[English] 日本語
Yorodumi
- EMDB-48079: Cryo-EM structure of 5E10 Fab in complex with H3 influenza Victor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-48079
TitleCryo-EM structure of 5E10 Fab in complex with H3 influenza Victoria 2011 HA trimer
Map dataSharpened map
Sample
  • Complex: 5E10 Fab in complex with H3 influenza Victoria 2011 HA trimer
    • Protein or peptide: 5E10 Fab Heavy chain
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: 5E10 Fab Light chain
    • Protein or peptide: Hemagglutinin HA2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHA / influenza / flu / N-term / H3 / IMMUNE SYSTEM
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 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.89 Å
AuthorsGorman J / Kwong PD
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Simons FoundationSF349247 United States
CitationJournal: Structure / Year: 2025
Title: The N terminus of H3-influenza hemagglutinin as a site-of-vulnerability to neutralizing antibody
Authors: Gorman J / Kwong PD
History
DepositionNov 25, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_48079.png

Downloads & links

-
Map

FileDownload / File: emd_48079.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 429.32 Å		1.07 Å/pix.
x 400 pix.
= 429.32 Å		1.07 Å/pix.
x 400 pix.
= 429.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0733 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.4103057 - 1.7865049
Average (Standard dev.)0.0019062381 (±0.04981953)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 429.32 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_48079_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_48079_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_48079_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : 5E10 Fab in complex with H3 influenza Victoria 2011 HA trimer

EntireName: 5E10 Fab in complex with H3 influenza Victoria 2011 HA trimer
Components
  • Complex: 5E10 Fab in complex with H3 influenza Victoria 2011 HA trimer
    • Protein or peptide: 5E10 Fab Heavy chain
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: 5E10 Fab Light chain
    • Protein or peptide: Hemagglutinin HA2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: 5E10 Fab in complex with H3 influenza Victoria 2011 HA trimer

SupramoleculeName: 5E10 Fab in complex with H3 influenza Victoria 2011 HA trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3, #1, #4, #2
Source (natural)Organism: Influenza A virus

-
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
Molecular weightTheoretical: 37.546414 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QKLPGNDNST ATLCLGHHAV PNGTIVKTIC NDQIEVTNAT ELVQNSSIGE ICDSPHQILD GENCTLIDAL LGDPQCDGFQ NKKWDLFVE RSKAYSNCYP YDVPDYASLR SLVASSGTLE FNNESFNWTG VTQNGTSSAC IRRSNNSFFS RLNWLTQLNF K YPALNVTM ...String:
QKLPGNDNST ATLCLGHHAV PNGTIVKTIC NDQIEVTNAT ELVQNSSIGE ICDSPHQILD GENCTLIDAL LGDPQCDGFQ NKKWDLFVE RSKAYSNCYP YDVPDYASLR SLVASSGTLE FNNESFNWTG VTQNGTSSAC IRRSNNSFFS RLNWLTQLNF K YPALNVTM PNNEQFDKLY IWGVHHPVTD KDQIFLYAQS SGRITVSTKR SQQAVIPNIG YRPRIRNIPS RISIYWTIVK PG DILLINS TGNLIAPRGY FKIRSGKSSI MRSDAPIGKC NSECITPNGS IPNDKPFQNV NRITYGACPR YVKQSTLKLA TGM RNVPEK QTRRRRRR

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
Molecular weightTheoretical: 25.234092 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GIFGAIAGFI ENGWEGMVDG WYGFRHQNSE GRGQAADLKS TQAAIDCING KLNRLIGKTN EKFHQIEKEF SEVEGRIQDL EKYVEDTKI DLWSYNAELL VALENQHTID LTDSEMNKLF EKTKKQLREN AEDMGNGCFK IYHKCDNACI GSIRNGTYDH D VYRDEALN ...String:
GIFGAIAGFI ENGWEGMVDG WYGFRHQNSE GRGQAADLKS TQAAIDCING KLNRLIGKTN EKFHQIEKEF SEVEGRIQDL EKYVEDTKI DLWSYNAELL VALENQHTID LTDSEMNKLF EKTKKQLREN AEDMGNGCFK IYHKCDNACI GSIRNGTYDH D VYRDEALN NRFQIKGVSG RLVPRGSPGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGHH HHHH

UniProtKB: Hemagglutinin

-
Macromolecule #3: 5E10 Fab Heavy chain

MacromoleculeName: 5E10 Fab Heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.463039 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVTLKESGPG ILQPSQTLSL TCSFSGFSLS TFGMGVGWIR QPSGKGLEWL AHIWWDNDEY CNPALKSRLT ISKDTSKNHI FLKIANVDT ADTATYYCAR IFANYGGDAM DYWGQGTSVT VSSA

-
Macromolecule #4: 5E10 Fab Light chain

MacromoleculeName: 5E10 Fab Light chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.615999 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QAVVTQESAL TTSPGGTVIL TCRSSTGAVT TSNYANWVQK KPDHLFTGLI GGTSNRVSGV PVRFSGSLIG DKAALTITGA QTEDDAMYF CALWFSTHYV FGGGTKVTVL SQ

-
Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 20 / 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

Concentration2 mg/mL
BufferpH: 7.4 / Details: PBS
GridModel: C-flat-1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 10.0 sec. / Average electron dose: 70.51 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 28277
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9ei9:
Cryo-EM structure of 5E10 Fab in complex with H3 influenza Victoria 2011 HA trimer

+
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