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- EMDB-20594: CryoEM-derived model of NA-63 Fab in complex with N9 Shanghai2 -

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Basic information

Entry
Database: EMDB / ID: EMD-20594
TitleCryoEM-derived model of NA-63 Fab in complex with N9 Shanghai2
Map dataCryoEM map of N9 Shanghai2 in complex with Fab-63
Sample
  • Complex: NA-63 Fab in complex with N9 Shanghai2
    • Complex: N9 Shanghai2
      • Protein or peptide: Neuraminidase
    • Complex: NA-63 Fab
      • Protein or peptide: Fab-63 Light Chain
      • Protein or peptide: Fab-63 Heavy Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNeuraminidase / NA / Sh2 / N9Shanghai / N9Sh2 / antibody / Fab / NA-63 / Influenza / VIRAL PROTEIN-IMMUNE SYSTEM complex / H7N9
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza A virus (A/environment/Shanghai/S1439/2013(H7N9)) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsWard AB / Turner HL
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI117905 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN 272201400024C United States
CitationJournal: Cell Host Microbe / Year: 2019
Title: Structural Basis of Protection against H7N9 Influenza Virus by Human Anti-N9 Neuraminidase Antibodies.
Authors: Xueyong Zhu / Hannah L Turner / Shanshan Lang / Ryan McBride / Sandhya Bangaru / Iuliia M Gilchuk / Wenli Yu / James C Paulson / James E Crowe / Andrew B Ward / Ian A Wilson /
Abstract: Influenza virus neuraminidase (NA) is a major target for small-molecule antiviral drugs. Antibodies targeting the NA surface antigen could also inhibit virus entry and egress to provide host ...Influenza virus neuraminidase (NA) is a major target for small-molecule antiviral drugs. Antibodies targeting the NA surface antigen could also inhibit virus entry and egress to provide host protection. However, our understanding of the nature and range of target epitopes is limited because of a lack of human antibody structures with influenza neuraminidase. Here, we describe crystal and cryogenic electron microscopy (cryo-EM) structures of NAs from human-infecting avian H7N9 viruses in complex with five human anti-N9 antibodies, systematically defining several antigenic sites and antibody epitope footprints. These antibodies either fully or partially block the NA active site or bind to epitopes distant from the active site while still showing neuraminidase inhibition. The inhibition of antibodies to NAs was further analyzed by glycan array and solution-based NA activity assays. Together, these structural studies provide insights into protection by anti-NA antibodies and templates for the development of NA-based influenza virus vaccines and therapeutics.
History
DepositionAug 13, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseDec 4, 2019-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6u02
  • Surface level: 1.01
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20594.png

Downloads & links

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Map

FileDownload / File: emd_20594.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of N9 Shanghai2 in complex with Fab-63
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 320 pix.
= 329.6 Å		1.03 Å/pix.
x 320 pix.
= 329.6 Å		1.03 Å/pix.
x 320 pix.
= 329.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.01 / Movie #1: 1.01
Minimum - Maximum-3.9822848 - 5.9704328
Average (Standard dev.)-0.00029748358 (±0.15957654)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 329.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z329.600329.600329.600
α/β/γ90.00090.00090.000
start NX/NY/NZ111-94150
NX/NY/NZ111123111
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-3.9825.970-0.000

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Supplemental data

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Mask #1

Fileemd_20594_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of N9 Shanghai2 in complex with Fab-63

Fileemd_20594_half_map_1.map
AnnotationHalf map A of N9 Shanghai2 in complex with Fab-63
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of N9 Shanghai2 in complex with Fab-63

Fileemd_20594_half_map_2.map
AnnotationHalf map B of N9 Shanghai2 in complex with Fab-63
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NA-63 Fab in complex with N9 Shanghai2

EntireName: NA-63 Fab in complex with N9 Shanghai2
Components
  • Complex: NA-63 Fab in complex with N9 Shanghai2
    • Complex: N9 Shanghai2
      • Protein or peptide: Neuraminidase
    • Complex: NA-63 Fab
      • Protein or peptide: Fab-63 Light Chain
      • Protein or peptide: Fab-63 Heavy Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: NA-63 Fab in complex with N9 Shanghai2

SupramoleculeName: NA-63 Fab in complex with N9 Shanghai2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: N9 Shanghai2

SupramoleculeName: N9 Shanghai2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Influenza A virus (A/environment/Shanghai/S1439/2013(H7N9))

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Supramolecule #3: NA-63 Fab

SupramoleculeName: NA-63 Fab / 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 A virus (A/environment/Shanghai/S1439/2013(H7N9))
Strain: A/environment/Shanghai/S1439/2013(H7N9)
Molecular weightTheoretical: 48.214508 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: LKPGCNCSHS QPETTNTSQT IINNYYNETN ITNIQMEERT SRNFNNLTKG LCTINSWHIY GKDNAVRIGE SSDVLVTREP YVSCDPDEC RFYALSQGTT IRGKHSNGTI HDRSQYRALI SWPLSSPPTV YNSRVECIGW SSTSCHDGKS RMSICISGPN N NASAVVWY ...String:
LKPGCNCSHS QPETTNTSQT IINNYYNETN ITNIQMEERT SRNFNNLTKG LCTINSWHIY GKDNAVRIGE SSDVLVTREP YVSCDPDEC RFYALSQGTT IRGKHSNGTI HDRSQYRALI SWPLSSPPTV YNSRVECIGW SSTSCHDGKS RMSICISGPN N NASAVVWY NRRPVAEINT WARNILRTQE SECVCHNGVC PVVFTDGSAT GPADTRIYYF KEGKILKWES LTGTAKHIEE CS CYGERTG ITCTCRDNWQ GSNRPVIQID PVAMTHTSQY ICSPVLTDNP RPNDPNIGKC NDPYPGNNNN GVKGFSYLDG ANT WLGRTI STASRSGYEM LKVPNALTDD RSKPIQGQTI VLNADWSGYS GSFMDYWAEG DCYRACFYVE LIRGRPKEDK VWWT SNSIV SMCSSTEFLG QWNWPDGAKI EYFL

UniProtKB: Neuraminidase

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Macromolecule #2: Fab-63 Light Chain

MacromoleculeName: Fab-63 Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.432014 KDa
Recombinant expressionOrganism: Cricetinae gen. sp. (mammal)
SequenceString: DIVMTQSPSS LSASVGDRVT ITCRASQSIS TYLNWYQQKP GKAPKLLIYA ASSLQGGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSYSTPLYTF GQGTKLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIVMTQSPSS LSASVGDRVT ITCRASQSIS TYLNWYQQKP GKAPKLLIYA ASSLQGGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSYSTPLYTF GQGTKLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #3: Fab-63 Heavy Chain

MacromoleculeName: Fab-63 Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.547318 KDa
Recombinant expressionOrganism: Cricetinae gen. sp. (mammal)
SequenceString: EVQLVESGGG LVQPGGSLRL SCAASGFTFS SYWMSWVRQA PGKGLDWVAN IKQDGSEKYY VDSVKGRFTI SRHNAKNSLY LQMNSLRAE DTAVYYCASS TAAEFFDYWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String:
EVQLVESGGG LVQPGGSLRL SCAASGFTFS SYWMSWVRQA PGKGLDWVAN IKQDGSEKYY VDSVKGRFTI SRHNAKNSLY LQMNSLRAE DTAVYYCASS TAAEFFDYWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP KSC

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration0.14 mg/mL
BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 8.25 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 91117
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5l14


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

PDB-6u02:
CryoEM-derived model of NA-63 Fab in complex with N9 Shanghai2

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