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- EMDB-21043: Structure of human 2E01 Fab in complex with influenza virus neura... -

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Basic information

Entry
Database: EMDB / ID: EMD-21043
TitleStructure of human 2E01 Fab in complex with influenza virus neuraminidase from B/Phuket/3073/2013
Map data
Sample
  • Complex: Structure of human 2E01 Fab in complex with influenza virus neuraminidase from B/Phuket/3073/2013
    • Complex: Influenza virus neuraminidase
      • Protein or peptide: Neuraminidase
    • Complex: Human antibody
      • Protein or peptide: Antibody Fab heavy chain
      • Protein or peptide: Antibody Fab light chain
  • Ligand: beta-D-mannopyranose
  • Ligand: CALCIUM ION
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
Similarity search - Domain/homology
Neuraminidase / Neuraminidase
Similarity search - Component
Biological speciesInfluenza B virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsDai YN / Fremont DH
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, 2019-
Header (metadata) releaseOct 7, 2020-
Map releaseOct 7, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6v4o
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21043.png

Downloads & links

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Map

FileDownload / File: emd_21043.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 250 pix.
= 275. Å		1.1 Å/pix.
x 250 pix.
= 275. Å		1.1 Å/pix.
x 250 pix.
= 275. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0123 / Movie #1: 0.018
Minimum - Maximum-0.0680078 - 0.14400901
Average (Standard dev.)0.0000055949945 (±0.0043729153)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 275.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z275.000275.000275.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ162182277
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0680.1440.000

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Supplemental data

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Sample components

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Entire : Structure of human 2E01 Fab in complex with influenza virus neura...

EntireName: Structure of human 2E01 Fab in complex with influenza virus neuraminidase from B/Phuket/3073/2013
Components
  • Complex: Structure of human 2E01 Fab in complex with influenza virus neuraminidase from B/Phuket/3073/2013
    • Complex: Influenza virus neuraminidase
      • Protein or peptide: Neuraminidase
    • Complex: Human antibody
      • Protein or peptide: Antibody Fab heavy chain
      • Protein or peptide: Antibody Fab light chain
  • Ligand: beta-D-mannopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: Structure of human 2E01 Fab in complex with influenza virus neura...

SupramoleculeName: Structure of human 2E01 Fab in complex with influenza virus neuraminidase from B/Phuket/3073/2013
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 400 KDa

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Supramolecule #2: Influenza virus neuraminidase

SupramoleculeName: Influenza virus neuraminidase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Influenza B virus / Strain: B/Phuket/3073/2013

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Supramolecule #3: Human antibody

SupramoleculeName: Human antibody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Neuraminidase

MacromoleculeName: Neuraminidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: exo-alpha-sialidase
Source (natural)Organism: Influenza B virus
Molecular weightTheoretical: 50.038824 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: ADPHHHHHHS SSDYSDLQRV KQELLEEVKK ELQKVKEEII EAFVQELRKR GSLVPRGSPS RWTYPRLSCP GSTFQKALLI SPHRFGETK GNSAPLIIRE PFIACGPKEC KHFALTHYAA QPGGYYNGTR EDRNKLRHLI SVKLGKIPTV ENSIFHMAAW S GSACHDGR ...String:
ADPHHHHHHS SSDYSDLQRV KQELLEEVKK ELQKVKEEII EAFVQELRKR GSLVPRGSPS RWTYPRLSCP GSTFQKALLI SPHRFGETK GNSAPLIIRE PFIACGPKEC KHFALTHYAA QPGGYYNGTR EDRNKLRHLI SVKLGKIPTV ENSIFHMAAW S GSACHDGR EWTYIGVDGP DSNALLKIKY GEAYTDTYHS YAKNILRTQE SACNCIGGDC YLMITDGPAS GISECRFLKI RE GRIIKEI FPTGRVKHTE ECTCGFASNK TIECACRDNS YTAKRPFVKL NVETDTAEIR LMCTKTYLDT PRPNDGSITG PCE SDGDEG SGGIKGGFVH QRMASKIGRW YSRTMSKTKR MGMGLYVKYD GDPWTDSEAL ALSGVMVSME EPGWYSFGFE IKDK KCDVP CIGIEMVHDG GKTTWHSAAT AIYCLMGSGQ LLWDTVTGVN MTL

UniProtKB: Neuraminidase

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Macromolecule #2: Antibody Fab heavy chain

MacromoleculeName: Antibody Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.840137 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVQSGAE VKKPGSSVKV SCKASGYTFI NHALSWVRQA PGQGLEWVGG IIPIFGLAKY GQKFQDRVTI TADESTKTAY MDLRSLRSD DTAVYYCARD TVAVYEDFDW SSPYFFYMDV WGKGTTVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT ...String:
EVQLVQSGAE VKKPGSSVKV SCKASGYTFI NHALSWVRQA PGQGLEWVGG IIPIFGLAKY GQKFQDRVTI TADESTKTAY MDLRSLRSD DTAVYYCARD TVAVYEDFDW SSPYFFYMDV WGKGTTVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCRSLVP RG SSGHHHH HH

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Macromolecule #3: Antibody Fab light chain

MacromoleculeName: Antibody Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.327992 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPAT LSLFPGERAT LSCRASQSAG SKSLAWYQHK VGQPPRLLIN GASSRATGIP DRFSGSGSGP DFNLTISRLE PEDFAVYYC QRYGTSLVTF GGGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
EIVLTQSPAT LSLFPGERAT LSCRASQSAG SKSLAWYQHK VGQPPRLLIN GASSRATGIP DRFSGSGSGP DFNLTISRLE PEDFAVYYC QRYGTSLVTF GGGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #5: beta-D-mannopyranose

MacromoleculeName: beta-D-mannopyranose / type: ligand / ID: 5 / Number of copies: 4 / Formula: BMA
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BMA:
beta-D-mannopyranose

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Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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

Concentration0.15 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 459004
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0-beta-2) / Number images used: 150730
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6v4n


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 89 / Target criteria: CORRELATION COEFFICIENT
Output model

PDB-6v4o:
Structure of human 2E01 Fab in complex with influenza virus neuraminidase from B/Phuket/3073/2013

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