[English] 日本語
Yorodumi
- EMDB-27990: HMPV F complex with 4I3 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-27990
TitleHMPV F complex with 4I3 Fab
Map data
Sample
  • Complex: MPV fusion protein complex with 4I3 Fab
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: 4I3 heavy chain protein
    • Protein or peptide: 4I3 light chain protein
Keywordshuman antibodies / RSV and MPV Fusion protein / complex Cryo-EM structure / viral protein and antiviral protein / BIOSYNTHETIC PROTEIN
Biological speciesHuman metapneumovirus / Human metapneumovirus A / Homo sapiens (human)
Methodsingle particle reconstruction / Resolution: 3.33 Å
AuthorsWen X / Jardetzky TS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI137523 United States
CitationJournal: Cell Host Microbe / Year: 2023
Title: Potent cross-neutralization of respiratory syncytial virus and human metapneumovirus through a structurally conserved antibody recognition mode.
Authors: Xiaolin Wen / Naveenchandra Suryadevara / Nurgun Kose / Jing Liu / Xiaoyan Zhan / Laura S Handal / Lauren E Williamson / Andrew Trivette / Robert H Carnahan / Theodore S Jardetzky / James E Crowe /
Abstract: Respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) infections pose a significant health burden. Using pre-fusion conformation fusion (F) proteins, we isolated a panel of anti-F ...Respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) infections pose a significant health burden. Using pre-fusion conformation fusion (F) proteins, we isolated a panel of anti-F antibodies from a human donor. One antibody (RSV-199) potently cross-neutralized 8 RSV and hMPV strains by recognizing antigenic site III, which is partially conserved in RSV and hMPV F. Next, we determined the cryoelectron microscopy (cryo-EM) structures of RSV-199 bound to RSV F trimers, hMPV F monomers, and an unexpected dimeric form of hMPV F. These structures revealed how RSV-199 engages both RSV and hMPV F proteins through conserved interactions of the antibody heavy-chain variable region and how variability within heavy-chain complementarity-determining region 3 (HCDR3) can be accommodated at the F protein interface in site-III-directed antibodies. Furthermore, RSV-199 offered enhanced protection against RSV A and B strains and hMPV in cotton rats. These findings highlight the mechanisms of broad neutralization and therapeutic potential of RSV-199.
History
DepositionAug 30, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateAug 23, 2023-
Current statusAug 23, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_27990.png

Downloads & links

-
Map

FileDownload / File: emd_27990.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 256 pix.
= 284.16 Å		1.11 Å/pix.
x 256 pix.
= 284.16 Å		1.11 Å/pix.
x 256 pix.
= 284.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.496
Minimum - Maximum-4.97388 - 8.235033
Average (Standard dev.)-0.00087320374 (±0.10104622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 284.16 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_27990_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_27990_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MPV fusion protein complex with 4I3 Fab

EntireName: MPV fusion protein complex with 4I3 Fab
Components
  • Complex: MPV fusion protein complex with 4I3 Fab
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: 4I3 heavy chain protein
    • Protein or peptide: 4I3 light chain protein

-
Supramolecule #1: MPV fusion protein complex with 4I3 Fab

SupramoleculeName: MPV fusion protein complex with 4I3 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human metapneumovirus

-
Macromolecule #1: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human metapneumovirus A
Molecular weightTheoretical: 45.044461 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LKESYLEESC STITEGYLSV LRTGWYTNVF TLEVGDVENL TCADGPSLIK TELDLTKSAL RELRTVSADQ LAREEQIENP RQSRFVLGA IALGVCTAAA VTAGVAIAKT IRLESEVTAI KNALKKTNEA VSTLGNGVRV LATAVRELKD FVSKNLTRAI N KNKCDIPD ...String:
LKESYLEESC STITEGYLSV LRTGWYTNVF TLEVGDVENL TCADGPSLIK TELDLTKSAL RELRTVSADQ LAREEQIENP RQSRFVLGA IALGVCTAAA VTAGVAIAKT IRLESEVTAI KNALKKTNEA VSTLGNGVRV LATAVRELKD FVSKNLTRAI N KNKCDIPD LKMAVSFSQF NRRFLNVVRQ FSDNAGITPA ISLDLMTDAE LARAVSNMPT SAGQIKLMLE NRAMVRRKGF GI LIGVYGS SVIYMVQLPI FGVIDTPCWI VKAAPSCSEK KGNYACLLRE DQGWYCQNAG STVYYPNEKD CETRGDHVFC DTA CGINVA EQSKECNINI STTNYPCKVS TGRHPISMVA LSPLGALVAC YKGVSCSIGS NRVGIIKQLN KGCSYITNQD ADTV TIDNT VYQLSKVEG

-
Macromolecule #2: 4I3 heavy chain protein

MacromoleculeName: 4I3 heavy chain protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.376045 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSETLSL TCTVSGGSIS NYYWNWIRQP PGKGLEWIGY FYYSGSTKYN PSLKSRVTIS LDMSKNQFSL KLRSVTAAD TAVYYCARGT MRESGMPDAF DIWGQGTVVT VS

-
Macromolecule #3: 4I3 light chain protein

MacromoleculeName: 4I3 light chain protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.438607 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SYELIQPPSV SVSPGQTAII TCSGNNLGNK YACWYQQKAG QSPVMIIYQD NRRPSGIPER FSGSNSGNTA TLTISGTQAM DEADYYCQA WDSSVVFGGG TKLTVLGQ

-
Experimental details

-
Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.8 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 36.522 µm / Nominal defocus min: 11.445 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2774162
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4dag

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 226482
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final 3D classificationNumber classes: 100 / Software - Name: cryoSPARC

-
Atomic model buiding 1

Initial modelPDB ID:

4dag


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8eay:
HMPV F complex with 4I3 Fab

+
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