[English] 日本語
Yorodumi
- EMDB-42529: CryoEM structure of A/Michigan/45/2015 H1 in complex with flu HA ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42529
TitleCryoEM structure of A/Michigan/45/2015 H1 in complex with flu HA central stem VH1-18 antibody 09-1B12
Map dataMich15H1 091B12_sharp
Sample
  • Complex: An 09-1B12 Fab complex with one protomer of a H1 trimer
    • Complex: 09-1B12 Fab
      • Protein or peptide: 09-1B12 HC Fv
      • Protein or peptide: 09-1B12 LC Fv
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsFlu Hemagglutinin / Central stem epitope / VH1-18 / 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 / apical plasma membrane / 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
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 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHuang J / Han J / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Immunity / Year: 2024
Title: Eliciting a single amino acid change by vaccination generates antibody protection against group 1 and group 2 influenza A viruses.
Authors: Rashmi Ray / Faez Amokrane Nait Mohamed / Daniel P Maurer / Jiachen Huang / Berk A Alpay / Larance Ronsard / Zhenfei Xie / Julianna Han / Monica Fernandez-Quintero / Quynh Anh Phan / Rebecca ...Authors: Rashmi Ray / Faez Amokrane Nait Mohamed / Daniel P Maurer / Jiachen Huang / Berk A Alpay / Larance Ronsard / Zhenfei Xie / Julianna Han / Monica Fernandez-Quintero / Quynh Anh Phan / Rebecca L Ursin / Mya Vu / Kathrin H Kirsch / Thavaleak Prum / Victoria C Rosado / Thalia Bracamonte-Moreno / Vintus Okonkwo / Julia Bals / Caitlin McCarthy / Usha Nair / Masaru Kanekiyo / Andrew B Ward / Aaron G Schmidt / Facundo D Batista / Daniel Lingwood /
Abstract: Broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem of influenza A viruses (IAVs) tend to be effective against either group 1 or group 2 viral diversity. In rarer cases, ...Broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem of influenza A viruses (IAVs) tend to be effective against either group 1 or group 2 viral diversity. In rarer cases, intergroup protective bnAbs can be generated by human antibody paratopes that accommodate the conserved glycan differences between the group 1 and group 2 stems. We applied germline-engaging nanoparticle immunogens to elicit a class of cross-group bnAbs from physiological precursor frequency within a humanized mouse model. Cross-group protection depended on the presence of the human bnAb precursors within the B cell repertoire, and the vaccine-expanded antibodies enriched for an N55T substitution in the CDRH2 loop, a hallmark of the bnAb class. Structurally, this single mutation introduced a flexible fulcrum to accommodate glycosylation differences and could alone enable cross-group protection. Thus, broad IAV immunity can be expanded from the germline repertoire via minimal antigenic input and an exceptionally simple antibody development pathway.
History
DepositionOct 30, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_42529.png

Downloads & links

-
Map

FileDownload / File: emd_42529.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMich15H1 091B12_sharp
Voxel sizeX=Y=Z: 0.725 Å
Density
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.33628196 - 0.55375403
Average (Standard dev.)0.000020915213 (±0.012572903)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 301.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Mich15H1 091B12 halfA

Fileemd_42529_half_map_1.map
AnnotationMich15H1 091B12_halfA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Mich15H1 091B12 halfB

Fileemd_42529_half_map_2.map
AnnotationMich15H1 091B12_halfB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : An 09-1B12 Fab complex with one protomer of a H1 trimer

EntireName: An 09-1B12 Fab complex with one protomer of a H1 trimer
Components
  • Complex: An 09-1B12 Fab complex with one protomer of a H1 trimer
    • Complex: 09-1B12 Fab
      • Protein or peptide: 09-1B12 HC Fv
      • Protein or peptide: 09-1B12 LC Fv
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: An 09-1B12 Fab complex with one protomer of a H1 trimer

SupramoleculeName: An 09-1B12 Fab complex with one protomer of a H1 trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Influenza A virus

-
Supramolecule #2: 09-1B12 Fab

SupramoleculeName: 09-1B12 Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Hemagglutinin HA1 chain

MacromoleculeName: Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 1 / Details: A/Michigan/45/2015 H1 HA1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 36.018465 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ADTLCIGYHA NNSTDTVDTV LEKNVTVTHS VNLLEDKHNG KLCKLRGVAP LHLGKCNIAG WILGNPECES LSTASSWSYI VETSNSDNG TCYPGDFINY EELREQLSSV SSFERFEIFP KTSSWPNHDS NKGVTAACPH AGAKSFYKNL IWLVKKGNSY P KLNQSYIN ...String:
ADTLCIGYHA NNSTDTVDTV LEKNVTVTHS VNLLEDKHNG KLCKLRGVAP LHLGKCNIAG WILGNPECES LSTASSWSYI VETSNSDNG TCYPGDFINY EELREQLSSV SSFERFEIFP KTSSWPNHDS NKGVTAACPH AGAKSFYKNL IWLVKKGNSY P KLNQSYIN DKGKEVLVLW GIHHPSTTAD QQSLYQNADA YVFVGTSRYS KKFKPEIATR PKVRDQEGRM NYYWTLVEPG DK ITFEATG NLVVPRYAFT MERNAGSGII ISDTPVHDCN TTCQTPEGAI NTSLPFQNIH PITIGKCPKY VKSTKLRLAT GLR NVPS

UniProtKB: Hemagglutinin

-
Macromolecule #2: Hemagglutinin HA2 chain

MacromoleculeName: Hemagglutinin HA2 chain / type: protein_or_peptide / ID: 2 / Details: A/Michigan/45/2015 H1 HA2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 28.359492 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IQSRGLFGAI AGFIEGGWTG MVDGWYGYHH QNEQGSGYAA DLKSTQNAID KITNKVNSVI EKMNTQFTAV GKEFNHLEKR IENLNKKVD DGFLDIWTYN AELLVLLENE RTLDYHDSNV KNLYEKVRNQ LKNNAKEIGN GCFEFYHKCD NTCMESVKNG T YDYPKYSE ...String:
IQSRGLFGAI AGFIEGGWTG MVDGWYGYHH QNEQGSGYAA DLKSTQNAID KITNKVNSVI EKMNTQFTAV GKEFNHLEKR IENLNKKVD DGFLDIWTYN AELLVLLENE RTLDYHDSNV KNLYEKVRNQ LKNNAKEIGN GCFEFYHKCD NTCMESVKNG T YDYPKYSE EAKLNREKID GVKGALEVLF QGPGSHHHHH HHHLGGSGYI PEAPRDGQAY VRKDGEWVLL STFLGSGGGL ND IFEAQKI EWH

UniProtKB: Hemagglutinin

-
Macromolecule #3: 09-1B12 HC Fv

MacromoleculeName: 09-1B12 HC Fv / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.967645 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSAPE VKRPGASVRL SCKASGYTFN TYGIIWVRQA PGQGLEWMGW ISAYTGNTNY AQKVQGRVTM TTDITTSTAY LELRGLRSD DTAVYYCARG LLQGAVILDS YHYALDFWGQ GTTVTVSS

-
Macromolecule #4: 09-1B12 LC Fv

MacromoleculeName: 09-1B12 LC Fv / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.121513 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPGT LSLSPGERAT LSCRASQSVT NRFIAWYQHK PGQSPRLLIY GASSRATGIP DRFSGRGSGT DFTLTISRLE PEDFAVYYC QQYDTSPRWT FGQGTKLEIK

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 18 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.7 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormula
50.0 nMTris
100.0 nMNaClSodium chloride
0.1 %Octyl-beta-Glucoside
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2

-
Image processing

Startup modelType of model: INSILICO MODEL / Details: CryoSPARC Ab-initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 89540
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