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Yorodumi- PDB-8sk7: Cryo-EM structure of designed Influenza HA binder, HA_20, bound t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8sk7 | ||||||
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Title | Cryo-EM structure of designed Influenza HA binder, HA_20, bound to Influenza HA (Strain: Iowa43) | ||||||
Components |
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Keywords | DE NOVO PROTEIN/Viral Protein / flu / 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 | ||||||
Biological species | Influenza A virus unidentified (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å | ||||||
Authors | Borst, A.J. / Bennett, N.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sk7.cif.gz | 533.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sk7.ent.gz | 436.6 KB | Display | PDB format |
PDBx/mmJSON format | 8sk7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/8sk7 ftp://data.pdbj.org/pub/pdb/validation_reports/sk/8sk7 | HTTPS FTP |
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-Related structure data
Related structure data | 40557MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 3 types, 9 molecules ABCGHIXYZ
#1: Protein | Mass: 35923.340 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Homo sapiens (human) / References: UniProt: A4GCK8 #2: Protein | Mass: 26623.463 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Homo sapiens (human) / References: UniProt: A4GCK8 #3: Protein | Mass: 7391.848 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli) |
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-Sugars , 3 types, 18 molecules
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | #6: Sugar | ChemComp-NAG / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Influenza HA (Iowa43) bound to RFdiffusion designed minibinder, HA_20 Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: Influenza A virus |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 64.273 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 308846 / Symmetry type: POINT | ||||||||||||||||||||||||
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