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- EMDB-41676: Fab 3864-6 in complex with influenza HA H3-VIC11 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-41676
TitleFab 3864-6 in complex with influenza HA H3-VIC11
Map data
Sample
  • Complex: Trimer
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Fab 3864-6 Heavy Chain
    • Protein or peptide: Fab 3864-6 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsantibody / influenza / ANTIVIRAL PROTEIN
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 (A/Victoria/361/2011(H3N2))
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsMorano NC / Shapiro L
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationFNIH SHAP19IUFV United States
CitationJournal: Structure / Year: 2025
Title: The N terminus of H3-influenza hemagglutinin as a site-of-vulnerability to neutralizing antibody
Authors: Rawi R / Morano NC / Cheung CSF / Du H / Gorman J / Prabhakaran M / Becker JE / Bylund T / Charaf S / Chen X / Lee M / Harris DR / Olia AS / Ou L / Wang L / Wang S / Zhang B / Kanekiyo M / ...Authors: Rawi R / Morano NC / Cheung CSF / Du H / Gorman J / Prabhakaran M / Becker JE / Bylund T / Charaf S / Chen X / Lee M / Harris DR / Olia AS / Ou L / Wang L / Wang S / Zhang B / Kanekiyo M / McDermott AB / Zhou T / Shapiro L / Kwong PD
History
DepositionAug 22, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41676.png

Downloads & links

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Map

FileDownload / File: emd_41676.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.696
Minimum - Maximum-2.5597525 - 3.485997
Average (Standard dev.)-0.00023171592 (±0.093791224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41676_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_41676_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 : Trimer

EntireName: Trimer
Components
  • Complex: Trimer
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Fab 3864-6 Heavy Chain
    • Protein or peptide: Fab 3864-6 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Trimer

SupramoleculeName: Trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Victoria/361/2011(H3N2)) / Strain: A/Victoria/361/2011(H3N2)
Molecular weightTheoretical: 39.303648 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKTIIALSHI LCLVFAQKLP GNDNSTATLC LGHHAVPNGT IVKTICNDQI EVTNATELVQ NSSIGEICDS PHQILDGENC TLIDALLGD PQCDGFQNKK WDLFVERSKA YSNCYPYDVP DYASLRSLVA SSGTLEFNNE SFNWTGVTQN GTSSACIRRS N NSFFSRLN ...String:
MKTIIALSHI LCLVFAQKLP GNDNSTATLC LGHHAVPNGT IVKTICNDQI EVTNATELVQ NSSIGEICDS PHQILDGENC TLIDALLGD PQCDGFQNKK WDLFVERSKA YSNCYPYDVP DYASLRSLVA SSGTLEFNNE SFNWTGVTQN GTSSACIRRS N NSFFSRLN WLTQLNFKYP ALNVTMPNNE QFDKLYIWGV HHPVTDKDQI FLYAQSSGRI TVSTKRSQQA VIPNIGYRPR IR NIPSRIS IYWTIVKPGD ILLINSTGNL IAPRGYFKIR SGKSSIMRSD APIGKCNSEC ITPNGSIPND KPFQNVNRIT YGA CPRYVK QSTLKLATGM RNVPEKQTRR RRRR

UniProtKB: Hemagglutinin

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Macromolecule #2: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Victoria/361/2011(H3N2))
Molecular weightTheoretical: 25.234092 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GIFGAIAGFI ENGWEGMVDG WYGFRHQNSE GRGQAADLKS TQAAIDCING KLNRLIGKTN EKFHQIEKEF SEVEGRIQDL EKYVEDTKI DLWSYNAELL VALENQHTID LTDSEMNKLF EKTKKQLREN AEDMGNGCFK IYHKCDNACI GSIRNGTYDH D VYRDEALN ...String:
GIFGAIAGFI ENGWEGMVDG WYGFRHQNSE GRGQAADLKS TQAAIDCING KLNRLIGKTN EKFHQIEKEF SEVEGRIQDL EKYVEDTKI DLWSYNAELL VALENQHTID LTDSEMNKLF EKTKKQLREN AEDMGNGCFK IYHKCDNACI GSIRNGTYDH D VYRDEALN NRFQIKGVSG RLVPRGSPGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGHH HHHH

UniProtKB: Hemagglutinin

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Macromolecule #3: Fab 3864-6 Heavy Chain

MacromoleculeName: Fab 3864-6 Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.862734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQQSGTD LVMPGASVKL SCKASGYTFI SWWIHWVKQR PGQGLEWIGE IDPSDSYTSY NQKFKGKATL TVDKSSSTAY MQLSSLTSE DSAVYYCARS GYSNYPFDYW GQGTTLPVSS ASTTPPSVYP LAPGSAAQTN SMVTLGCLVK GYFPEPVTVT W NSGSLSSG ...String:
QVQLQQSGTD LVMPGASVKL SCKASGYTFI SWWIHWVKQR PGQGLEWIGE IDPSDSYTSY NQKFKGKATL TVDKSSSTAY MQLSSLTSE DSAVYYCARS GYSNYPFDYW GQGTTLPVSS ASTTPPSVYP LAPGSAAQTN SMVTLGCLVK GYFPEPVTVT W NSGSLSSG VHTFPAVLQS DLYTLSSSVT VPSSTWPSET VTCNVAHPAS STKVDKKIVP RDCDKGLEVL FQ

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Macromolecule #4: Fab 3864-6 Light Chain

MacromoleculeName: Fab 3864-6 Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.583883 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQTTSS LSASLGDRVT ISCSASQGIS NYLNWYQQKP DGTVKLLIYY TSSLHSGVPS RFSGSGSGTD YSLTISNLEP EDIATYYCQ QSSKLPWTFG GGTKLEIKRT DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String:
DIQMTQTTSS LSASLGDRVT ISCSASQGIS NYLNWYQQKP DGTVKLLIYY TSSLHSGVPS RFSGSGSGTD YSLTISNLEP EDIATYYCQ QSSKLPWTFG GGTKLEIKRT DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNEC

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.06 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
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: PDB ENTRY
PDB model - PDB ID:

7kc1

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 590963
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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