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

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Basic information

Database: PDB / ID: 6u02
TitleCryoEM-derived model of NA-63 Fab in complex with N9 Shanghai2
  • Fab-63 Heavy ChainFragment antigen-binding
  • Fab-63 Light ChainFragment antigen-binding
  • Neuraminidase
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Neuraminidase / NA / Sh2 / N9Shanghai / N9Sh2 / antibody / Fab / NA-63 / Influenza / VIRAL PROTEIN-IMMUNE SYSTEM complex / H7N9
Function / homology
Function and homology information

exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / exo-alpha-(2->3)-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / integral component of membrane / metal ion binding
Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily / Sialidase, Influenza viruses A/B / Neuraminidase - #10 / 6 Propeller / Neuraminidase / Mainly Beta
Neuraminidase / polysac:dmanpa1-2dmanpa1-2dmanpa1-3[dmanpa1-3[dmanpa1-6]dmanpa1-6]dmanpb1-4dglcpnacb1-4dglcpnacb1-:
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsWard, A.B. / Turner, H.L. / Zhu, X.
Funding support United States, 2items
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.
Validation Report
SummaryFull reportAbout validation report
DepositionAug 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / em_entity_assembly / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _em_entity_assembly.entity_id_list / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure visualization

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Deposited unit
A: Neuraminidase
L: Fab-63 Light Chain
H: Fab-63 Heavy Chain
B: Neuraminidase
C: Fab-63 Light Chain
D: Fab-63 Heavy Chain
E: Neuraminidase
F: Fab-63 Light Chain
G: Fab-63 Heavy Chain
J: Neuraminidase
I: Fab-63 Light Chain
K: Fab-63 Heavy Chain
hetero molecules

Theoretical massNumber of molelcules
Total (without water)388,78324

TypeNameSymmetry operationNumber
identity operation1_5551


#1: Protein
Neuraminidase /

Mass: 48214.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/environment/Shanghai/S1439/2013(H7N9))
Strain: A/environment/Shanghai/S1439/2013(H7N9) / Gene: NA / Cell line (production host): SF6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: S5MF06, exo-alpha-sialidase
#2: Antibody
Fab-63 Light Chain / Fragment antigen-binding

Mass: 23432.014 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetinae gen. sp. (mammal)
#3: Antibody
Fab-63 Heavy Chain / Fragment antigen-binding

Mass: 23547.318 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetinae gen. sp. (mammal)
#4: Polysaccharide
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1WURCSPDB2Glycan 1.1.0
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
Has ligand of interestN

Experimental details


EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

Sample preparation

IDNameTypeEntity IDParent-IDSource
1NA-63 Fab in complex with N9 Shanghai2COMPLEX#1-#30MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Influenza A virus (A/environment/Shanghai/S1439/2013(H7N9))1347105
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Spodoptera frugiperda (fall armyworm)7108
23Cricetinae gen. sp. (mammal)36483
Buffer solutionpH: 7.4
SpecimenConc.: 0.14 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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 FIELDBright-field microscopy / Nominal magnification: 29000 X / Nominal defocus max: 1500 nm / Calibrated defocus min: 500 nm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Image recordingAverage exposure time: 8.25 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 33


EM software
1DoG Pickerparticle selection
2Leginonimage acquisition
4Gctf1.06CTF correction
7UCSF Chimeramodel fitting
9Cootmodel refinement
10Rosetta3.1model refinementrelax
11cryoSPARC2initial Euler assignment
12cryoSPARC2final Euler assignment
14cryoSPARC23D reconstruction
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91117 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 5L14

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