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- EMDB-70235: Cryo-EM structure of NI04359_d30_240 Fab in complex with influenz... -

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Basic information

Entry
Database: EMDB / ID: EMD-70235
TitleCryo-EM structure of NI04359_d30_240 Fab in complex with influenza virus hemagglutinin from A/Hong Kong/485197/2014 (H3N2)
Map datastructure of NI04359_d30_240 Fab in complex with influenza virus hemagglutinin from A/Hong Kong/485197/2014 (H3N2)
Sample
  • Complex: Cryo-EM structure of NI04359_d30_240 Fab in complex with influenza virus hemagglutinin from A/Hong Kong/485197/2014 (H3N2)
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: Hemagglutinin HA2
    • Protein or peptide: NI04359_d30_240 Fab heavy chain
    • Protein or peptide: NI04359_d30_240 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsInfluenza / Hemagglutinin / Antibody complex / Viral protein / 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 (A/Hong Kong/485197/2014(H3N2)) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsJo G / Ward AB
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: A single amino acid substitution in hemagglutinin stalk drives heterosubtypic imprinting of cross-group reactive B cells in children
Authors: Jo G / Ward AB
History
DepositionApr 16, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70235.png

Downloads & links

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Map

FileDownload / File: emd_70235.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of NI04359_d30_240 Fab in complex with influenza virus hemagglutinin from A/Hong Kong/485197/2014 (H3N2)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 440 pix.
= 315.92 Å		0.72 Å/pix.
x 440 pix.
= 315.92 Å		0.72 Å/pix.
x 440 pix.
= 315.92 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: 0.05
Minimum - Maximum-0.20962061 - 0.3728503
Average (Standard dev.)-0.0001476665 (±0.009288116)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 315.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_70235_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_70235_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 : Cryo-EM structure of NI04359_d30_240 Fab in complex with influenz...

EntireName: Cryo-EM structure of NI04359_d30_240 Fab in complex with influenza virus hemagglutinin from A/Hong Kong/485197/2014 (H3N2)
Components
  • Complex: Cryo-EM structure of NI04359_d30_240 Fab in complex with influenza virus hemagglutinin from A/Hong Kong/485197/2014 (H3N2)
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: Hemagglutinin HA2
    • Protein or peptide: NI04359_d30_240 Fab heavy chain
    • Protein or peptide: NI04359_d30_240 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of NI04359_d30_240 Fab in complex with influenz...

SupramoleculeName: Cryo-EM structure of NI04359_d30_240 Fab in complex with influenza virus hemagglutinin from A/Hong Kong/485197/2014 (H3N2)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Influenza A virus (A/Hong Kong/485197/2014(H3N2))

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Macromolecule #1: Hemagglutinin HA1

MacromoleculeName: Hemagglutinin HA1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Hong Kong/485197/2014(H3N2))
Molecular weightTheoretical: 38.435547 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKTIIALSYI LCLVFAQKIP GNDNSTATLC LGHHAVPNGT IVKTITNDRI EVTNATELVQ NSSIGEICDS PHQILDGENC TLIDALLGD PQCDGFQNKK WDLFVERSKA YSNCYPYDVP DYASLRSLVA TSGTLEFNNE SFNWTGVTQN GTSSACIRRS S SSFFSRLN ...String:
MKTIIALSYI LCLVFAQKIP GNDNSTATLC LGHHAVPNGT IVKTITNDRI EVTNATELVQ NSSIGEICDS PHQILDGENC TLIDALLGD PQCDGFQNKK WDLFVERSKA YSNCYPYDVP DYASLRSLVA TSGTLEFNNE SFNWTGVTQN GTSSACIRRS S SSFFSRLN WLTHLNYTYP ALNVTMPNNE QFDKLYIWGV HHPGTDKDQI FLYAQSSGRI TVSTKRSQQA VIPNIGSRPR IR DIPSRIS IYWTIVKPGD ILLINSTGNL IAPRGYFKIR SGKSSIMRSD APIGKCKSEC ITPNGSIPND KPFQNVNRIT YGA CPRYVK HSTLKLATGM RNVPEKQTR

UniProtKB: Hemagglutinin

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Macromolecule #2: Hemagglutinin HA2

MacromoleculeName: Hemagglutinin HA2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Hong Kong/485197/2014(H3N2))
Molecular weightTheoretical: 26.760545 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GIFGAIAGFI ENGWEGMVDG WYGFRHQNSE GRGQAADLKS TQAAIDQING KLNRLIGKTN EKFHQIEKEF SEVEGRIQDL EKYVEDTKI DLWSYNAELL VALENQHTID LTDSEMNKLF EKTKKQLREN AEDMGNGCFK IYHKCDNACI GSIRNGTYDH N VYRDEALN ...String:
GIFGAIAGFI ENGWEGMVDG WYGFRHQNSE GRGQAADLKS TQAAIDQING KLNRLIGKTN EKFHQIEKEF SEVEGRIQDL EKYVEDTKI DLWSYNAELL VALENQHTID LTDSEMNKLF EKTKKQLREN AEDMGNGCFK IYHKCDNACI GSIRNGTYDH N VYRDEALN NRFQIKGVGY IPEAPRDGQA YVRKDGEWVL LSTFLGSENL YFQGSAWSHP QFEKGGGSGG GSHHHHHH

UniProtKB: Hemagglutinin

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Macromolecule #3: NI04359_d30_240 Fab heavy chain

MacromoleculeName: NI04359_d30_240 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.020549 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DVQLLESGGG LVHPGGSLRL SCAASGFTFS SYGMNWVRQA PGKGLEWVSG ISGSGGTTYY ADSVKGRFTV SRDNSKNTLF LQMNSLRAE DTAVYYCAKD RGCRSSNCYI VGYYYYGMDV WGQGTTVTVS S

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Macromolecule #4: NI04359_d30_240 Fab light chain

MacromoleculeName: NI04359_d30_240 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.497644 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDRVT FTCRASQSIS SYLNWYQQKP GKAPKLLIYA ASSLQNEVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSSSTPLTFG GGTTVEIK

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 18 / 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

Concentration0.8 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 2516 / Average exposure time: 2.67 sec. / Average electron dose: 45.09 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab initio (cryoSPARC)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 196828
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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