[English] 日本語
Yorodumi
- EMDB-67556: CryoEM structure of H5N1 A/Texas/37/2024 HA bound to 3CF5 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-67556
TitleCryoEM structure of H5N1 A/Texas/37/2024 HA bound to 3CF5 Fab
Map data
Sample
  • Complex: CryoEM structure of H5N1 A/Texas/37/2024 HA bound to 3CF5 Fab
    • Protein or peptide: The light chain of 3CF5 Fab
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: The heavy chain of 3CF5 Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHemagglutinin / Antibody Fab fragment / Complex / VIRAL PROTEIN/IMMUNE SYSTEM / VIRUS
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / virion 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
Biological speciesInfluenza A virus / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsNiu C / Liu B / Li Z / Xiong X
Funding support China, 8 items
OrganizationGrant numberCountry
Other government2021YFA1300903
National Natural Science Foundation of China (NSFC)82341085 China
Other governmentEKPG21-06
Other governmentSRPG22-002
Other government2021A1515011289
Other government2023B1212060050
Other government2023B1212120009
Other governmentGIBHBRP24-02
CitationJournal: To Be Published
Title: A broadly neutralizing monoclonal antibody targeting a conserved non-RBS epitope on hemagglutinins of emerging and historical H5Nx influenza viruses
Authors: Niu X / Liang H / Niu C / Cheng Y / Liew K / Zheng Z / Liu B / Li Z / Feng H / Tan Y / Xiong X / Chen L
History
DepositionDec 6, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_67556.png

Downloads & links

-
Map

FileDownload / File: emd_67556.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 220 pix.
= 264. Å		1.2 Å/pix.
x 220 pix.
= 264. Å		1.2 Å/pix.
x 220 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.5281091 - 2.0887642
Average (Standard dev.)0.0019944403 (±0.06370748)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_67556_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_67556_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CryoEM structure of H5N1 A/Texas/37/2024 HA bound to 3CF5 Fab

EntireName: CryoEM structure of H5N1 A/Texas/37/2024 HA bound to 3CF5 Fab
Components
  • Complex: CryoEM structure of H5N1 A/Texas/37/2024 HA bound to 3CF5 Fab
    • Protein or peptide: The light chain of 3CF5 Fab
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: The heavy chain of 3CF5 Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: CryoEM structure of H5N1 A/Texas/37/2024 HA bound to 3CF5 Fab

SupramoleculeName: CryoEM structure of H5N1 A/Texas/37/2024 HA bound to 3CF5 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Influenza A virus

-
Macromolecule #1: The light chain of 3CF5 Fab

MacromoleculeName: The light chain of 3CF5 Fab / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.303951 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT IACRTSQEIS NSLAWYQQKP GKAPKLLIYA ASTLKDGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QRKSFPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVT IACRTSQEIS NSLAWYQQKP GKAPKLLIYA ASTLKDGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QRKSFPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

-
Macromolecule #2: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: strain A/Texas/37/2024 H5N1
Molecular weightTheoretical: 62.840508 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DQICIGYHAN NSTEQVDTIM EKNVTVTHAQ DILEKTHNGK LCDLNGVKPL ILKDCSVAGW LLGNPMCDEF IRVPEWSYIV ERANPANDL CYPGSLNDYE ELKHMLSRIN HFEKIQIIPK SSWPNHETSL GVSAACPYQG APSFFRNVVW LIKKNDAYPT I KISYNNTN ...String:
DQICIGYHAN NSTEQVDTIM EKNVTVTHAQ DILEKTHNGK LCDLNGVKPL ILKDCSVAGW LLGNPMCDEF IRVPEWSYIV ERANPANDL CYPGSLNDYE ELKHMLSRIN HFEKIQIIPK SSWPNHETSL GVSAACPYQG APSFFRNVVW LIKKNDAYPT I KISYNNTN REDLLILWGI HHSNNAEEQT NLYKNPITYI SVGTSTLNQR LAPKIATRSQ VNGQRGRMDF FWTILKPDDA IH FESNGNF IAPEYAYKIV KKGDSTIMKS GVEYGHCNTK CQTPVGAINS SMPFHNIHPL TIGECPKYVK SNKLVLATGL RNS PLREKR RKRGLFGAIA GFIEGGWQGM VDGWYGYHHS NEQGSGYAAD KESTQKAIDG VTNKVNSIID KMNTQFEAVG REFN NLERR IENLNKKMED GFLDVWTYNA ELLVLMENER TLDFHDSNVK NLYDKVRLQL RDNAKELGNG CFEFYHKCDN ECMES VRNG TYDYPQYSEE ARLKREEISG SGRENLYFQG GGGSGYIPEA PRDGQAYVRK DGEWVLLSTF LGHHHHHH

UniProtKB: Hemagglutinin

-
Macromolecule #3: The heavy chain of 3CF5 Fab

MacromoleculeName: The heavy chain of 3CF5 Fab / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 24.726707 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QLQLQESGPG LVKPSETLSL TCAVSGASIR TNYWSWIRQS PGRGLEWIGL ISGYDGKTDY NPSLKSRVTI SRDVSDNRFS LTLNSVTAA DTAVYYCARE GPLPFCSGET CYTVFYFDFW GPGTPITISS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV ...String:
QLQLQESGPG LVKPSETLSL TCAVSGASIR TNYWSWIRQS PGRGLEWIGL ISGYDGKTDY NPSLKSRVTI SRDVSDNRFS LTLNSVTAA DTAVYYCARE GPLPFCSGET CYTVFYFDFW GPGTPITISS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK D YFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKVE PKSC

-
Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 9 / 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: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9ekf

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 242333
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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