[English] 日本語
Yorodumi
- EMDB-70808: Structure of Fab HB420 in complex with influenza H3N2 A/Moscow/10... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-70808
TitleStructure of Fab HB420 in complex with influenza H3N2 A/Moscow/10/1999 neuraminidase
Map data
Sample
  • Complex: Structure of Fab HB420 in complex with influenza H3N2 A/Moscow/10/1999 neuraminidase
    • Protein or peptide: Neuraminidase
    • Protein or peptide: Variable domain of the heavy chain of Fab hb420
    • Protein or peptide: Variable domain of the light chain of Fab HB420
KeywordsInfluenza / Neuraminidase / Antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
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
Methodsingle particle reconstruction / cryo EM / Resolution: 2.16 Å
AuthorsLv H / Wu NC
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)Emerging Pathogens Initiative United States
CitationJournal: To Be Published
Title: Evolution of antibody cross-reactivity to influenza H5N1 neuraminidase from an N2-specific germline
Authors: Lv H / Wu NC
History
DepositionMay 25, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_70808.png

Downloads & links

-
Map

FileDownload / File: emd_70808.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 360 pix.
= 380.88 Å		1.06 Å/pix.
x 360 pix.
= 380.88 Å		1.06 Å/pix.
x 360 pix.
= 380.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.095
Minimum - Maximum-0.0017491005 - 1.6169193
Average (Standard dev.)0.0007444206 (±0.018703492)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 380.87997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_70808_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_70808_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Structure of Fab HB420 in complex with influenza H3N2 A/Moscow/10...

EntireName: Structure of Fab HB420 in complex with influenza H3N2 A/Moscow/10/1999 neuraminidase
Components
  • Complex: Structure of Fab HB420 in complex with influenza H3N2 A/Moscow/10/1999 neuraminidase
    • Protein or peptide: Neuraminidase
    • Protein or peptide: Variable domain of the heavy chain of Fab hb420
    • Protein or peptide: Variable domain of the light chain of Fab HB420

-
Supramolecule #1: Structure of Fab HB420 in complex with influenza H3N2 A/Moscow/10...

SupramoleculeName: Structure of Fab HB420 in complex with influenza H3N2 A/Moscow/10/1999 neuraminidase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Neuraminidase was expressed recombinantly in SF9 cells. Fab HB420 was expressed recombinantly in Expi293F cells.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 350 KDa

-
Macromolecule #1: Neuraminidase

MacromoleculeName: Neuraminidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: exo-alpha-sialidase
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 42.767715 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: AEYRNWSKPQ CNITGFAPFS KDNSIRLSAG GDIWVTREPY VSCDPDKCYQ FALGQGTTLN NGHSNDTVHD RTPYRTLLMN ELGVPFHLG TKQVCIAWSS SSCHDGKAWL HVCVTGDDEN ATASFIYNGR LVDSIGSWSK KILRTQESEC VCINGTCTVV M TDGSASGK ...String:
AEYRNWSKPQ CNITGFAPFS KDNSIRLSAG GDIWVTREPY VSCDPDKCYQ FALGQGTTLN NGHSNDTVHD RTPYRTLLMN ELGVPFHLG TKQVCIAWSS SSCHDGKAWL HVCVTGDDEN ATASFIYNGR LVDSIGSWSK KILRTQESEC VCINGTCTVV M TDGSASGK ADTKILFIEE GKIVHTSPLS GSAQHVEECS CYPRYPGVRC VCRDNWKGSN RPIVDINVKD YSIVSSYVCS GL VGDTPRK NDSSSSSHCL DPNNEEGGHG VKGWAFDDGN DVWMGRTISE KLRSGYETFK VIEGWSKPNS KLQINRQVIV DRG NRSGYS GIFSVEGKSC INRCFYVELI RGRKQETEVL WTSNSIVVFC GTSGTYGTGS WPDGADINLM PI

UniProtKB: Neuraminidase

-
Macromolecule #2: Variable domain of the heavy chain of Fab hb420

MacromoleculeName: Variable domain of the heavy chain of Fab hb420 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.544985 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGAE VKKPGSSVKV SCMASGGSFG SYGFSWVRQA PGQGLEWMGG IIPLFDTPNY AQKFQGRVTI TADASTSTVY MELSSLRSE DTAVYYCARD SLPYGDQNYY YGMHVWGQGT TVTVSS

-
Macromolecule #3: Variable domain of the light chain of Fab HB420

MacromoleculeName: Variable domain of the light chain of Fab HB420 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.460441 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSALTQPASL SGSPGQSITI SCSGSSSDIG DYNYVSWYQQ HPGKAPKLII YDVTNRPSGV SDRLSGSKSG TTASLTISGL QAEDEADYY CSSYGGNYNL VFGGGTKLTV L

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 8 / Details: 20 mM Tris-HCl, 100 mM NaCl, 10 mM CaCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III
DetailsThe sample was also mixed with octyl glucoside to 0.1% w/v of the detergent final concentration piror to applying on the grid.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.35 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Details: Initial model was built directly into the map using automated model building algorithm ModelAngelo (DOI: 10.1038/s41586-024-07215-4)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 355667
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)

+
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