[English] 日本語
Yorodumi
- EMDB-76453: Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-76453
TitleCryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-3F4 Fab fragments
Map datastructure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-3F4 Fab fragments
Sample
  • Complex: Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-3F4 Fab fragments
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: KL-BHA-3F4 heavy chain
    • Protein or peptide: KL-BHA-3F4 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordshemagglutinin / Fab / viral glycoprotein / Viral Protein-Immune System complex
Function / homology:
Function and homology information
Biological speciesMus musculus (house mouse) / Influenza B virus (B/Lee/1940)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsCivljak A / Bonnettaz B / Bajic G
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI117287 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI109946 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI097092 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400008C United States
Other private United States
CitationJournal: To Be Published
Title: Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-3F4 Fab fragments
Authors: Civljak A / Bonnettaz B / Bajic G
History
DepositionApr 7, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_76453.png

Downloads & links

-
Map

FileDownload / File: emd_76453.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-3F4 Fab fragments
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 397.92 Å		0.83 Å/pix.
x 480 pix.
= 397.92 Å		0.83 Å/pix.
x 480 pix.
= 397.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.0018391435 - 1.6625237
Average (Standard dev.)0.0006202831 (±0.017114071)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 397.91998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half Map B

Fileemd_76453_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map A

Fileemd_76453_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex w...

EntireName: Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-3F4 Fab fragments
Components
  • Complex: Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-3F4 Fab fragments
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: KL-BHA-3F4 heavy chain
    • Protein or peptide: KL-BHA-3F4 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex w...

SupramoleculeName: Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-3F4 Fab fragments
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: B/Lee/1940 hemagglutinin expressed using Sf9 insect cells
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza B virus (B/Lee/1940) / Strain: B/Lee/1940
Molecular weightTheoretical: 56.640168 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DRICTGITSS NSPHVIKTAT QGEVNVTGVI PLTTTPTRSH FANLKGTQTR GKLCPNCFDC TDLDVALGRP KCMGNIPSAK VSILHEVKP VTSGCFPIMH DRTKIRQLPN LLRGYENIRL STSNVINAET APGGPYKVGT SGSCPNVANR NGFFNTMAWV I PQDNNKTA ...String:
DRICTGITSS NSPHVIKTAT QGEVNVTGVI PLTTTPTRSH FANLKGTQTR GKLCPNCFDC TDLDVALGRP KCMGNIPSAK VSILHEVKP VTSGCFPIMH DRTKIRQLPN LLRGYENIRL STSNVINAET APGGPYKVGT SGSCPNVANR NGFFNTMAWV I PQDNNKTA INPVTVEVPY ICSEGEDQIT VWGFHSDDKT QMERLYGDSN PQKFTSSANG VTTHYVSQIG GFPNQTEDEG LK QSGRIVV DYMVQKPGKT GTIVYQRGIL LPQKVWCASG RSKVIKGSLP LIGEADCLHE KYGGLNKSKP YYTGEHAKAI GNC PIWVKT PLKLANGTKY RPPAKLLKER GFFGAIAGFL EGGWEGMIAG WHGYTSHGAH GVAVAADLKS TQEAINKITK NLNS LSELE VKNLQRLSGA MNGLHDEILE LDEKVDDLRA DTISSQIELA VLLSNEGIIN SEDEHLLALE RKLKKMLGPS AVEIG NGCF ETKHKCNQTC LDRIAAGTFN AGDFSLPTFD SLNITAAS

UniProtKB: UNIPROTKB: Q0PLR5

-
Macromolecule #2: KL-BHA-3F4 heavy chain

MacromoleculeName: KL-BHA-3F4 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.816409 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
KVQLQQSGAG LVKPGASVKL SCKASGYTFT EYIIHWVKQR SGQGLEWIGW FYPGSGSIRF NEKFKDKATL TADKSSSTVY MELSRLTSE DSAVYFCARH GSIYYDYQGY FDYWGQGTTL TVSS

-
Macromolecule #3: KL-BHA-3F4 light chain

MacromoleculeName: KL-BHA-3F4 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.934287 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
DIVMTQSHKF MSTSVGDRVS ITCKASQDVS STIAWYQQKP GQSPKLLIYW ASTRHTGVPD RFTGSGSGTD FTLTISNVRA EDLTLYYCQ QHYSSPWTFG GGTYLEIK

-
Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 10 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.59 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 154216
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
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