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Yorodumi- PDB-6v4o: Structure of human 2E01 Fab in complex with influenza virus neura... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v4o | ||||||
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Title | Structure of human 2E01 Fab in complex with influenza virus neuraminidase from B/Phuket/3073/2013 | ||||||
Components |
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Keywords | VIRAL PROTEIN / neuraminidase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information : / : / : / exo-alpha-sialidase / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Influenza B virus Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Dai, Y.N. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Immunity / Year: 2020 Title: Human Antibodies Targeting Influenza B Virus Neuraminidase Active Site Are Broadly Protective. Authors: Anders Madsen / Ya-Nan Dai / Meagan McMahon / Aaron J Schmitz / Jackson S Turner / Jessica Tan / Tingting Lei / Wafaa B Alsoussi / Shirin Strohmeier / Mostafa Amor / Bassem M Mohammed / ...Authors: Anders Madsen / Ya-Nan Dai / Meagan McMahon / Aaron J Schmitz / Jackson S Turner / Jessica Tan / Tingting Lei / Wafaa B Alsoussi / Shirin Strohmeier / Mostafa Amor / Bassem M Mohammed / Philip A Mudd / Viviana Simon / Rebecca J Cox / Daved H Fremont / Florian Krammer / Ali H Ellebedy / Abstract: Influenza B virus (IBV) infections can cause severe disease in children and the elderly. Commonly used antivirals have lower clinical effectiveness against IBV compared to influenza A viruses (IAV). ...Influenza B virus (IBV) infections can cause severe disease in children and the elderly. Commonly used antivirals have lower clinical effectiveness against IBV compared to influenza A viruses (IAV). Neuraminidase (NA), the second major surface protein on the influenza virus, is emerging as a target of broadly protective antibodies that recognize the NA active site of IAVs. However, similarly broadly protective antibodies against IBV NA have not been identified. Here, we isolated and characterized human monoclonal antibodies (mAbs) that target IBV NA from an IBV-infected patient. Two mAbs displayed broad and potent capacity to inhibit IBV NA enzymatic activity, neutralize the virus in vitro, and protect against lethal IBV infection in mice in prophylactic and therapeutic settings. These mAbs inserted long CDR-H3 loops into the NA active site, engaging residues highly conserved among IBV NAs. These mAbs provide a blueprint for the development of improved vaccines and therapeutics against IBVs. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6v4o.cif.gz | 547.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v4o.ent.gz | 461.7 KB | Display | PDB format |
PDBx/mmJSON format | 6v4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v4o_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6v4o_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6v4o_validation.xml.gz | 87.2 KB | Display | |
Data in CIF | 6v4o_validation.cif.gz | 127.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/6v4o ftp://data.pdbj.org/pub/pdb/validation_reports/v4/6v4o | HTTPS FTP |
-Related structure data
Related structure data | 21043MC 6v4nC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Antibody , 2 types, 8 molecules ACDHBEGL
#2: Antibody | Mass: 26840.137 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Antibody | Mass: 23327.992 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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-Protein / Non-polymers , 2 types, 8 molecules IMNW
#1: Protein | Mass: 50038.824 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza B virus / Gene: NA / Production host: Trichoplusia ni (cabbage looper) References: UniProt: A0A4P8YQ63, UniProt: A0A1S5RAG6*PLUS, exo-alpha-sialidase #6: Chemical | ChemComp-CA / |
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-Sugars , 2 types, 8 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-BMA / |
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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 |
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Molecular weight | Value: 0.4 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Conc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 66 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
Particle selection | Num. of particles selected: 459004 | ||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150730 / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | B value: 89 / Protocol: OTHER / Space: REAL / Target criteria: CORRELATION COEFFICIENT | ||||||||||||||||||||
Atomic model building | PDB-ID: 6V4N | ||||||||||||||||||||
Refinement | Highest resolution: 2.8 Å |