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- EMDB-46727: Structure of AG11-2F01 Fab in complex with A/Solomon Islands/3/20... -

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Basic information

Entry
Database: EMDB / ID: EMD-46727
TitleStructure of AG11-2F01 Fab in complex with A/Solomon Islands/3/2006 (H1N1) influenza virus hemagglutinin
Map data
Sample
  • Complex: Structure of AG11-2F01 Fab in complex with A/Solomon Islands/3/2006 (H1N1) influenza virus hemagglutinin
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
    • Protein or peptide: Heavy chain of influenza virus hemagglutinin antibody AG11-2F01
    • Protein or peptide: Light chain of influenza virus hemagglutinin antibody AG11-2F01
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsantibody-antigen complex / 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 speciesInfluenza A virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMou Z / Lei R / Dai X / Wu N
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI167910 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)DP2 AT011966 United States
Michelson Medical Research FoundationPrize for Human Immunology and Vaccine Research United States
Searle Scholars Program United States
CitationJournal: To Be Published
Title: Structure of AG11-2F01 Fab in complex with A/Solomon Islands/3/2006 (H1N1) influenza virus hemagglutinin
Authors: Mou Z / Lei R / Ouyang W / Dai X / Wu N
History
DepositionAug 23, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46727.png

Downloads & links

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Map

FileDownload / File: emd_46727.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 512 pix.
= 337.92 Å		0.66 Å/pix.
x 512 pix.
= 337.92 Å		0.66 Å/pix.
x 512 pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.1856133 - 1.8306562
Average (Standard dev.)-0.00008917441 (±0.05557885)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_46727_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_46727_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of AG11-2F01 Fab in complex with A/Solomon Islands/3/20...

EntireName: Structure of AG11-2F01 Fab in complex with A/Solomon Islands/3/2006 (H1N1) influenza virus hemagglutinin
Components
  • Complex: Structure of AG11-2F01 Fab in complex with A/Solomon Islands/3/2006 (H1N1) influenza virus hemagglutinin
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
    • Protein or peptide: Heavy chain of influenza virus hemagglutinin antibody AG11-2F01
    • Protein or peptide: Light chain of influenza virus hemagglutinin antibody AG11-2F01
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Structure of AG11-2F01 Fab in complex with A/Solomon Islands/3/20...

SupramoleculeName: Structure of AG11-2F01 Fab in complex with A/Solomon Islands/3/2006 (H1N1) influenza virus hemagglutinin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Influenza A virus / Strain: A/Solomon Islands/3/2006(H1N1)

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Macromolecule #1: Hemagglutinin HA1 chain

MacromoleculeName: Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: A/Solomon Islands/3/2006(H1N1)
Molecular weightTheoretical: 35.809098 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCRLGIAPLQ LGNCSVAGWI LGNPECELLI SRESWSYIVE KPNPENGTC YPGHFADYEE LREQLSSVSS FERFEIFPKE SSWPNHTTTG VSASCSHNGE SSFYKNLLWL TGKNGLYPNL S KSYANNKE ...String:
DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCRLGIAPLQ LGNCSVAGWI LGNPECELLI SRESWSYIVE KPNPENGTC YPGHFADYEE LREQLSSVSS FERFEIFPKE SSWPNHTTTG VSASCSHNGE SSFYKNLLWL TGKNGLYPNL S KSYANNKE KEVLVLWGVH HPPNIGDQRA LYHKENAYVS VVSSHYSRKF TPEIAKRPKV RDQEGRINYY WTLLEPGDTI IF EANGNLI APRYAFALSR GFGSGIINSN APMDECDAKC QTPQGAINSS LPFQNVHPVT IGECPKYVRS AKLRMVTGLR NIP S

UniProtKB: Hemagglutinin

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Macromolecule #2: Hemagglutinin HA2 chain

MacromoleculeName: Hemagglutinin HA2 chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: A/Solomon Islands/3/2006(H1N1)
Molecular weightTheoretical: 19.395527 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
IAGFIEGGWT GMVDGWYGYH HQNEQGSGYA ADQKSTQNAI NGITNKVNSV IEKMNTQFTA VGKEFNKLER RMENLNKKVD DGFIDIWTY NAELLVLLEN ERTLDFHDSN VKNLYEKVKS QLKNNAKEIG NGCFEFYHKC NDECMESVKN GTYDYPKYSE E SKLNREKI

UniProtKB: Hemagglutinin

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Macromolecule #3: Heavy chain of influenza virus hemagglutinin antibody AG11-2F01

MacromoleculeName: Heavy chain of influenza virus hemagglutinin antibody AG11-2F01
type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.794432 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSETLSL TCAVSGNSIS SEYYWAWIRQ PPGMPPEWVG TIYHTGNTYY NPSLKSRTTI SMDTSKNQFS LRLRSVTAA DSAVYYCARA GVTIFGLTLP NYFHHWGQGT LVTVSS

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Macromolecule #4: Light chain of influenza virus hemagglutinin antibody AG11-2F01

MacromoleculeName: Light chain of influenza virus hemagglutinin antibody AG11-2F01
type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.486814 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
IQMTQSPSTL SASVGDRVTI TCRASQSISN WMAWYQQKPG KAPKLLIYKA STLESGVPSR FSGGGSGPEF TLTISSLQPD DSATYYCQQ YNSYMYTFGQ GTKVEI

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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: 6 / 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: 8
Component:
ConcentrationNameFormula
20.0 mMTris Hydrochloric acid
100.0 mMSodium ChlorideNaCl
10.0 mMCalcium ChlorideCaCl2

Details: 20 mM Tris-HCl, 100 mM NaCl, 10 mM CaCl2, pH 8.0
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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 reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 359720
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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