[English] 日本語
Yorodumi
- EMDB-29711: Neuraminidase of B/Massachusetts/02/2012 (Yamagata) in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-29711
TitleNeuraminidase of B/Massachusetts/02/2012 (Yamagata) in complex with 4 FNI17 Fab molecules
Map data
Sample
  • Complex: 4 FNI17 Fabs in complex with tetrameric NA protein from B/Massachusetts/02/2012 (Yamagata) strain
    • Protein or peptide: FNI17 Fab heavy chain
    • Protein or peptide: FNI17 Fab light chain
    • Protein or peptide: Neuraminidase
  • Ligand: CALCIUM IONCalcium
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsviral 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 speciesInfluenza A virus / Homo sapiens (human) / Influenza B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsDang HV / Snell G
Funding support United States, 1 items
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, 2023-
Header (metadata) releaseMay 31, 2023-
Map releaseMay 31, 2023-
UpdateJun 28, 2023-
Current statusJun 28, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_29711.png

Downloads & links

-
Map

FileDownload / File: emd_29711.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.18550974 - 0.6349805
Average (Standard dev.)0.0023227981 (±0.023404801)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 262.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_29711_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_29711_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_29711_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_29711_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : 4 FNI17 Fabs in complex with tetrameric NA protein from B/Massach...

EntireName: 4 FNI17 Fabs in complex with tetrameric NA protein from B/Massachusetts/02/2012 (Yamagata) strain
Components
  • Complex: 4 FNI17 Fabs in complex with tetrameric NA protein from B/Massachusetts/02/2012 (Yamagata) strain
    • Protein or peptide: FNI17 Fab heavy chain
    • Protein or peptide: FNI17 Fab light chain
    • Protein or peptide: Neuraminidase
  • Ligand: CALCIUM IONCalcium
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: 4 FNI17 Fabs in complex with tetrameric NA protein from B/Massach...

SupramoleculeName: 4 FNI17 Fabs in complex with tetrameric NA protein from B/Massachusetts/02/2012 (Yamagata) strain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Fab fragment generated by proteolytic cleavage of FNI17 IgG1 antibody
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 0.42 kDa/nm

-
Macromolecule #1: FNI17 Fab heavy chain

MacromoleculeName: FNI17 Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.580527 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLVQSGAE VKRPGSSVKV SCKPSGGTFS NNVISWVRQA PGQGLEWMGG IIPTSGIANY AQKFQGRVAI IADKSTSTVY MALSSLRSE DSAVYFCARA RSDYFNRDLG WEDYYFENWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS ...String:
QVQLVQSGAE VKRPGSSVKV SCKPSGGTFS NNVISWVRQA PGQGLEWMGG IIPTSGIANY AQKFQGRVAI IADKSTSTVY MALSSLRSE DSAVYFCARA RSDYFNRDLG WEDYYFENWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP KSC

-
Macromolecule #2: FNI17 Fab light chain

MacromoleculeName: FNI17 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.479061 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EIVMTQSPAT LSVSPGERAT LSCRASQSVG SSLVWYQQKP GQAPRLLIYG ASTRATGVPA RFSGSGSGTE FTLTISSLQS EDFAVYYCQ HYNNWPPWTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
EIVMTQSPAT LSVSPGERAT LSCRASQSVG SSLVWYQQKP GQAPRLLIYG ASTRATGVPA RFSGSGSGTE FTLTISSLQS EDFAVYYCQ HYNNWPPWTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

-
Macromolecule #3: Neuraminidase

MacromoleculeName: Neuraminidase / type: protein_or_peptide / ID: 3 / Details: B/Massachusetts/02/2012 (Yamagata) / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Influenza B virus
Molecular weightTheoretical: 55.145559 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METDTLLLWV LLLWVPGSTG DHHHHHHGSG LNDIFEAQKI EWHEGSIINE TADDIVYRLT VIIDDRYESL KNLITLRADR LEMIINDNV STILASGLVP RGSGSLPEPE WTYPRLSCPG STFQKALLIS PHRFGEIKGN SAPLIIREPF IACGPTECKH F ALTHYAAQ ...String:
METDTLLLWV LLLWVPGSTG DHHHHHHGSG LNDIFEAQKI EWHEGSIINE TADDIVYRLT VIIDDRYESL KNLITLRADR LEMIINDNV STILASGLVP RGSGSLPEPE WTYPRLSCPG STFQKALLIS PHRFGEIKGN SAPLIIREPF IACGPTECKH F ALTHYAAQ PGGYYNGTRE DRNKLRHLIS VKLGKIPTVE NSIFHMAAWS GSACHDGKEW TYIGVDGPDS NALLKIKYGE AY TDTYHSY AKNILRTQES ACNCIGGDCY LMITDGPASG VSECRFLKIR EGRIIKEIFP TGRVKHTEEC TCGFASNKTI ECA CRDNRY TAKRPFVKLN VETDTAEIRL MCTETYLDTP RPNDGSITGP CESDGDKGSG GIKGGFVHQR MASKIGRWYS RTMS KTKRM GMGLYVKYDG DPWTDSEALA LSGVMVSMEE PGWYSFGFEI KDKKCDVPCI GIEMVHDGGK TTWHSAATAI YCLMG SGQL LWDTVTGVDM AL

-
Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
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 / N-Acetylglucosamine

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.25 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
50.0 mMC4H11NO3Tris
10.0 mMCaCl2calcium chloride

Details: 50 mM Tris-HCl, 150 mM NaCl, 10 mM CaCl2, pH 8.0
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.61 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER / Details: ab initio
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 177249

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more