS TGNLIAPRGY FKIRSGKSSI MRSDAPIGKC NSECITPNGS IPNDKPFQNV NRITYGACPR YVKQNTLKLA TGM RNVPEK QTRGIFGAIA GFIENGWEGM VDGWYGFRHQ NSEGRGQAAD LKSTQAAIDQ INGKLNRLIG KTNEKFHQIE KEFS EVEGR IQDLEKYVED TKIDLWSYNA ELLVALENQH TIDLTDSEMN KLFEKTKKQL RENAEDMGNG CFKIYHKCDN ACIGS IRNG TYDHDVYRDE ALNNRFQIKG GSGYIPEAPR DGQAYVRKDG EWVLLSTFLG SGLNDIFEAQ KIEWHEGHHH HHH

UniProtKB: Hemagglutinin

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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: 21 / 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

Concentration0.7 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormula
50.0 nMTris
100.0 nMNaCl
0.1 %Octyl-beta-Glucoside
GridModel: UltrAuFoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm

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Image processing

Startup modelType of model: INSILICO MODEL / Details: CryoSPARC Ab-initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 469712
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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