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

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Basic information

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 / 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: 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: To Be Published
Title: Persistence of germinal center B cell responses after influenza virus vaccination in humans
Authors: McIntire KM / Meng H / Lin TH / Kim W / Moore NE / Han J / McMahon M / Wang M / Malladi SK / Mohammed BM / Zhou JQ / Schmitz AJ / Hoehn K / Suessen T / Middleton WD / Teefey SA / Presti RM / ...Authors: McIntire KM / Meng H / Lin TH / Kim W / Moore NE / Han J / McMahon M / Wang M / Malladi SK / Mohammed BM / Zhou JQ / Schmitz AJ / Hoehn K / Suessen T / Middleton WD / Teefey SA / Presti RM / Krammer F / Turner JS / Ward AB / Wilson IA / Kleinstein SH / Ellebedy AH
History
DepositionSep 8, 2023-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing 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
Voxel sizeX=Y=Z: 1.045 Å
Density
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

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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