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- PDB-8g3v: N2 neuraminidase of A/Hong_Kong/2671/2019 in complex with 4 FNI19... -

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Basic information

Entry
Database: PDB / ID: 8g3v
TitleN2 neuraminidase of A/Hong_Kong/2671/2019 in complex with 4 FNI19 Fab molecules
Components
  • FNI19 Fab heavy chain
  • FNI19 Fab light chain
  • Neuraminidase
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / viral glycoprotein / antibody / Fab / influenza / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsDang, H.V. / Snell, G.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nature / Year: 2023
Title: A pan-influenza antibody inhibiting neuraminidase via receptor mimicry.
Authors: Corey Momont / Ha V Dang / Fabrizia Zatta / Kevin Hauser / Caihong Wang / Julia di Iulio / Andrea Minola / Nadine Czudnochowski / Anna De Marco / Kaitlin Branch / David Donermeyer / Siddhant ...Authors: Corey Momont / Ha V Dang / Fabrizia Zatta / Kevin Hauser / Caihong Wang / Julia di Iulio / Andrea Minola / Nadine Czudnochowski / Anna De Marco / Kaitlin Branch / David Donermeyer / Siddhant Vyas / Alex Chen / Elena Ferri / Barbara Guarino / Abigail E Powell / Roberto Spreafico / Samantha S Yim / Dale R Balce / Istvan Bartha / Marcel Meury / Tristan I Croll / David M Belnap / Michael A Schmid / William Timothy Schaiff / Jessica L Miller / Elisabetta Cameroni / Amalio Telenti / Herbert W Virgin / Laura E Rosen / Lisa A Purcell / Antonio Lanzavecchia / Gyorgy Snell / Davide Corti / Matteo Samuele Pizzuto /
Abstract: Rapidly evolving influenza A viruses (IAVs) and influenza B viruses (IBVs) are major causes of recurrent lower respiratory tract infections. Current influenza vaccines elicit antibodies ...Rapidly evolving influenza A viruses (IAVs) and influenza B viruses (IBVs) are major causes of recurrent lower respiratory tract infections. Current influenza vaccines elicit antibodies predominantly to the highly variable head region of haemagglutinin and their effectiveness is limited by viral drift and suboptimal immune responses. Here we describe a neuraminidase-targeting monoclonal antibody, FNI9, that potently inhibits the enzymatic activity of all group 1 and group 2 IAVs, as well as Victoria/2/87-like, Yamagata/16/88-like and ancestral IBVs. FNI9 broadly neutralizes seasonal IAVs and IBVs, including the immune-evading H3N2 strains bearing an N-glycan at position 245, and shows synergistic activity when combined with anti-haemagglutinin stem-directed antibodies. Structural analysis reveals that D107 in the FNI9 heavy chain complementarity-determinant region 3 mimics the interaction of the sialic acid carboxyl group with the three highly conserved arginine residues (R118, R292 and R371) of the neuraminidase catalytic site. FNI9 demonstrates potent prophylactic activity against lethal IAV and IBV infections in mice. The unprecedented breadth and potency of the FNI9 monoclonal antibody supports its development for the prevention of influenza illness by seasonal and pandemic viruses.
History
DepositionFeb 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 28, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Neuraminidase
A: FNI19 Fab heavy chain
L: FNI19 Fab light chain
H: Neuraminidase
B: FNI19 Fab heavy chain
M: FNI19 Fab light chain
I: Neuraminidase
C: FNI19 Fab heavy chain
N: FNI19 Fab light chain
J: Neuraminidase
D: FNI19 Fab heavy chain
O: FNI19 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)422,20537
Polymers411,25112
Non-polymers10,95425
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11G
21H
12G
22I
13G
23J
14A
24B
15A
25C
16A
26D
17L
27M
18L
28N
19L
29O
110H
210I
111H
211J
112B
212C
113B
213D
114M
214N
115M
215O
116I
216J
117C
217D
118N
218O

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALATHRTHRGA82 - 469105 - 492
21ALAALATHRTHRHD82 - 469105 - 492
12ALAALATHRTHRGA82 - 469105 - 492
22ALAALATHRTHRIG82 - 469105 - 492
13ALAALATHRTHRGA82 - 469105 - 492
23ALAALATHRTHRJJ82 - 469105 - 492
14VALVALALAALAAB2 - 1292 - 129
24VALVALALAALABE2 - 1292 - 129
15VALVALALAALAAB2 - 1292 - 129
25VALVALALAALACH2 - 1292 - 129
16VALVALALAALAAB2 - 1292 - 129
26VALVALALAALADK2 - 1292 - 129
17GLUGLUARGARGLC1 - 1091 - 109
27GLUGLUARGARGMF1 - 1091 - 109
18GLUGLUARGARGLC1 - 1091 - 109
28GLUGLUARGARGNI1 - 1091 - 109
19GLUGLUARGARGLC1 - 1091 - 109
29GLUGLUARGARGOL1 - 1091 - 109
110ALAALATHRTHRHD82 - 469105 - 492
210ALAALATHRTHRIG82 - 469105 - 492
111ALAALATHRTHRHD82 - 469105 - 492
211ALAALATHRTHRJJ82 - 469105 - 492
112VALVALALAALABE2 - 1292 - 129
212VALVALALAALACH2 - 1292 - 129
113VALVALALAALABE2 - 1292 - 129
213VALVALALAALADK2 - 1292 - 129
114GLUGLUARGARGMF1 - 1091 - 109
214GLUGLUARGARGNI1 - 1091 - 109
115GLUGLUARGARGMF1 - 1091 - 109
215GLUGLUARGARGOL1 - 1091 - 109
116ALAALATHRTHRIG82 - 469105 - 492
216ALAALATHRTHRJJ82 - 469105 - 492
117VALVALALAALACH2 - 1292 - 129
217VALVALALAALADK2 - 1292 - 129
118GLUGLUARGARGNI1 - 1091 - 109
218GLUGLUARGARGOL1 - 1091 - 109

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18

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Components

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Antibody , 2 types, 8 molecules ABCDLMNO

#2: Antibody
FNI19 Fab heavy chain


Mass: 24692.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody
FNI19 Fab light chain


Mass: 23549.264 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Protein / Non-polymers , 2 types, 9 molecules GHIJ

#1: Protein
Neuraminidase /


Mass: 54570.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: A/Hong_Kong/2671/2019 / Source: (gene. exp.) Influenza A virus / Gene: NA / Production host: Homo sapiens (human) / References: UniProt: A0A411D019
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION

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Sugars , 3 types, 20 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.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Polysaccharide
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...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: 1397.245 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY

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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

ComponentName: 4 FNI19 Fabs in complex with tetrameric N2 NA protein from A/Hong_Kong/2671/2019 strain
Type: COMPLEX
Details: Fab fragment generated by proteolytic cleavage of FNI19 IgG1 antibody
Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.42 MDa / Experimental value: NO
Source (natural)Organism: Influenza A virus
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8 / Details: 50 mM Tris-HCl, 150 mM NaCl, 10 mM CaCl2, pH 8.0
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisC4H11NO31
2150 mMsodium chlorideNaClSodium chloride1
310 mMcalcium chlorideCaCl21
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 52.61 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0267 / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 885566 / Symmetry type: POINT
RefinementResolution: 2.21→141.1 Å / Cor.coef. Fo:Fc: 0.813 / SU B: 4.425 / SU ML: 0.104 / ESU R: 0.185
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.35217 --
obs0.35217 436047 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 54.201 Å2
Refinement stepCycle: 1 / Total: 20045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.010.01320592
ELECTRON MICROSCOPYr_bond_other_d00.01418431
ELECTRON MICROSCOPYr_angle_refined_deg1.671.69428080
ELECTRON MICROSCOPYr_angle_other_deg1.4091.62442595
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.81252488
ELECTRON MICROSCOPYr_dihedral_angle_2_deg30.78321.7581024
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.101153148
ELECTRON MICROSCOPYr_dihedral_angle_4_deg16.71815136
ELECTRON MICROSCOPYr_chiral_restr0.0890.22844
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.0223072
ELECTRON MICROSCOPYr_gen_planes_other0.0020.024887
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it4.5065.4049988
ELECTRON MICROSCOPYr_mcbond_other4.5065.4029987
ELECTRON MICROSCOPYr_mcangle_it6.6528.11812464
ELECTRON MICROSCOPYr_mcangle_other6.6518.1212465
ELECTRON MICROSCOPYr_scbond_it5.4326.02810604
ELECTRON MICROSCOPYr_scbond_other5.4326.0310605
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other8.5428.8115617
ELECTRON MICROSCOPYr_long_range_B_refined12.24485334
ELECTRON MICROSCOPYr_long_range_B_other12.24485335
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: ELECTRON MICROSCOPY / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11G267580.01
12H267580.01
21G267720.01
22I267720.01
31G267660.02
32J267660.02
41A81760
42B81760
51A81700.02
52C81700.02
61A81740.02
62D81740.02
71L68140
72M68140
81L68100
82N68100
91L67960.02
92O67960.02
101H267780.01
102I267780.01
111H267480.02
112J267480.02
121B81700.02
122C81700.02
131B81720.02
132D81720.02
141M68080
142N68080
151M67940.02
152O67940.02
161I267860.01
162J267860.01
171C81740
172D81740
181N67960.02
182O67960.02
LS refinement shellResolution: 2.21→2.267 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.053 32375 -
obs--100 %

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