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- PDB-6v4o: Structure of human 2E01 Fab in complex with influenza virus neura... -

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Basic information

Entry
Database: PDB / ID: 6v4o
TitleStructure of human 2E01 Fab in complex with influenza virus neuraminidase from B/Phuket/3073/2013
Components
  • (Antibody Fab ...) x 2
  • Neuraminidase
KeywordsVIRAL PROTEIN / neuraminidase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-D-mannopyranose / Neuraminidase / Neuraminidase
Similarity search - Component
Biological speciesInfluenza B virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsDai, Y.N. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: 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
DepositionNov 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-21043
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
I: Neuraminidase
M: Neuraminidase
N: Neuraminidase
W: Neuraminidase
A: Antibody Fab heavy chain
C: Antibody Fab heavy chain
D: Antibody Fab heavy chain
H: Antibody Fab heavy chain
B: Antibody Fab light chain
E: Antibody Fab light chain
G: Antibody Fab light chain
L: Antibody Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)403,40624
Polymers400,82812
Non-polymers2,57912
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Antibody , 2 types, 8 molecules ACDHBEGL

#2: Antibody
Antibody Fab heavy chain


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
Antibody Fab light chain


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
Neuraminidase


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 / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: 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


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
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
#5: Sugar
ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG 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

Component
IDNameTypeEntity IDParent-IDSource
1Structure of human 2E01 Fab in complex with influenza virus neuraminidase from B/Phuket/3073/2013COMPLEX#1-#30MULTIPLE SOURCES
2Influenza virus neuraminidaseCOMPLEX#11RECOMBINANT
3Human antibodyCOMPLEX#2-#31RECOMBINANT
Molecular weightValue: 0.4 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
12Influenza B virus11520B/Phuket/3073/2013
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Trichoplusia ni (cabbage looper)7111
23Homo sapiens (human)9606
Buffer solutionpH: 7.4
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 66 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
4Gctf1.06CTF correction
7UCSF Chimera1.13.1model fitting
12RELION3.0-beta-23D reconstruction
13PHENIX1.15.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 459004
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150730 / Symmetry type: POINT
Atomic model buildingB value: 89 / Protocol: OTHER / Space: REAL / Target criteria: CORRELATION COEFFICIENT
Atomic model buildingPDB-ID: 6V4N

6v4n


Accession code: 6V4N / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.8 Å

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