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- EMDB-76462: CryoEM structure of monoclonal Fab 047-09 1A02 binding the latera... -

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Basic information

Entry
Database: EMDB / ID: EMD-76462
TitleCryoEM structure of monoclonal Fab 047-09 1A02 binding the lateral patch of influenza virus H1 HA (A/California/04/2009 H1N1)
Map datastructure of monoclonal Fab 047-09 1A02 binding the lateral patch of influenza virus H1 HA (A/California/04/2009 H1N1)
Sample
  • Complex: Fab 047-09 1A02 in complex with A/California/04/2009
    • Protein or peptide: Light chain 1A02
    • Protein or peptide: Heavy chain 1A02
    • Protein or peptide: Hemagglutinin HA2
    • Protein or peptide: Hemagglutinin HA1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAntibody / Hemagglutinin / IMMUNE SYSTEM / IMMUNE SYSTEM-Viral Protein 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 / metal ion binding / 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 (A/California/04/2009(H1N1))
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsFernandez-Quintero ML / Han J / Ward AB
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Temporal and cross-species convergence of influenza H1 lateral patch antigenic drift
Authors: Fernandez-Quintero ML / Han J / Ward AB
History
DepositionApr 7, 2026-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76462.png

Downloads & links

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Map

FileDownload / File: emd_76462.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of monoclonal Fab 047-09 1A02 binding the lateral patch of influenza virus H1 HA (A/California/04/2009 H1N1)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 512 pix.
= 367.616 Å		0.72 Å/pix.
x 512 pix.
= 367.616 Å		0.72 Å/pix.
x 512 pix.
= 367.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.718 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.37938723 - 0.45057756
Average (Standard dev.)-0.0002041974 (±0.012596118)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 367.616 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_76462_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_76462_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Fab 047-09 1A02 in complex with A/California/04/2009

EntireName: Fab 047-09 1A02 in complex with A/California/04/2009
Components
  • Complex: Fab 047-09 1A02 in complex with A/California/04/2009
    • Protein or peptide: Light chain 1A02
    • Protein or peptide: Heavy chain 1A02
    • Protein or peptide: Hemagglutinin HA2
    • Protein or peptide: Hemagglutinin HA1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Fab 047-09 1A02 in complex with A/California/04/2009

SupramoleculeName: Fab 047-09 1A02 in complex with A/California/04/2009 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #4, #3, #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 330 kDa/nm

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Macromolecule #1: Hemagglutinin HA2

MacromoleculeName: Hemagglutinin HA2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/California/04/2009(H1N1))
Molecular weightTheoretical: 18.543518 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GGWTGMVDGW YGYHHQNEQG SGYAADLKST QNAIDKITNK VNSVIEKMNT QFTAVGKEFN HLEKRIENLN KKVDDGFLDI WTYNAELLV LLENERTLDY HDSNVKNLYE KVRSQLKNNA KEIGNGCFEF YHKCDNTCME SVKNGTYDYP KYSEEAKLNR E

UniProtKB: Hemagglutinin

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Macromolecule #2: Hemagglutinin HA1

MacromoleculeName: Hemagglutinin HA1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/California/04/2009(H1N1))
Molecular weightTheoretical: 35.701344 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TLCIGYHANN STDTVDTVLE KNVTVTHSVN LLEDKHNGKL CKLRGVAPLH LGKCNIAGWI LGNPECESLS TASSWSYIVE TPSSDNGTC YPGDFIDYEE LREQLSSVSS FERFEIFPKT SSWPNHDSNK GVTAACPHAG AKSFYKNLIW LVKKGNSYPK L SKSYINDK ...String:
TLCIGYHANN STDTVDTVLE KNVTVTHSVN LLEDKHNGKL CKLRGVAPLH LGKCNIAGWI LGNPECESLS TASSWSYIVE TPSSDNGTC YPGDFIDYEE LREQLSSVSS FERFEIFPKT SSWPNHDSNK GVTAACPHAG AKSFYKNLIW LVKKGNSYPK L SKSYINDK GKEVLVLWGI HHPSTSADQQ SLYQNADTYV FVGSSRYSKK FKPEIAIRPK VRDQEGRMNY YWTLVEPGDK IT FEATGNL VVPRYAFAME RNAGSGIIIS DTPVHDCNTT CQTPKGAINT SLPFQNIHPI TIGKCPKYVK STKLRLATGL RNI P

UniProtKB: Hemagglutinin

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Macromolecule #3: Heavy chain 1A02

MacromoleculeName: Heavy chain 1A02 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.095723 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLLESGGA LVQPGGSLRL SCTASGFTLG HFAMAWVRQA PGKGLEWLSA ISGGGGTTYY ADSVKGRFTI SRDNSKNTLY LQLSGLRAE DTALYFCGKY DSSGHHYVRR MHFWGQGTLV TV

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Macromolecule #4: Light chain 1A02

MacromoleculeName: Light chain 1A02 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.543765 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDRVT ITCRASQDIN NNLNWYQQKP GKAPKLLMYD ASNLEAGVPS RFSGTGSGTD FTFTISSLQA EDIATYYCQ QYRNPLLTFG GGTKVEI

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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: 14 / 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: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm

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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: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 87530
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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