[English] 日本語
Yorodumi
- EMDB-47877: H5N1 HA in complex with HC-5 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-47877
TitleH5N1 HA in complex with HC-5 Fab
Map dataMap has good resolution in the area of interest, but loses resolution towards the bottom of chain B, D, and F.
Sample
  • Complex: Complex of trimeric HA with three HC-5 Fabs
    • Protein or peptide: Hemagglutinin HA2
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: HC-5 Fab heavy chain
    • Protein or peptide: HC-5 Fab light chain
KeywordsComplex / Viral / Antibody / Monoclonal / VIRAL PROTEIN-IMMUNE SYSTEM complex
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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsSalas E / Liang B
Funding support United States, 1 items
OrganizationGrant numberCountry
Other government United States
CitationJournal: To Be Published
Title: H5N1 HA in complex with HC-5 Fab
Authors: Salas E / Liang B
History
DepositionNov 12, 2024-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_47877.png

Downloads & links

-
Map

FileDownload / File: emd_47877.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap has good resolution in the area of interest, but loses resolution towards the bottom of chain B, D, and F.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 384 pix.
= 346.499 Å		0.9 Å/pix.
x 384 pix.
= 346.499 Å		0.9 Å/pix.
x 384 pix.
= 346.499 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.90234 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.144
Minimum - Maximum-1.0031095 - 1.4440151
Average (Standard dev.)0.00029283713 (±0.02695185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 346.49857 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_47877_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_47877_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of trimeric HA with three HC-5 Fabs

EntireName: Complex of trimeric HA with three HC-5 Fabs
Components
  • Complex: Complex of trimeric HA with three HC-5 Fabs
    • Protein or peptide: Hemagglutinin HA2
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: HC-5 Fab heavy chain
    • Protein or peptide: HC-5 Fab light chain

-
Supramolecule #1: Complex of trimeric HA with three HC-5 Fabs

SupramoleculeName: Complex of trimeric HA with three HC-5 Fabs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1, #3-#4
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 300 KDa

-
Macromolecule #1: Hemagglutinin HA1

MacromoleculeName: Hemagglutinin HA1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: H5N1
Molecular weightTheoretical: 35.712555 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DQICIGYHAN NSTEQVDTIM EKNVTVTHAQ DILEKTHNGK LCDLNGVKPL ILKDCSVAGW LLGNPMCDEF IRVPEWSYIV ERANPANDL CYPGSLNDYE ELKHMLSRIN HFEKILIIPK SSWPNHETSL GVSAACPYQG APSFFRNVVW LIKKNDAYPT I KISYNNTN ...String:
DQICIGYHAN NSTEQVDTIM EKNVTVTHAQ DILEKTHNGK LCDLNGVKPL ILKDCSVAGW LLGNPMCDEF IRVPEWSYIV ERANPANDL CYPGSLNDYE ELKHMLSRIN HFEKILIIPK SSWPNHETSL GVSAACPYQG APSFFRNVVW LIKKNDAYPT I KISYNNTN REDLLILWGI HHSNNAEEQT NLYKNPTTYI SVGTSTLNQR LAPKIATRSQ VNGQRGRMDF FWTILKPDDA IH FESNGNF IAPEYAYKIV KKGDSTIMKS GVEYGHCNTK CQTPVGAINS SMPFHNIHPL TIGECPKYVK SNKLVLATGL

UniProtKB: Hemagglutinin

-
Macromolecule #2: Hemagglutinin HA2

MacromoleculeName: Hemagglutinin HA2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: H5N1
Molecular weightTheoretical: 17.491254 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
WQGMVDGWYG YHHSNEQGSG YAADKESTQK AIDGVTNKVN SIIDKMNTQF EAVGREFNNL ERRIENLNKK MEDGFLDVWT YNAELLVLM ENERTLDFHD SNVKNLYDKV RLQLRDNAKE LGNGCFEFYH KCDNECMESV RNGTYDYPQY

UniProtKB: Hemagglutinin

-
Macromolecule #3: HC-5 Fab heavy chain

MacromoleculeName: HC-5 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 14.07667 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VQLLESGGGL VQSGGSLRLS CAASGFTFSS CALSWVRQAP GKGLEWVSGI RGSGDTTYYA DSVRGRFTIS RVNSKNSLYL QMNSLRAED TAVYFCAKTP YDFWNTYYPY SYYYYMDVWG KGTTVTVS

-
Macromolecule #4: HC-5 Fab light chain

MacromoleculeName: HC-5 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.149724 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMTQTPLS LSVTPGQPAS ISCKSSQSLL HSDGKTYLYW YLQKPGQSPQ LLIYEVSSRF SGVPDRFSGS GSGTDFTLKI SRVEAEDVG AYYCMQGIHL PLTFGGGTKV EIK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 10 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / 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: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5jw4

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49611
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
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