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- PDB-8g3z: Neuraminidase of B/Massachusetts/02/2012 (Yamagata) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8g3z
TitleNeuraminidase of B/Massachusetts/02/2012 (Yamagata) in complex with 4 FNI17 Fab molecules
Components
  • FNI17 Fab heavy chain
  • FNI17 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 / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Influenza B virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 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 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
H: FNI17 Fab heavy chain
L: FNI17 Fab light chain
E: FNI17 Fab heavy chain
F: FNI17 Fab light chain
G: FNI17 Fab heavy chain
I: FNI17 Fab light chain
J: FNI17 Fab heavy chain
K: FNI17 Fab light chain
A: Neuraminidase
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)414,79125
Polymers412,82112
Non-polymers1,97013
Water0
1


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

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
11VALVALSERSERHA2 - 1302 - 130
21VALVALSERSEREC2 - 1302 - 130
12VALVALSERSERHA2 - 1302 - 130
22VALVALSERSERGE2 - 1302 - 130
13VALVALSERSERHA2 - 1302 - 130
23VALVALSERSERJG2 - 1302 - 130
14ILEILETHRTHRLB2 - 1102 - 110
24ILEILETHRTHRFD2 - 1102 - 110
15ILEILETHRTHRLB2 - 1102 - 110
25ILEILETHRTHRIF2 - 1102 - 110
16ILEILETHRTHRLB2 - 1102 - 110
26ILEILETHRTHRKH2 - 1102 - 110
17VALVALSERSEREC2 - 1302 - 130
27VALVALSERSERGE2 - 1302 - 130
18VALVALSERSEREC2 - 1302 - 130
28VALVALSERSERJG2 - 1302 - 130
19ILEILETHRTHRFD2 - 1102 - 110
29ILEILETHRTHRIF2 - 1102 - 110
110ILEILETHRTHRFD2 - 1102 - 110
210ILEILETHRTHRKH2 - 1102 - 110
111VALVALSERSERGE2 - 1302 - 130
211VALVALSERSERJG2 - 1302 - 130
112ILEILETHRTHRIF2 - 1102 - 110
212ILEILETHRTHRKH2 - 1102 - 110
113GLUGLULEULEUAI77 - 466107 - 496
213GLUGLULEULEUBJ77 - 466107 - 496
114GLUGLULEULEUAI77 - 466107 - 496
214GLUGLULEULEUCK77 - 466107 - 496
115GLUGLULEULEUAI77 - 466107 - 496
215GLUGLULEULEUDL77 - 466107 - 496
116GLUGLULEULEUBJ77 - 466107 - 496
216GLUGLULEULEUCK77 - 466107 - 496
117GLUGLULEULEUBJ77 - 466107 - 496
217GLUGLULEULEUDL77 - 466107 - 496
118GLUGLULEULEUCK77 - 466107 - 496
218GLUGLULEULEUDL77 - 466107 - 496

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

#1: Antibody
FNI17 Fab heavy chain


Mass: 24580.527 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
FNI17 Fab light chain


Mass: 23479.061 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: Protein
Neuraminidase /


Mass: 55145.559 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: B/Massachusetts/02/2012 (Yamagata) / Source: (gene. exp.) Influenza B virus / Gene: NA / Production host: Homo sapiens (human) / References: UniProt: A0A0D6A730
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: 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
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 FNI17 Fabs in complex with tetrameric NA protein from B/Massachusetts/02/2012 (Yamagata) strain
Type: COMPLEX
Details: Fab fragment generated by proteolytic cleavage of FNI17 IgG1 antibody
Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.42 kDa/nm / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Influenza A virus11320
31Influenza B virus11520
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Homo sapiens (human)9606
Buffer solutionpH: 8 / Details: 50 mM Tris-HCl, 150 mM NaCl, 10 mM CaCl2, pH 8.0
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaClSodium chloride1
250 mMTrisC4H11NO31
310 mMcalcium chlorideCaCl21
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 177249 / Symmetry type: POINT
RefinementResolution: 2.3→178.76 Å / Cor.coef. Fo:Fc: 0.898 / SU B: 5.206 / SU ML: 0.117 / ESU R: 0.159
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.34412 --
obs0.34412 563160 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 55.63 Å2
Refinement stepCycle: 1 / Total: 19485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.01319999
ELECTRON MICROSCOPYr_bond_other_d0.0320.01518270
ELECTRON MICROSCOPYr_angle_refined_deg1.5951.65627121
ELECTRON MICROSCOPYr_angle_other_deg1.341.58642239
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.9852500
ELECTRON MICROSCOPYr_dihedral_angle_2_deg29.6121.369964
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.608153256
ELECTRON MICROSCOPYr_dihedral_angle_4_deg19.21815132
ELECTRON MICROSCOPYr_chiral_restr0.0880.22620
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.0222649
ELECTRON MICROSCOPYr_gen_planes_other0.0020.024670
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_it2.5375.79310036
ELECTRON MICROSCOPYr_mcbond_other2.5375.79310035
ELECTRON MICROSCOPYr_mcangle_it4.2238.69412524
ELECTRON MICROSCOPYr_mcangle_other4.2238.69412525
ELECTRON MICROSCOPYr_scbond_it3.0266.0399963
ELECTRON MICROSCOPYr_scbond_other3.0266.0399964
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other5.0858.91514598
ELECTRON MICROSCOPYr_long_range_B_refined9.67582906
ELECTRON MICROSCOPYr_long_range_B_other9.67582907
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)
11H78340.07
12E78340.07
21H77880.08
22G77880.08
31H78240.07
32J78240.07
41L65000.1
42F65000.1
51L64980.1
52I64980.1
61L63640.12
62K63640.12
71E79600.04
72G79600.04
81E78660.06
82J78660.06
91F66360.08
92I66360.08
101F65120.1
102K65120.1
111G78380.07
112J78380.07
121I64960.1
122K64960.1
131A256440.09
132B256440.09
141A255360.08
142C255360.08
151A259480.07
152D259480.07
161B254100.09
162C254100.09
171B255540.09
172D255540.09
181C255060.09
182D255060.09
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.817 41717 -
obs--100 %

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