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- EMDB-49098: H1 hemagglutinin (A/California/04/2009) with E47K mutation in HA2... -

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Basic information

Entry
Database: EMDB / ID: EMD-49098
TitleH1 hemagglutinin (A/California/04/2009) with E47K mutation in HA2 in complex with central stem-targeting Fab ST10
Map data
Sample
  • Complex: H1 hemagglutinin (A/California/04/2009) with E47K mutation in HA2 in complex with central stem-targeting Fab ST10
    • Protein or peptide: H1 HA2
    • Protein or peptide: ST10 Light Chain Fab
    • Protein or peptide: H1 HA1
    • Protein or peptide: ST10 Heavy Chain Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsinfluenza / hemagglutinin / H1 / monoclonal / complex / fab complex / viral fusion protein / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHomo sapiens (human) / Influenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsBrouwer PJM / Loeffler JR / Ferguson JA / Rodriguez AJ / Han J / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N39019C00051 United States
CitationJournal: To Be Published
Title: Individualized IG genotyping coupled with high throughput isolation of influenza HA-specific monoclonal antibodies
Authors: Fisher A / Corcoran M / Chernyshev M / Brouwer PJM / Gillespie R / Nicoletto A / Loeffler JR / Ferguson JA / Rodriguez AJ / Narang S / Adori M / Angeletti D / van Gils MJ / Castro Dopico X / ...Authors: Fisher A / Corcoran M / Chernyshev M / Brouwer PJM / Gillespie R / Nicoletto A / Loeffler JR / Ferguson JA / Rodriguez AJ / Narang S / Adori M / Angeletti D / van Gils MJ / Castro Dopico X / Kanekiyo M / Ward AB / Han J / Karlsson Hedestam GB
History
DepositionFeb 6, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49098.png

Downloads & links

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Map

FileDownload / File: emd_49098.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.)
0.73 Å/pix.
x 512 pix.
= 371.2 Å		0.73 Å/pix.
x 512 pix.
= 371.2 Å		0.73 Å/pix.
x 512 pix.
= 371.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.29207262 - 0.39513656
Average (Standard dev.)0.000010024106 (±0.0076225386)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 371.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49098_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49098_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49098_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 : H1 hemagglutinin (A/California/04/2009) with E47K mutation in HA2...

EntireName: H1 hemagglutinin (A/California/04/2009) with E47K mutation in HA2 in complex with central stem-targeting Fab ST10
Components
  • Complex: H1 hemagglutinin (A/California/04/2009) with E47K mutation in HA2 in complex with central stem-targeting Fab ST10
    • Protein or peptide: H1 HA2
    • Protein or peptide: ST10 Light Chain Fab
    • Protein or peptide: H1 HA1
    • Protein or peptide: ST10 Heavy Chain Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: H1 hemagglutinin (A/California/04/2009) with E47K mutation in HA2...

SupramoleculeName: H1 hemagglutinin (A/California/04/2009) with E47K mutation in HA2 in complex with central stem-targeting Fab ST10
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: H1 HA2

MacromoleculeName: H1 HA2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: A/California/04/2009
Molecular weightTheoretical: 26.030748 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADLKS TQNAIDKITN KVNSVIEKMN TQFTAVGKEF NHLEKRIENL NKKVDDGFL DIWTYNAELL VLLENERTLD YHDSNVKNLY EKVRSQLKNN AKEIGNGCFE FYHKCDNTCM ESVKNGTYDY P KYSEEAKL ...String:
GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADLKS TQNAIDKITN KVNSVIEKMN TQFTAVGKEF NHLEKRIENL NKKVDDGFL DIWTYNAELL VLLENERTLD YHDSNVKNLY EKVRSQLKNN AKEIGNGCFE FYHKCDNTCM ESVKNGTYDY P KYSEEAKL NREEIDGSGY IPEAPRDGQA YVRKDGEWVL LSTFLGSGLN DIFEAQKIEW HEGHHHHHH

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Macromolecule #2: ST10 Light Chain Fab

MacromoleculeName: ST10 Light Chain Fab / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.498836 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVLTQSPDS LAVSLGERAS INCRSSQSLL NRSNNKNFLA WYQQTPGQPP KLLIYWASTR ESGVPDRFTG SGSGADFTLT ISSLQAEDV AVYYCQQYYT TPRTFGQGTK VEIK

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Macromolecule #3: H1 HA1

MacromoleculeName: H1 HA1 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: A/California/04/2009
Molecular weightTheoretical: 38.211297 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKAILVVLLY TFATANADTL CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDKHNGKLCK LRGVAPLHLG KCNIAGWILG NPECESLST ASSWSYIVET PSSDNGTCYP GDFIDYEELR EQLSSVSSFE RFEIFPKTSS WPNHDSNKGV TAACPHAGAK S FYKNLIWL ...String:
MKAILVVLLY TFATANADTL CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDKHNGKLCK LRGVAPLHLG KCNIAGWILG NPECESLST ASSWSYIVET PSSDNGTCYP GDFIDYEELR EQLSSVSSFE RFEIFPKTSS WPNHDSNKGV TAACPHAGAK S FYKNLIWL VKKGNSYPKL SKSYINDKGK EVLVLWGIHH PSTSADQQSL YQNADTYVFV GSSRYSKKFK PEIAIRPKVR DQ EGRMNYY WTLVEPGDKI TFEATGNLVV PRYAFAMERN AGSGIIISDT PVHDCNTTCQ TPKGAINTSL PFQNIHPITI GKC PKYVKS TKLRLATGLR NIPSIQSR

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Macromolecule #4: ST10 Heavy Chain Fab

MacromoleculeName: ST10 Heavy Chain Fab / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.591262 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSGTLSL TCAVSGGSIS SNNWWTWVRQ SPGKGLEWMG EIFHSGSTSY NPSLNSRVTM SVDKSKNQFS LRLNSLTAA DTAVYYCARL QQIMIYGLIR GGAMDVWGQG TTVTVSS

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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: 15 / 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

Concentration0.9 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Details: 15mA
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: 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 / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.7000000000000001 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: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133491
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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