[English] 日本語
Yorodumi
- EMDB-44112: Hemagglutinin H1 New Caledonia 1999 in complex with monoclonal an... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-44112
TitleHemagglutinin H1 New Caledonia 1999 in complex with monoclonal antibody Fab 43_S0008
Map dataHemagglutinin H1 NC99 in complex with the monoclonal antibody Fab43_S0008
Sample
  • Complex: Hemagglutinin H1 New Caledonia 1999 in complex with monoclonal antibody Fab 43_S0008
    • Protein or peptide: Hemagglutinin HA2 chain
    • Protein or peptide: Heavy chain monoclonal antibody Fab 3_S0008
    • Protein or peptide: Light chain monoclonal antibody Fab 3_S0008
  • Protein or peptide: Hemagglutinin HA1 chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsinfluenza virus / broadly neutralizing antibody / bnAb / VH1-69 / DH3-9 / hemagglutinin / HA / stem / stalk / germline-targeting / VIRAL PROTEIN / 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
Biological speciesHomo sapiens (human) / Influenza A virus / Mus sp. (mice)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsTorrents de la Pena A / de Paiva Froes Rocha R / Ward AB / Ataca S / Kanekiyo M
Funding support United States, 2 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Cell Rep / Year: 2024
Title: Modulating the immunodominance hierarchy of immunoglobulin germline-encoded structural motifs targeting the influenza hemagglutinin stem.
Authors: Sila Ataca / Maya Sangesland / Rebeca de Paiva Fróes Rocha / Alba Torrents de la Peña / Larance Ronsard / Seyhan Boyoglu-Barnum / Rebecca A Gillespie / Yaroslav Tsybovsky / Tyler Stephens ...Authors: Sila Ataca / Maya Sangesland / Rebeca de Paiva Fróes Rocha / Alba Torrents de la Peña / Larance Ronsard / Seyhan Boyoglu-Barnum / Rebecca A Gillespie / Yaroslav Tsybovsky / Tyler Stephens / Syed M Moin / Julia Lederhofer / Adrian Creanga / Sarah F Andrews / Ralston M Barnes / Daniel Rohrer / Nils Lonberg / Barney S Graham / Andrew B Ward / Daniel Lingwood / Masaru Kanekiyo /
Abstract: Antibodies targeting epitopes through germline-encoded motifs can be found in different individuals. While these public antibodies are often beneficial, they also pose hurdles for subdominant ...Antibodies targeting epitopes through germline-encoded motifs can be found in different individuals. While these public antibodies are often beneficial, they also pose hurdles for subdominant antibodies to emerge. Here, we use transgenic mice that reproduce the human IGHV1-6901 germline-encoded antibody response to the conserved stem epitope on group 1 hemagglutinin (HA) of influenza A virus to show that this germline-endowed response can be overridden by a subdominant yet cross-group reactive public antibody response. Immunization with a non-cognate group 2 HA stem enriched B cells harboring the IGHD3-9 gene, thereby switching from IGHV1-69- to IGHD3-9-encoded motif-dependent epitope recognition. These IGHD3-9 antibodies bound, neutralized, and conferred cross-group protection in mice against influenza A viruses. A cryoelectron microscopy (cryo-EM) structure of an IGHD3-9 antibody resembled the human broadly neutralizing antibody FI6v3, which uses IGHD3-9. Together, our findings offer insights into vaccine regimens that engage an immunoglobulin repertoire with broader cross-reactivity to influenza A viruses.
History
DepositionMar 15, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_44112.png

Downloads & links

-
Map

FileDownload / File: emd_44112.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHemagglutinin H1 NC99 in complex with the monoclonal antibody Fab43_S0008
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 334.4 Å		1.05 Å/pix.
x 320 pix.
= 334.4 Å		1.05 Å/pix.
x 320 pix.
= 334.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.8243744 - 2.2472174
Average (Standard dev.)0.00085465214 (±0.037908882)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 334.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Hemagglutinin H1 NC99 in complex with the monoclonal...

Fileemd_44112_additional_1.map
AnnotationHemagglutinin H1 NC99 in complex with the monoclonal antibody Fab43_S0008
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Hemagglutinin H1 NC99 in complex with the monoclonal...

Fileemd_44112_half_map_1.map
AnnotationHemagglutinin H1 NC99 in complex with the monoclonal antibody Fab43_S0008
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Hemagglutinin H1 NC99 in complex with the monoclonal...

Fileemd_44112_half_map_2.map
AnnotationHemagglutinin H1 NC99 in complex with the monoclonal antibody Fab43_S0008
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Hemagglutinin H1 New Caledonia 1999 in complex with monoclonal an...

EntireName: Hemagglutinin H1 New Caledonia 1999 in complex with monoclonal antibody Fab 43_S0008
Components
  • Complex: Hemagglutinin H1 New Caledonia 1999 in complex with monoclonal antibody Fab 43_S0008
    • Protein or peptide: Hemagglutinin HA2 chain
    • Protein or peptide: Heavy chain monoclonal antibody Fab 3_S0008
    • Protein or peptide: Light chain monoclonal antibody Fab 3_S0008
  • Protein or peptide: Hemagglutinin HA1 chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Hemagglutinin H1 New Caledonia 1999 in complex with monoclonal an...

SupramoleculeName: Hemagglutinin H1 New Caledonia 1999 in complex with monoclonal antibody Fab 43_S0008
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#4
Details: Fab fragment was generated using papain digestion and size exclusion chromatography. The complex was incubated overnight and the sample was purified using size exclusion chromatography
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 330 KDa

-
Macromolecule #1: Hemagglutinin HA1 chain

MacromoleculeName: Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 1 / Details: Hemagglutinin New Caledonia 1999 HA1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 37.803648 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKAKLLVLLC TFTATYADTI CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDSHNGKLCL LKGIAPLQLG NCSVAGWILG NPECELLIS KESWSYIVET PNPENGTCYP GYFADYEELR EQLSSVSSFE RFEIFPKESS WPNHTVTGVS ASCSHNGKSS F YRNLLWLT ...String:
MKAKLLVLLC TFTATYADTI CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDSHNGKLCL LKGIAPLQLG NCSVAGWILG NPECELLIS KESWSYIVET PNPENGTCYP GYFADYEELR EQLSSVSSFE RFEIFPKESS WPNHTVTGVS ASCSHNGKSS F YRNLLWLT GKNGLYPNLS KSYVNNKEKE VLVLWGVHHP PNIGNQRALY HTENAYVSVV SSHYSRRFTP EIAKRPKVRD QE GRINYYW TLLEPGDTII FEANGNLIAP WYAFALSRGF GSGIITSNAP MDECDAKCQT PQGAINSSLP FQNVHPVTIG ECP KYVRSA KLRMVTGLRN IPS

UniProtKB: Hemagglutinin

-
Macromolecule #2: Hemagglutinin HA2 chain

MacromoleculeName: Hemagglutinin HA2 chain / type: protein_or_peptide / ID: 2 / Details: Hemagglutinin H1 New Caledonia 1999 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 25.550836 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IQSRGLFGAI AGFIEGGWTG MVDGWYGYHH QNEQGSGYAA DQKSTQNAIN GITNKVNSVI EKMNTQFTAV GKEFNKLERR MENLNKKVD DGFLDIWTYN AELLVLLENE RTLDFHDSNV KNLYEKVKSQ LKNNAKEIGN GCFEFYHKCN NECMESVKNG T YDYPKYSE ...String:
IQSRGLFGAI AGFIEGGWTG MVDGWYGYHH QNEQGSGYAA DQKSTQNAIN GITNKVNSVI EKMNTQFTAV GKEFNKLERR MENLNKKVD DGFLDIWTYN AELLVLLENE RTLDFHDSNV KNLYEKVKSQ LKNNAKEIGN GCFEFYHKCN NECMESVKNG T YDYPKYSE ESKLNREKID GVKLESMGVY QILAIYSTVA SSLVLLVSLG AISFWMCSNG SLQCRICI

UniProtKB: Hemagglutinin

-
Macromolecule #3: Heavy chain monoclonal antibody Fab 3_S0008

MacromoleculeName: Heavy chain monoclonal antibody Fab 3_S0008 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus sp. (mice)
Molecular weightTheoretical: 24.914199 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGSSVKV SCKASGGTFR TFGISWVRQA PGQGLEWMGW IIPIIGTPNY AQKFQGRVII TADESSNTAY MELNSLKSE DTAVYYCAKE GRALLRYFDW LPLDAFDIWG QGTMVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS ...String:
QVQLVQSGAE VKKPGSSVKV SCKASGGTFR TFGISWVRQA PGQGLEWMGW IIPIIGTPNY AQKFQGRVII TADESSNTAY MELNSLKSE DTAVYYCAKE GRALLRYFDW LPLDAFDIWG QGTMVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP KSCDK

-
Macromolecule #4: Light chain monoclonal antibody Fab 3_S0008

MacromoleculeName: Light chain monoclonal antibody Fab 3_S0008 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus sp. (mice)
Molecular weightTheoretical: 24.034838 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVLTQTPLS LPVSLGDQAS ISCRSSQSLV HSDGNTYLHW YLQKPGQSPK LLIYKVSNRF SGVPDRFSGS GSGTDFTLKI SRVEAEDLG VYFCSQSTHV PPLTFGAGTK LELKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES ...String:
DIVLTQTPLS LPVSLGDQAS ISCRSSQSLV HSDGNTYLHW YLQKPGQSPK LLIYKVSNRF SGVPDRFSGS GSGTDFTLKI SRVEAEDLG VYFCSQSTHV PPLTFGAGTK LELKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES VTEQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNRG EC

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 15 / 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: TBS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 40 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4m4y

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 190711
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

4m4y


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9b2m:
Hemagglutinin H1 New Caledonia 1999 in complex with monoclonal antibody Fab 43_S0008

+
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