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- EMDB-40557: Cryo-EM structure of designed Influenza HA binder, HA_20, bound t... -

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Basic information

Entry
Database: EMDB / ID: EMD-40557
TitleCryo-EM structure of designed Influenza HA binder, HA_20, bound to Influenza HA (Strain: Iowa43)
Map dataunsharpened
Sample
  • Complex: Influenza HA (Iowa43) bound to RFdiffusion designed minibinder, HA_20
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: HA_20 minibinder (RFdiffusion-designed)
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsflu / influenza / hemagglutinin / HA / Iowa43 / HA_20 / DE NOVO PROTEIN / minibinder / binder / designed protein / fusion protein / glycoprotein / DE NOVO PROTEIN-Viral Protein 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 / unidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsBorst AJ / Bennett NR
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2023
Title: De novo design of protein structure and function with RFdiffusion.
Authors: Joseph L Watson / David Juergens / Nathaniel R Bennett / Brian L Trippe / Jason Yim / Helen E Eisenach / Woody Ahern / Andrew J Borst / Robert J Ragotte / Lukas F Milles / Basile I M Wicky / ...Authors: Joseph L Watson / David Juergens / Nathaniel R Bennett / Brian L Trippe / Jason Yim / Helen E Eisenach / Woody Ahern / Andrew J Borst / Robert J Ragotte / Lukas F Milles / Basile I M Wicky / Nikita Hanikel / Samuel J Pellock / Alexis Courbet / William Sheffler / Jue Wang / Preetham Venkatesh / Isaac Sappington / Susana Vázquez Torres / Anna Lauko / Valentin De Bortoli / Emile Mathieu / Sergey Ovchinnikov / Regina Barzilay / Tommi S Jaakkola / Frank DiMaio / Minkyung Baek / David Baker /
Abstract: There has been considerable recent progress in designing new proteins using deep-learning methods. Despite this progress, a general deep-learning framework for protein design that enables solution of ...There has been considerable recent progress in designing new proteins using deep-learning methods. Despite this progress, a general deep-learning framework for protein design that enables solution of a wide range of design challenges, including de novo binder design and design of higher-order symmetric architectures, has yet to be described. Diffusion models have had considerable success in image and language generative modelling but limited success when applied to protein modelling, probably due to the complexity of protein backbone geometry and sequence-structure relationships. Here we show that by fine-tuning the RoseTTAFold structure prediction network on protein structure denoising tasks, we obtain a generative model of protein backbones that achieves outstanding performance on unconditional and topology-constrained protein monomer design, protein binder design, symmetric oligomer design, enzyme active site scaffolding and symmetric motif scaffolding for therapeutic and metal-binding protein design. We demonstrate the power and generality of the method, called RoseTTAFold diffusion (RFdiffusion), by experimentally characterizing the structures and functions of hundreds of designed symmetric assemblies, metal-binding proteins and protein binders. The accuracy of RFdiffusion is confirmed by the cryogenic electron microscopy structure of a designed binder in complex with influenza haemagglutinin that is nearly identical to the design model. In a manner analogous to networks that produce images from user-specified inputs, RFdiffusion enables the design of diverse functional proteins from simple molecular specifications.
History
DepositionApr 18, 2023-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateSep 13, 2023-
Current statusSep 13, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40557.png

Downloads & links

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Map

FileDownload / File: emd_40557.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.044
Minimum - Maximum-0.20553379 - 0.44938546
Average (Standard dev.)0.000694502 (±0.0117027005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 282.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: deepEMhancer

Fileemd_40557_additional_1.map
AnnotationdeepEMhancer
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: autosharpened

Fileemd_40557_additional_2.map
Annotationautosharpened
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Half map: half map a

Fileemd_40557_half_map_1.map
Annotationhalf map a
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Half map: half map b

Fileemd_40557_half_map_2.map
Annotationhalf map b
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Sample components

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Entire : Influenza HA (Iowa43) bound to RFdiffusion designed minibinder, HA_20

EntireName: Influenza HA (Iowa43) bound to RFdiffusion designed minibinder, HA_20
Components
  • Complex: Influenza HA (Iowa43) bound to RFdiffusion designed minibinder, HA_20
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: HA_20 minibinder (RFdiffusion-designed)
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Influenza HA (Iowa43) bound to RFdiffusion designed minibinder, HA_20

SupramoleculeName: Influenza HA (Iowa43) bound to RFdiffusion designed minibinder, HA_20
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Influenza A virus

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Macromolecule #1: Hemagglutinin HA1 chain

MacromoleculeName: Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
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 #2: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
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 #3: HA_20 minibinder (RFdiffusion-designed)

MacromoleculeName: HA_20 minibinder (RFdiffusion-designed) / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 7.391848 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MEKEKELKEY AEKIKKEIGD IESVEVKDGK ILVKAKKITD KTVDAIMKLT VKAARLGFKV EVELV

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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 / N-Acetylglucosamine

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 64.273 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3lzg

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 308846
FSC plot (resolution estimation)

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