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- PDB-8g30: N2 neuraminidase of A/Tanzania/205/2010 H3N2 in complex with 4 FN... -

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Basic information

Entry
Database: PDB / ID: 8g30
TitleN2 neuraminidase of A/Tanzania/205/2010 H3N2 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 / virus / 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 speciesHomo sapiens (human)
Influenza A virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDang, H.V. / Snell, G.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
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 6, 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
E: FNI19 Fab heavy chain
F: FNI19 Fab light chain
M: Neuraminidase
G: FNI19 Fab heavy chain
I: FNI19 Fab light chain
N: Neuraminidase
H: FNI19 Fab heavy chain
L: FNI19 Fab light chain
O: Neuraminidase
J: FNI19 Fab heavy chain
K: FNI19 Fab light chain
P: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)428,53541
Polymers411,98812
Non-polymers16,54729
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11E
21G
12E
22H
13E
23J
14F
24I
15F
25L
16F
26K
17M
27N
18M
28O
19M
29P
110M
210N
111M
211O
112M
212P
113G
213H
114G
214J
115I
215L
116I
216K
117N
217O
118N
218P
119H
219J
120L
220K
121O
221P

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALSERSEREA2 - 1302 - 130
21VALVALSERSERGD2 - 1302 - 130
12VALVALSERSEREA2 - 1302 - 130
22VALVALSERSERHG2 - 1302 - 130
13VALVALSERSEREA2 - 1302 - 130
23VALVALSERSERJJ2 - 1302 - 130
14GLUGLUTHRTHRFB1 - 1101 - 110
24GLUGLUTHRTHRIE1 - 1101 - 110
15GLUGLUTHRTHRFB1 - 1101 - 110
25GLUGLUTHRTHRLH1 - 1101 - 110
16GLUGLUTHRTHRFB1 - 1101 - 110
26GLUGLUTHRTHRKK1 - 1101 - 110
17ALAALAASPASPMC82 - 243105 - 266
27ALAALAASPASPNF82 - 243105 - 266
18ALAALAASPASPMC82 - 243105 - 266
28ALAALAASPASPOI82 - 243105 - 266
19ALAALAASPASPMC82 - 243105 - 266
29ALAALAASPASPPL82 - 243105 - 266
110ALAALAPROPROMC250 - 468273 - 491
210ALAALAPROPRONF250 - 468273 - 491
111ALAALAPROPROMC250 - 468273 - 491
211ALAALAPROPROOI250 - 468273 - 491
112ALAALAPROPROMC250 - 468273 - 491
212ALAALAPROPROPL250 - 468273 - 491
113VALVALSERSERGD2 - 1302 - 130
213VALVALSERSERHG2 - 1302 - 130
114VALVALSERSERGD2 - 1302 - 130
214VALVALSERSERJJ2 - 1302 - 130
115GLUGLUTHRTHRIE1 - 1101 - 110
215GLUGLUTHRTHRLH1 - 1101 - 110
116GLUGLUTHRTHRIE1 - 1101 - 110
216GLUGLUTHRTHRKK1 - 1101 - 110
117ALAALAILEILENF82 - 469105 - 492
217ALAALAILEILEOI82 - 469105 - 492
118ALAALAILEILENF82 - 469105 - 492
218ALAALAILEILEPL82 - 469105 - 492
119VALVALSERSERHG2 - 1302 - 130
219VALVALSERSERJJ2 - 1302 - 130
120GLUGLUTHRTHRLH1 - 1101 - 110
220GLUGLUTHRTHRKK1 - 1101 - 110
121ALAALAILEILEOI82 - 469105 - 492
221ALAALAILEILEPL82 - 469105 - 492

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21

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Components

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Antibody , 2 types, 8 molecules EGHJFILK

#1: 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)
#2: 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 MNOP

#3: Protein
Neuraminidase


Mass: 54755.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: A/Tanzania/205/2010 H3N2 / Source: (gene. exp.) Influenza A virus / Gene: NA / Production host: Homo sapiens (human) / References: UniProt: V9SU56
#8: 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 , 4 types, 24 molecules

#4: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: 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
#7: 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

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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: N2 neuraminidase of A/Tanzania/205/2010 H3N2 in complex with 4 FNI19 Fab molecules
Type: COMPLEX
Details: Fab fragment generated by proteolytic cleavage of FNI19 IgG1 antibody
Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.42 kDa/nm / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Influenza A virus11320
31Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Cricetulus griseus (Chinese hamster)10029
Buffer solutionpH: 8 / Details: 50 mM Tris-HCl, 150 mM NaCl, 10 mM CaCl2, pH 8.0
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
250 mMTrisC4H11NO31
310 mMcalcium chlorideCaCl21
SpecimenConc.: 0.2 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

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 19.35 e/Å2 / Film or detector model: FEI FALCON IV (4k 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 170901 / Symmetry type: POINT
RefinementResolution: 3.1→174.28 Å / Cor.coef. Fo:Fc: 0.909 / SU B: 10.118 / SU ML: 0.178 / ESU R: 0.38
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.34631 --
obs0.34631 245419 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 113.566 Å2
Refinement stepCycle: 1 / Total: 20449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0140.01321029
ELECTRON MICROSCOPYr_bond_other_d0.0010.01418718
ELECTRON MICROSCOPYr_angle_refined_deg1.8911.72328734
ELECTRON MICROSCOPYr_angle_other_deg1.4821.64743382
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.93852490
ELECTRON MICROSCOPYr_dihedral_angle_2_deg30.63621.7651020
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.585153150
ELECTRON MICROSCOPYr_dihedral_angle_4_deg16.59215136
ELECTRON MICROSCOPYr_chiral_restr0.0880.23002
ELECTRON MICROSCOPYr_gen_planes_refined0.010.0223218
ELECTRON MICROSCOPYr_gen_planes_other0.0030.024885
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_it14.0510.6379999
ELECTRON MICROSCOPYr_mcbond_other14.0510.6349998
ELECTRON MICROSCOPYr_mcangle_it19.58616.02412476
ELECTRON MICROSCOPYr_mcangle_other19.58516.02712477
ELECTRON MICROSCOPYr_scbond_it16.49213.27811030
ELECTRON MICROSCOPYr_scbond_other16.49113.2811031
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other25.69419.2716259
ELECTRON MICROSCOPYr_long_range_B_refined32.54585577
ELECTRON MICROSCOPYr_long_range_B_other32.54485578
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)
11E79020.02
12G79020.02
21E79020.02
22H79020.02
31E79060.02
32J79060.02
41F68800.02
42I68800.02
51F68780.01
52L68780.01
61F68720.01
62K68720.01
71M101640.01
72N101640.01
81M101680.01
82O101680.01
91M101660.01
92P101660.01
101M142820.02
102N142820.02
111M142820.02
112O142820.02
121M142820.02
122P142820.02
131G79540
132H79540
141G79520
142J79520
151I69080.02
152L69080.02
161I69020.02
162K69020.02
171N266800
172O266800
181N266780
182P266780
191H79520
192J79520
201L69060
202K69060
211O266780
212P266780
LS refinement shellResolution: 3.1→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.539 18091 -
obs--100 %

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