[English] 日本語
Yorodumi
- EMDB-48613: Structure of porcine Fab 24-1G23 in complex with influenza H1N1 A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-48613
TitleStructure of porcine Fab 24-1G23 in complex with influenza H1N1 A/Hawaii/70/2019 hemagglutinin
Map data
Sample
  • Complex: A complex of hemagglutinin from A A/Hawaii/70/2019 with pig Fab 24-1G17
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Heavy chain of Fab from porcine antibody 24-1G23
  • Protein or peptide: Light chain of Fab from porcine antibody 24-1G23
  • Protein or peptide: Hemagglutinin
KeywordsInfluenza / Hemagglutinin / Antibody / Immune response / Pig / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesHomo sapiens (human) / Influenza A virus / Sus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.41 Å
AuthorsLv H / Pholcharee T / 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: Structural analysis of broadly neutralizing porcine antibodies to influenza hemagglutinin stem
Authors: Lv H / Pholcharee T / Wu NC
History
DepositionJan 11, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_48613.png

Downloads & links

-
Map

FileDownload / File: emd_48613.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: 0.04
Minimum - Maximum-0.001788739 - 1.4716309
Average (Standard dev.)0.0006456784 (±0.01792515)
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_48613_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_48613_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : A complex of hemagglutinin from A A/Hawaii/70/2019 with pig Fab 2...

EntireName: A complex of hemagglutinin from A A/Hawaii/70/2019 with pig Fab 24-1G17
Components
  • Complex: A complex of hemagglutinin from A A/Hawaii/70/2019 with pig Fab 24-1G17
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Heavy chain of Fab from porcine antibody 24-1G23
  • Protein or peptide: Light chain of Fab from porcine antibody 24-1G23
  • Protein or peptide: Hemagglutinin

-
Supramolecule #1: A complex of hemagglutinin from A A/Hawaii/70/2019 with pig Fab 2...

SupramoleculeName: A complex of hemagglutinin from A A/Hawaii/70/2019 with pig Fab 24-1G17
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Hemagglutinin was expressed recombinantly in SF9 cells. Fab 24-1G17 was expressed recombinantly in Expi293F cells.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.19 KDa

-
Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 36.484098 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DTLCIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDKHNGK LCKLRGVAPL HLGKCNIAGW ILGNPECESL STARSWSYIV ETSNSDNGT CYPGDFINYE ELREQLSSVS SFERFEIFPK TSSWPNHDSD KGVTAACPHA GAKSFYKNLI WLVKKGNSYP K LNQTYIND ...String:
DTLCIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDKHNGK LCKLRGVAPL HLGKCNIAGW ILGNPECESL STARSWSYIV ETSNSDNGT CYPGDFINYE ELREQLSSVS SFERFEIFPK TSSWPNHDSD KGVTAACPHA GAKSFYKNLI WLVKKGNSYP K LNQTYIND KGKEVLVLWG IHHPPTIAAQ ESLYQNADAY VFVGTSRYSK KFKPEIATRP KVRDQEGRMN YYWTLVEPGD KI TFEATGN LVVPRYAFTM ERDAGSGIII SDTPVHDCNT TCQTPEGAIN TSLPFQNVHP ITIGKCPKYV KSTKLRLATG LRN VPSIQS R

UniProtKB: Hemagglutinin

-
Macromolecule #2: Heavy chain of Fab from porcine antibody 24-1G23

MacromoleculeName: Heavy chain of Fab from porcine antibody 24-1G23 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 13.840352 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EEKLVESGGG LVQPGGSLRL SCVGSGFTFS STYIGWVRQA PGGGLEWLGS ISVNGDITDY AESAEGRFTI SKDNSQNMAW LQMNSLRTE DTARYYCATG RFFGIVVTYA MNLWGPGVEV VVSSASTKGP S

-
Macromolecule #3: Light chain of Fab from porcine antibody 24-1G23

MacromoleculeName: Light chain of Fab from porcine antibody 24-1G23 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 12.289744 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QTVIQEPAMS VSPGGTVTLT CAFRSGSVTT SNYPSWFQQT PGQPPRLLIY NTNSRPTGVP SRFSGRISGN KAALTITGAQ TEDEADYFC ALYKTALNVR FGGGTHLTVL GQPKAAP

-
Macromolecule #4: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 20.004217 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADLKS TQNAIDKITN KVNSVIEKMN TQFTAVGKEF NHLEKRIENL NKKVDDGFL DIWTYNAELL VLLENERTLD YHDSNVKNLY EKVRNQLKNN AKEIGNGCFE FYHKCDNTCM ESVKNGTYDY P KYSEEAKL NREKID

UniProtKB: Hemagglutinin

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 8 / Details: 20 mM Tris-HCl, 100 mM NaCl
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: 2.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 247438
Initial angle assignmentType: MAXIMUM LIKELIHOOD
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