[English] 日本語
Yorodumi
- EMDB-50547: Cryo-EM structure of Influenza B/Washington/02/2019 virus neurami... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-50547
TitleCryo-EM structure of Influenza B/Washington/02/2019 virus neuraminidase in complex with single-domain antibody hVHH-525.
Map dataSharpened map of Influenza B/Washington/02/2019 virus Neuraminidase in complex with single-chain antibody hVHH-525.
Sample
  • Complex: Complex between Influenza B/Washington/02/2019 virus neuraminidase (tetramer) and one copy of single-domain antibody hVHH-525
    • Protein or peptide: Single-domain antibody hVHH-525
    • Protein or peptide: Neuraminidase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsneuraminidase / single-domain antibody / complex / ANTIVIRAL PROTEIN
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza B virus / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsFelix J / Matthys A / Savvides SN / Saelens X
Funding support Belgium, 3 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1S93223N Belgium
Other privateFlanders Institute for Biotechnology (VIB) grant C0101 Belgium
Other privateFlanders Institute for Biotechnology (VIB) grant C0301 Belgium
CitationJournal: Nat Commun / Year: 2025
Title: Single-domain antibodies directed against hemagglutinin and neuraminidase protect against influenza B viruses
Authors: Matthys A / Felix J / Catani JPP / Roose K / Nerinckx W / Van Buyten B / Fijalkowska D / Callewaert N / Savvides SN / Saelens X
History
DepositionJun 5, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_50547.png

Downloads & links

-
Map

FileDownload / File: emd_50547.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of Influenza B/Washington/02/2019 virus Neuraminidase in complex with single-chain antibody hVHH-525.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.44 Å/pix.
x 140 pix.
= 201.6 Å		1.44 Å/pix.
x 140 pix.
= 201.6 Å		1.44 Å/pix.
x 140 pix.
= 201.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.6656399 - 0.9984864
Average (Standard dev.)0.0031092467 (±0.0380508)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 201.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_50547_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened, unfiltered full map of Influenza B/Washington/02/2019 virus...

Fileemd_50547_additional_1.map
AnnotationUnsharpened, unfiltered full map of Influenza B/Washington/02/2019 virus Neuraminidase in complex with single-chain antibody hVHH-525, used for map and model validation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: DeepEMhancer sharpened map of Influenza B/Washington/02/2019 virus Neuraminidase...

Fileemd_50547_additional_2.map
AnnotationDeepEMhancer sharpened map of Influenza B/Washington/02/2019 virus Neuraminidase in complex with single-chain antibody hVHH-525, used for model building and map visualization.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Local sharpened map of Influenza B/Washington/02/2019 virus Neuraminidase...

Fileemd_50547_additional_3.map
AnnotationLocal sharpened map of Influenza B/Washington/02/2019 virus Neuraminidase in complex with single-chain antibody hVHH-525, used for model refinement in Phenix.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2 of Influenza B/Washington/02/2019 virus Neuraminidase...

Fileemd_50547_half_map_1.map
AnnotationHalf map 2 of Influenza B/Washington/02/2019 virus Neuraminidase in complex with single-chain antibody hVHH-525.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1 of Influenza B/Washington/02/2019 virus Neuraminidase...

Fileemd_50547_half_map_2.map
AnnotationHalf map 1 of Influenza B/Washington/02/2019 virus Neuraminidase in complex with single-chain antibody hVHH-525.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex between Influenza B/Washington/02/2019 virus neuraminidas...

EntireName: Complex between Influenza B/Washington/02/2019 virus neuraminidase (tetramer) and one copy of single-domain antibody hVHH-525
Components
  • Complex: Complex between Influenza B/Washington/02/2019 virus neuraminidase (tetramer) and one copy of single-domain antibody hVHH-525
    • Protein or peptide: Single-domain antibody hVHH-525
    • Protein or peptide: Neuraminidase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Complex between Influenza B/Washington/02/2019 virus neuraminidas...

SupramoleculeName: Complex between Influenza B/Washington/02/2019 virus neuraminidase (tetramer) and one copy of single-domain antibody hVHH-525
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Influenza B virus
Molecular weightTheoretical: 264 KDa

-
Macromolecule #1: Single-domain antibody hVHH-525

MacromoleculeName: Single-domain antibody hVHH-525 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.09438 KDa
Recombinant expressionOrganism: Komagataella phaffii (fungus)
SequenceString:
DVQLVESGGG LVQPGGSLRL SCAASGDIFS THIMGWYRQA PGKQRELVAT IDTDGSTNYA DSVKGRFTIS RDNAKNTVYL QMNSLRPED TAVYYCNAES AYSDYRLPDY WGQGTLVTVS S

-
Macromolecule #2: Neuraminidase

MacromoleculeName: Neuraminidase / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: exo-alpha-sialidase
Source (natural)Organism: Influenza B virus
Molecular weightTheoretical: 53.540992 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLSAWSHPQ FEKGSGIINE TADDIVYRLT VIIDDRYESL KNLITLRADR LEMIINDNVS TILASIGSG VTLLLPEPEW TYPRLSCPGS TFQKALLISP HRFGETKGNS APLIIREPFV ACGPNECKHF ALTHYAAQPG G YYNGTRGD ...String:
MPMGSLQPLA TLYLLGMLVA SVLSAWSHPQ FEKGSGIINE TADDIVYRLT VIIDDRYESL KNLITLRADR LEMIINDNVS TILASIGSG VTLLLPEPEW TYPRLSCPGS TFQKALLISP HRFGETKGNS APLIIREPFV ACGPNECKHF ALTHYAAQPG G YYNGTRGD RNKLRHLISV KLGKIPTVEN SIFHMAAWSG SACHDGKEWT YIGVDGPDNN ALLKVKYGEA YTDTYHSYAN NI LRTQESA CNCIGGNCYL MITDGSASGV SECRFLKIRE GRIIKEIFPT GRVKHTEECT CGFASNKTIE CACRDNRYTA KRP FVKLNV ETDTAEIRLM CTDTYLDTPR PNDGSITGPC ESDGDKGSGG IKGGFVHQRM KSKIGRWYSR TMSKTERMGM GLYV KYGGD PWADSDALTF SGVMVSMKEP GWYSFGFEIK DKKCDVPCIG IEMVHDGGKE TWHSAATAIY CLMGSGQLLW DTVTG VDMA L

UniProtKB: Neuraminidase

-
Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.12 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
0.137 MSodium chloride
0.0027 MPotassium Chloride
0.01 MSodium Phosphate Dibasic
0.0018 MPotassium Phosphate Monobasic
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 28057 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

+
Image processing

Particle selectionNumber selected: 697697
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2)
Details: Compositional heterogeneity of the sample necessitated the use of a 3D processing strategy combining symmetry expansion, focused 3D classification without alignment, signal subtraction and ...Details: Compositional heterogeneity of the sample necessitated the use of a 3D processing strategy combining symmetry expansion, focused 3D classification without alignment, signal subtraction and localized refinement. The final particle set consists of 158674 symmetry expanded and signal subtracted particles.
Number images used: 158674
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 4.2)
FSC plot (resolution estimation)

+
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