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- EMDB-49405: CryoEM Structure of De Novo VHH, VHH_flu_01, bound to influenza H... -

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Basic information

Entry
Database: EMDB / ID: EMD-49405
TitleCryoEM Structure of De Novo VHH, VHH_flu_01, bound to influenza HA, strain A/USA:Iowa/1943 H1N1
Map dataDeepEMhancer
Sample
  • Complex: De Novo VHH, VHH_flu_01, bound to influenza HA, strain A/USA:Iowa/1943 H1N1.
    • Protein or peptide: VHH_flu_01
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsInfluenza / Flu / HA / hemagglutinin / H1N1 / antibody / De Novo / protein design / VHH_flu_01 / De Novo Antibody / DE NOVO PROTEIN / RFdiffusion / RFantibody
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 speciessynthetic construct (others) / Influenza A virus (strain A/USA:Iowa/1943 H1N1)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsBorst AJ / Weidle C
Funding support United States, European Union, United Kingdom, 11 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Department of Energy (DOE, United States)DE-SC0018940 MOD03 United States
National Institutes of Health/National Eye Institute (NIH/NEI)T32EY032448 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA260415 United States
Bill & Melinda Gates FoundationINV-010680 United States
European Molecular Biology Organization (EMBO)ALTF 292-2022European Union
Defense Threat Reduction Agency (DTRA)HDTRA1-21-1-0007 United States
National Science Foundation (NSF, United States)NERSC award BER-ERCAP0022018 United States
Cancer Research UKCGCATF-2021/100002 United Kingdom
National Institutes of Health/National Cancer Institute (NIH/NCI)CA278687-01 United States
Defense Threat Reduction Agency (DTRA)HDTRA1-21-1-0038 United States
CitationJournal: Nature / Year: 2025
Title: Atomically accurate de novo design of antibodies with RFdiffusion
Authors: Bennett NR / Watson JL / Ragotte RJ / Borst AJ / See DL / Weidle C / Biswas R / Yu Y / Shrock EL / Ault R / Leung PJY / Huang B / Goreshnik I / Tam J / Carr KD / Singer B / Criswell C / ...Authors: Bennett NR / Watson JL / Ragotte RJ / Borst AJ / See DL / Weidle C / Biswas R / Yu Y / Shrock EL / Ault R / Leung PJY / Huang B / Goreshnik I / Tam J / Carr KD / Singer B / Criswell C / Wicky BIM / Vafeados D / Sanchez MG / Kim HM / Torres ST / Chan S / Sun SM / Spear T / Sun Y / O'Reilly K / Maris JM / Sgourakis NG / Melnyk RA / Liu CC / Baker D
History
DepositionFeb 24, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49405.png

Downloads & links

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Map

FileDownload / File: emd_49405.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 340 pix.
= 285.6 Å		0.84 Å/pix.
x 340 pix.
= 285.6 Å		0.84 Å/pix.
x 340 pix.
= 285.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00909
Minimum - Maximum-0.028199285 - 1.6458527
Average (Standard dev.)0.0010399796 (±0.021002438)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 285.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened

Fileemd_49405_additional_1.map
AnnotationUnsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened

Fileemd_49405_additional_2.map
AnnotationSharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_49405_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_49405_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 : De Novo VHH, VHH_flu_01, bound to influenza HA, strain A/USA:Iowa...

EntireName: De Novo VHH, VHH_flu_01, bound to influenza HA, strain A/USA:Iowa/1943 H1N1.
Components
  • Complex: De Novo VHH, VHH_flu_01, bound to influenza HA, strain A/USA:Iowa/1943 H1N1.
    • Protein or peptide: VHH_flu_01
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: De Novo VHH, VHH_flu_01, bound to influenza HA, strain A/USA:Iowa...

SupramoleculeName: De Novo VHH, VHH_flu_01, bound to influenza HA, strain A/USA:Iowa/1943 H1N1.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Influenza HA, strain A/USA:Iowa/1943 H1N1 was expressed and purified. VHH_flu_01 was expressed and purified. VHH_flu_01 was mixed with Influenza HA, strain A/USA:Iowa/1943 H1N1 at a 3:1 molar ratio.
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 92.44733 KDa

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Macromolecule #1: VHH_flu_01

MacromoleculeName: VHH_flu_01 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.032718 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGQVQLVES GGGLVQPGGS LRLSCAASGK YVNLMSLGWF RQAPGQGLEA VAAISFDGKK TYYADSVKGR FTISRDNSKN TLYLQMNSL RAEDTAVYYC AASVVDSLGV GFYSYWGQGT LVTVSGSGSH HWGSTHHHHH H

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Macromolecule #2: Hemagglutinin HA1 chain

MacromoleculeName: Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (strain A/USA:Iowa/1943 H1N1) / Strain: A/USA:Iowa/1943 H1N1
Molecular weightTheoretical: 35.92334 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCRLKGIAPL QLGKCNIAGW ILGNPECESL LSERSWSYIV ETPNSENGT CFPGDFIDYE ELREQLSSVS SFERFEIFSK ESSWPKHTTG GVTAACSHAG KSSFYRNLLW LTEKDGSYPN L NNSYVNKK ...String:
DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCRLKGIAPL QLGKCNIAGW ILGNPECESL LSERSWSYIV ETPNSENGT CFPGDFIDYE ELREQLSSVS SFERFEIFSK ESSWPKHTTG GVTAACSHAG KSSFYRNLLW LTEKDGSYPN L NNSYVNKK GKEVLVLWGV HHPSNIKDQQ TLYQKENAYV SVVSSNYNRR FTPEIAERPK VRGQAGRINY YWTLLKPGDT IM FEANGNL IAPWYAFALS RGFGSGIITS NASMHECDTK CQTPQGAINS SLPFQNIHPI TIGECPKYVR STKLRMVTGL RNI P

UniProtKB: Hemagglutinin

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Macromolecule #3: Hemagglutinin HA2 chain

MacromoleculeName: Hemagglutinin HA2 chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (strain A/USA:Iowa/1943 H1N1) / Strain: A/USA:Iowa/1943 H1N1
Molecular weightTheoretical: 26.623463 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SIQSRGLFGA IAGFIEGGWT GMIDGWYGYH WQNEQGSGYA ADQKSTQNAI NGITNIVNSV IEKMNTQFTA VGKEFNNLEK RMENLNKKV DDGFLDIWTY NAELLVLLIN ERTLDFHDSN VKNLYEKVKN QLRNNAKEIG NGCFEFYHKC NNECMESVKN G TYDYPKYS ...String:
SIQSRGLFGA IAGFIEGGWT GMIDGWYGYH WQNEQGSGYA ADQKSTQNAI NGITNIVNSV IEKMNTQFTA VGKEFNNLEK RMENLNKKV DDGFLDIWTY NAELLVLLIN ERTLDFHDSN VKNLYEKVKN QLRNNAKEIG NGCFEFYHKC NNECMESVKN G TYDYPKYS EESKLNREKI DGSGYIPEAP RDGQAYVRKD GEWVLLSTFL GSGLNDIFEA QKIEWHEGHH HHHH

UniProtKB: Hemagglutinin

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 12 / 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

Concentration0.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
40.0 nMTris/HCltris(hydroxymethyl)aminomethane/Hydrochloric Acid

Details: 150 mM NaCl, 40 mM Tris/ HCl pH 7.5
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 16954 / Average exposure time: 5.0 sec. / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 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: 0.8 µm / Nominal magnification: 105000
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

Particle selectionNumber selected: 5869679
CTF correctionSoftware - Name: cryoSPARC / Details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: 3D Ab Initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 288441
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: Non Uniform Refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: Non Uniform Refinement
Final 3D classificationNumber classes: 2 / Avg.num./class: 17141 / Software - Name: cryoSPARC / Details: 3D Classification
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

8sk7

source_name: PDB, initial_model_type: experimental modelTrimeric influenza HA glycoprotein (strain A/USA:Iowa/1943 H1N1
source_name: Other, initial_model_type: in silico modelDe Novo Design
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9nh7:
CryoEM Structure of De Novo VHH, VHH_flu_01, bound to influenza HA, strain A/USA:Iowa/1943 H1N1.

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