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- EMDB-41874: CryoEM structure of A/Solomon Islands/3/2006 H1 HA in complex wit... -

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Entry
Database: EMDB / ID: EMD-41874
TitleCryoEM structure of A/Solomon Islands/3/2006 H1 HA in complex with 05.GC.w2.3C10-H1_SI06
Map dataCryoEM map of A/Solomon Islands/3/2006 H1 HA in complex with 3C10 mAb
Sample
  • Complex: Immune complex of A/Solomon Islands/3/2006 H1 HA with Fab 3C10
    • Complex: Fab
      • Protein or peptide: 05.GC.w2.3C10-H1_SI06 Heavy chain
      • Protein or peptide: 05.GC.w2.3C10-H1_SI06 Light chain
    • Complex: HA
      • Protein or peptide: Hemagglutinin HA1 chain
      • Protein or peptide: Hemagglutinin HA2 chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsInfluenza virus / hemagglutinin / H1 / monoclonal antibody / virus / 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 / 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 / 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: 3.41 Å
AuthorsMoore N / Han J / Ward AB / Wilson IA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: J Exp Med / Year: 2024
Title: Maturation of germinal center B cells after influenza virus vaccination in humans.
Authors: Katherine M McIntire / Hailong Meng / Ting-Hui Lin / Wooseob Kim / Nina E Moore / Julianna Han / Meagan McMahon / Meng Wang / Sameer Kumar Malladi / Bassem M Mohammed / Julian Q Zhou / Aaron ...Authors: Katherine M McIntire / Hailong Meng / Ting-Hui Lin / Wooseob Kim / Nina E Moore / Julianna Han / Meagan McMahon / Meng Wang / Sameer Kumar Malladi / Bassem M Mohammed / Julian Q Zhou / Aaron J Schmitz / Kenneth B Hoehn / Juan Manuel Carreño / Temima Yellin / Teresa Suessen / William D Middleton / Sharlene A Teefey / Rachel M Presti / Florian Krammer / Jackson S Turner / Andrew B Ward / Ian A Wilson / Steven H Kleinstein / Ali H Ellebedy /
Abstract: Germinal centers (GC) are microanatomical lymphoid structures where affinity-matured memory B cells and long-lived bone marrow plasma cells are primarily generated. It is unclear how the maturation ...Germinal centers (GC) are microanatomical lymphoid structures where affinity-matured memory B cells and long-lived bone marrow plasma cells are primarily generated. It is unclear how the maturation of B cells within the GC impacts the breadth and durability of B cell responses to influenza vaccination in humans. We used fine needle aspiration of draining lymph nodes to longitudinally track antigen-specific GC B cell responses to seasonal influenza vaccination. Antigen-specific GC B cells persisted for at least 13 wk after vaccination in two out of seven individuals. Monoclonal antibodies (mAbs) derived from persisting GC B cell clones exhibit enhanced binding affinity and breadth to influenza hemagglutinin (HA) antigens compared with related GC clonotypes isolated earlier in the response. Structural studies of early and late GC-derived mAbs from one clonal lineage in complex with H1 and H5 HAs revealed an altered binding footprint. Our study shows that inducing sustained GC reactions after influenza vaccination in humans supports the maturation of responding B cells.
History
DepositionSep 8, 2023-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41874.png

Downloads & links

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Map

FileDownload / File: emd_41874.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of A/Solomon Islands/3/2006 H1 HA in complex with 3C10 mAb
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 288 pix.
= 300.96 Å		1.05 Å/pix.
x 288 pix.
= 300.96 Å		1.05 Å/pix.
x 288 pix.
= 300.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.34325728 - 0.98822445
Average (Standard dev.)0.0002080827 (±0.03179192)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 300.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41874_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM half map A of A/Solomon Islands/3/2006 H1...

Fileemd_41874_half_map_1.map
AnnotationCryoEM half map A of A/Solomon Islands/3/2006 H1 HA in complex with 3C10 mAb
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM half map B of A/Solomon Islands/3/2006 H1...

Fileemd_41874_half_map_2.map
AnnotationCryoEM half map B of A/Solomon Islands/3/2006 H1 HA in complex with 3C10 mAb
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Immune complex of A/Solomon Islands/3/2006 H1 HA with Fab 3C10

EntireName: Immune complex of A/Solomon Islands/3/2006 H1 HA with Fab 3C10
Components
  • Complex: Immune complex of A/Solomon Islands/3/2006 H1 HA with Fab 3C10
    • Complex: Fab
      • Protein or peptide: 05.GC.w2.3C10-H1_SI06 Heavy chain
      • Protein or peptide: 05.GC.w2.3C10-H1_SI06 Light chain
    • Complex: HA
      • Protein or peptide: Hemagglutinin HA1 chain
      • Protein or peptide: Hemagglutinin HA2 chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Immune complex of A/Solomon Islands/3/2006 H1 HA with Fab 3C10

SupramoleculeName: Immune complex of A/Solomon Islands/3/2006 H1 HA with Fab 3C10
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#4, #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Fab

SupramoleculeName: Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: HA

SupramoleculeName: HA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 05.GC.w2.3C10-H1_SI06 Heavy chain

MacromoleculeName: 05.GC.w2.3C10-H1_SI06 Heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.771057 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: METDTLLLWV LLLWVPGSTG DEVQLVQSGA EVKKPGSSVR VSCKASGGTF SAISWVRQAP GQGLEWMGGI IPVFGTANYA QKFQGRVTI TADDSTSTAY MEVSSLRSDD TAVYYCAREE TWKGATIGVM GIWGQGTMVT VSSASTKGPS VFPLAPSSKS T SGGTAALG ...String:
METDTLLLWV LLLWVPGSTG DEVQLVQSGA EVKKPGSSVR VSCKASGGTF SAISWVRQAP GQGLEWMGGI IPVFGTANYA QKFQGRVTI TADDSTSTAY MEVSSLRSDD TAVYYCAREE TWKGATIGVM GIWGQGTMVT VSSASTKGPS VFPLAPSSKS T SGGTAALG CLVKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RV EPKSC

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Macromolecule #2: 05.GC.w2.3C10-H1_SI06 Light chain

MacromoleculeName: 05.GC.w2.3C10-H1_SI06 Light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.706625 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: METDTLLLWV LLLWVPGSTG DDIQMTQSPS SLSASVGDRV TITCRASQSI SSYLNWYQHK PGKAPKLLIF TASNLQSGVP SRFSGGGSG TDFTLTISSL QPEDFATYYC QQSYTSPRTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ ...String:
METDTLLLWV LLLWVPGSTG DDIQMTQSPS SLSASVGDRV TITCRASQSI SSYLNWYQHK PGKAPKLLIF TASNLQSGVP SRFSGGGSG TDFTLTISSL QPEDFATYYC QQSYTSPRTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ WKVDNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #3: Hemagglutinin HA1 chain

MacromoleculeName: Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 40.835902 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAAD PGDTICIGYH ANNSTDTVDT VLEKNVTVTH SVNLLEDSHN GKLCRLKGI APLQLGNCSV AGWILGNPEC ELLISRESWS YIVEKPNPEN GTCYPGHFAD YEELREQLSS VSSFERFEIF P KESSWPNH ...String:
MVLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFAAD PGDTICIGYH ANNSTDTVDT VLEKNVTVTH SVNLLEDSHN GKLCRLKGI APLQLGNCSV AGWILGNPEC ELLISRESWS YIVEKPNPEN GTCYPGHFAD YEELREQLSS VSSFERFEIF P KESSWPNH TTTGVSASCS HNGESSFYKN LLWLTGKNGL YPNLSKSYAN NKEKEVLVLW GVHHPPNIGD QRALYHKENA YV SVVSSHY SRKFTPEIAK RPKVRDQEGR INYYWTLLEP GDTIIFEANG NLIAPRYAFA LSRGFGSGII NSNAPMDECD AKC QTPQGA INSSLPFQNV HPVTIGECPK YVRSAKLRMV TGLRNIPSIQ SR

UniProtKB: Hemagglutinin

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Macromolecule #4: Hemagglutinin HA2 chain

MacromoleculeName: Hemagglutinin HA2 chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 26.988895 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADQKS TQNAINGITN KVNSVIEKMN TQFTAVGKEF NKLERRMENL NKKVDDGFI DIWTYNAELL VLLENERTLD FHDSNVKNLY EKVKSQLKNN AKEIGNGCFE FYHKCNDECM ESVKNGTYDY P KYSEESKL ...String:
GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADQKS TQNAINGITN KVNSVIEKMN TQFTAVGKEF NKLERRMENL NKKVDDGFI DIWTYNAELL VLLENERTLD FHDSNVKNLY EKVKSQLKNN AKEIGNGCFE FYHKCNDECM ESVKNGTYDY P KYSEESKL NREKIDSGGG GLNDIFEAQK IEWHERLVPR GSPGSGYIPE APRDGQAYVR KDGEWVLLST FLGHHHHHH

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: 9 / 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

Concentration0.6 mg/mL
BufferpH: 7.6 / Details: Tris-buffered saline
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 25 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4m4y

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3) / Number images used: 53000
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. v3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. v3)
FSC plot (resolution estimation)

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