[English] 日本語
Yorodumi
- EMDB-52444: Respiratory Syncytial Virus Fusion protein in the postfusion conf... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52444
TitleRespiratory Syncytial Virus Fusion protein in the postfusion conformation in complex with monoclonal antibody 131-2a Fab
Map dataRSV-F postfusion in complex with 131-2a Fab
Sample
  • Complex: RSV-F in postfusion conformation in complex with 131-2a Fab
    • Complex: 131-2a Fab
      • Protein or peptide: 131-2a heavy chain
      • Protein or peptide: 131-2a light chain
    • Complex: RSV-F
      • Protein or peptide: Fusion glycoprotein F0
      • Protein or peptide: Fusion glycoprotein F1,Probable N-acetylmuramidase
Keywordsantigenic site I / VIRAL PROTEIN
Function / homology
Function and homology information


peptidoglycan N-acetylglucosaminidase activity / amidase activity / Translation of respiratory syncytial virus mRNAs / symbiont-mediated induction of syncytium formation / division septum assembly / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry ...peptidoglycan N-acetylglucosaminidase activity / amidase activity / Translation of respiratory syncytial virus mRNAs / symbiont-mediated induction of syncytium formation / division septum assembly / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / cell wall organization / lysozyme / lysozyme activity / killing of cells of another organism / entry receptor-mediated virion attachment to host cell / defense response to bacterium / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
: / Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / Lysin motif / LysM domain superfamily / Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / LysM domain / LysM domain profile. / LysM domain
Similarity search - Domain/homology
Probable N-acetylmuramidase / Fusion glycoprotein F0
Similarity search - Component
Biological specieshuman respiratory syncytial virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSnijder J
Funding support Netherlands, European Union, 2 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: Structural basis for postfusion-specific binding to Respiratory Syncytial Virus F protein by the canonical antigenic site I antibody 131-2a
Authors: Peng W / Siborova M / Wu X / Du W / Schulte D / Pronker MF / De Haan CAM / Snijder J
History
DepositionJan 2, 2025-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52444.png

Downloads & links

-
Map

FileDownload / File: emd_52444.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRSV-F postfusion in complex with 131-2a Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 240 pix.
= 300. Å		1.25 Å/pix.
x 240 pix.
= 300. Å		1.25 Å/pix.
x 240 pix.
= 300. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.8751532 - 2.9144058
Average (Standard dev.)0.0004596001 (±0.0496678)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 300.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_52444_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_52444_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_52444_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : RSV-F in postfusion conformation in complex with 131-2a Fab

EntireName: RSV-F in postfusion conformation in complex with 131-2a Fab
Components
  • Complex: RSV-F in postfusion conformation in complex with 131-2a Fab
    • Complex: 131-2a Fab
      • Protein or peptide: 131-2a heavy chain
      • Protein or peptide: 131-2a light chain
    • Complex: RSV-F
      • Protein or peptide: Fusion glycoprotein F0
      • Protein or peptide: Fusion glycoprotein F1,Probable N-acetylmuramidase

-
Supramolecule #1: RSV-F in postfusion conformation in complex with 131-2a Fab

SupramoleculeName: RSV-F in postfusion conformation in complex with 131-2a Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: human respiratory syncytial virus
Molecular weightTheoretical: 213 kDa/nm

-
Supramolecule #2: 131-2a Fab

SupramoleculeName: 131-2a Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Mus musculus (house mouse)

-
Supramolecule #3: RSV-F

SupramoleculeName: RSV-F / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: human respiratory syncytial virus

-
Macromolecule #1: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: human respiratory syncytial virus
Molecular weightTheoretical: 8.930087 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QNITEEFYQS TCSAVSKGYL SALRTGWYTS VITIELSNIK ENKCNGTDAK VKLIKQELDK YKNAVTELQL LMQSTPAANS

UniProtKB: Fusion glycoprotein F0

-
Macromolecule #2: Fusion glycoprotein F1,Probable N-acetylmuramidase

MacromoleculeName: Fusion glycoprotein F1,Probable N-acetylmuramidase / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: lysozyme
Source (natural)Organism: human respiratory syncytial virus
Molecular weightTheoretical: 55.75102 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: FLGFLLGVGS AIASGIAVSK VLHLEGEVNK IKSALLSTNK AVVSLSNGVS VLTSKVLDLK NYIDKQLLPI VNKQSCSISN IETVIEFQQ KNNRLLEITR EFSVNAGVTT PVSTYMLTNS ELLSLINDMP ITNDQKKLMS NNVQIVRQQS YSIMSIIKEE V LAYVVQLP ...String:
FLGFLLGVGS AIASGIAVSK VLHLEGEVNK IKSALLSTNK AVVSLSNGVS VLTSKVLDLK NYIDKQLLPI VNKQSCSISN IETVIEFQQ KNNRLLEITR EFSVNAGVTT PVSTYMLTNS ELLSLINDMP ITNDQKKLMS NNVQIVRQQS YSIMSIIKEE V LAYVVQLP LYGVIDTPCW KLHTSPLCTT NTKEGSNICL TRTDRGWYCD NAGSVSFFPQ AETCKVQSNR VFCDTMNSLT LP SEVNLCN IDIFNPKYDC KIMTSKTDVS SSVITSLGAI VSCYGKTKCT ASNKNRGIIK TFSNGCDYVS NKGVDTVSVG NTL YYVNKQ EGKSLYVKGE PIINFYDPLV FPSDEFDASI SQVNEKINQS LAFIRKSDEL LHNLIKRMKQ IEDKIEEIES KQKK IENEI ARIKKGNTNS GGSTTTITNN NSGTNSSSTT YTVKSGDTLW GISQRYGISV AQIQSANNLK STIIYIGQKL VLTGS ASST NSGGSNNSAS TTPTTSVTPA KPTSQTT

UniProtKB: Fusion glycoprotein F0, Probable N-acetylmuramidase

-
Macromolecule #3: 131-2a heavy chain

MacromoleculeName: 131-2a heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.162569 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLQQSGPE LVKPGASVKI SCKASGFTFT DFSIHWVKQS QGKSLDWVGY IYPYTGGNGY NLKFQSKATL TVDTSSTTAY MELRSLTSE DSAVYYCARR EGNFVGAMDY WGQGTSVTVS S

-
Macromolecule #4: 131-2a light chain

MacromoleculeName: 131-2a light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.88026 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVLTQSPAS LAVSLGQRAT ISCRASESVD NFGISFINWF QQKPGQPPKL LIYGASNQGS GVPARFSGSG SGTDFSLNIH PMEEVDTAV YFCHQSKEVP YTFGGGTKLE IK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS 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: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 394000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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