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- PDB-9nh7: CryoEM Structure of De Novo VHH, VHH_flu_01, bound to influenza H... -

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Basic information

Entry
Database: PDB / ID: 9nh7
TitleCryoEM Structure of De Novo VHH, VHH_flu_01, bound to influenza HA, strain A/USA:Iowa/1943 H1N1.
Components
  • (Hemagglutinin ...) x 2
  • VHH_flu_01
KeywordsDE NOVO PROTEIN / Influenza / Flu / HA / hemagglutinin / H1N1 / antibody / De Novo / protein design / VHH_flu_01 / De Novo Antibody / 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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsBorst, A.J. / Weidle, C.
Funding support United States, European Union, United Kingdom, 11items
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, N.R. / Watson, J.L. / Ragotte, R.J. / Borst, A.J. / See, D.L. / Weidle, C. / Biswas, R. / Yu, Y. / Shrock, E.L. / Ault, R. / Leung, P.J.Y. / Huang, B. / Goreshnik, I. / Tam, J. / ...Authors: Bennett, N.R. / Watson, J.L. / Ragotte, R.J. / Borst, A.J. / See, D.L. / Weidle, C. / Biswas, R. / Yu, Y. / Shrock, E.L. / Ault, R. / Leung, P.J.Y. / Huang, B. / Goreshnik, I. / Tam, J. / Carr, K.D. / Singer, B. / Criswell, C. / Wicky, B.I.M. / Vafeados, D. / Sanchez, M.G. / Kim, H.M. / Torres, S.T. / Chan, S. / Sun, S.M. / Spear, T. / Sun, Y. / O'Reilly, K. / Maris, J.M. / Sgourakis, N.G. / Melnyk, R.A. / Liu, C.C. / Baker, D.
History
DepositionFeb 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: VHH_flu_01
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA1 chain
C: Hemagglutinin HA1 chain
F: VHH_flu_01
G: Hemagglutinin HA2 chain
H: Hemagglutinin HA2 chain
I: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,71726
Polymers217,7068
Non-polymers6,01218
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Hemagglutinin ... , 2 types, 6 molecules ABCGHI

#2: Protein Hemagglutinin HA1 chain


Mass: 35923.340 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/USA:Iowa/1943 H1N1)
Strain: A/USA:Iowa/1943 H1N1 / Gene: HA / Production host: Homo sapiens (human) / References: UniProt: A4GCK8
#3: Protein Hemagglutinin HA2 chain


Mass: 26623.463 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/USA:Iowa/1943 H1N1)
Strain: A/USA:Iowa/1943 H1N1 / Gene: HA / Production host: Homo sapiens (human) / References: UniProt: A4GCK8

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Antibody , 1 types, 2 molecules EF

#1: Antibody VHH_flu_01


Mass: 15032.718 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Sugars , 3 types, 18 molecules

#4: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: De Novo VHH, VHH_flu_01, bound to influenza HA, strain A/USA:Iowa/1943 H1N1.
Type: COMPLEX
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.
Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.09244733 MDa / Experimental value: NO
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5 / Details: 150 mM NaCl, 40 mM Tris/ HCl pH 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
240 nMtris(hydroxymethyl)aminomethane/Hydrochloric AcidTris/HCl1
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5 sec. / Electron dose: 53 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 16954
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7UCSF Chimeramodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIX1.21.2_5419model refinement
14PyMOLmodel refinement
15Cootmodel refinement
16ISOLDEmodel refinement
17UCSF ChimeraXmodel refinement
CTF correctionDetails: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5869679
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 288441 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1

IDPDB-IDAccession codeDetailsInitial refinement model-IDSource nameType
18SK7

8sk7

8SK7Trimeric influenza HA glycoprotein (strain A/USA:Iowa/1943 H1N11PDBexperimental model
2De Novo DesignOtherin silico model
RefinementHighest resolution: 3.02 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00413249
ELECTRON MICROSCOPYf_angle_d0.56917990
ELECTRON MICROSCOPYf_dihedral_angle_d12.8414696
ELECTRON MICROSCOPYf_chiral_restr0.0492053
ELECTRON MICROSCOPYf_plane_restr0.0042300

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