[English] 日本語
Yorodumi
- EMDB-23933: Cryo-EM structure of Prefusion-stabilized RSV F (DS-Cav1) in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-23933
TitleCryo-EM structure of Prefusion-stabilized RSV F (DS-Cav1) in complex with Fab AM14
Map dataCryo-EM structure of RSV DS-Cav1 in complex with FabAM14.
Sample
  • Complex: Homo sapiens respiratory syncytial virus A
    • Complex: Fusion glycoprotein F1 and F2 fused with Fibritin trimerization domain.
      • Protein or peptide: Fusion glycoprotein F0,Envelope glycoprotein
    • Complex: Fab AM14 heavy and light chain
      • Protein or peptide: AM14 Fab Heavy Chain
      • Protein or peptide: AM14 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsantigen / antibody / epitope / vaccine / structural vaccinology / IMMUNE SYSTEM
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / host cell plasma membrane / virion membrane / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
Fusion glycoprotein F0 / Envelope glycoprotein
Similarity search - Component
Biological speciesRespiratory syncytial virus A2 / Homo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsAbeyrathne PD / Malito E
CitationJournal: MAbs / Year: 2021
Title: Improved epitope resolution of the prefusion trimer-specific antibody AM14 bound to the RSV F glycoprotein.
Authors: Wayne Harshbarger / Priyanka D Abeyrathne / Sai Tian / Ying Huang / Sumana Chandramouli / Matthew James Bottomley / Enrico Malito /
Abstract: Respiratory syncytial virus (RSV) is the most common cause of acute lower respiratory tract infections resulting in medical intervention and hospitalizations during infancy and early childhood, and ...Respiratory syncytial virus (RSV) is the most common cause of acute lower respiratory tract infections resulting in medical intervention and hospitalizations during infancy and early childhood, and vaccination against RSV remains a public health priority. The RSV F glycoprotein is a major target of neutralizing antibodies, and the prefusion stabilized form of F (DS-Cav1) is under investigation as a vaccine antigen. AM14 is a human monoclonal antibody with the exclusive capacity of binding an epitope on prefusion F (PreF), which spans two F protomers. The quality of recognizing a trimer-specific epitope makes AM14 valuable for probing PreF-based immunogen conformation and functionality during vaccine production. Currently, only a low-resolution (5.5 Å) X-ray structure is available of the PreF-AM14 complex, revealing few reliable details of the interface. Here, we perform complementary structural studies using X-ray crystallography and cryo-electron microscopy (cryo-EM) to provide improved resolution structures at 3.6 Å and 3.4 Å resolutions, respectively. Both X-ray and cryo-EM structures provide clear side-chain densities, which allow for accurate mapping of the AM14 epitope on DS-Cav1. The structures help rationalize the molecular basis for AM14 loss of binding to RSV F monoclonal antibody-resistant mutants and reveal flexibility for the side chain of a key antigenic residue on PreF. This work provides the basis for a comprehensive understanding of RSV F trimer specificity with implications in vaccine design and quality assessment of PreF-based immunogens.
History
DepositionMay 4, 2021-
Header (metadata) releaseSep 8, 2021-
Map releaseSep 8, 2021-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.9
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 5.9
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7mpg
  • Surface level: 5.9
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23933.png

Downloads & links

-
Map

FileDownload / File: emd_23933.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of RSV DS-Cav1 in complex with FabAM14.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 428. Å		1.07 Å/pix.
x 400 pix.
= 428. Å		1.07 Å/pix.
x 400 pix.
= 428. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.94 / Movie #1: 5.9
Minimum - Maximum-19.019707 - 30.022686
Average (Standard dev.)0.000000000003571 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 428.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z428.000428.000428.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-19.02030.0230.000

-
Supplemental data

-
Sample components

-
Entire : Homo sapiens respiratory syncytial virus A

EntireName: Homo sapiens respiratory syncytial virus A
Components
  • Complex: Homo sapiens respiratory syncytial virus A
    • Complex: Fusion glycoprotein F1 and F2 fused with Fibritin trimerization domain.
      • Protein or peptide: Fusion glycoprotein F0,Envelope glycoprotein
    • Complex: Fab AM14 heavy and light chain
      • Protein or peptide: AM14 Fab Heavy Chain
      • Protein or peptide: AM14 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Homo sapiens respiratory syncytial virus A

SupramoleculeName: Homo sapiens respiratory syncytial virus A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 285 KDa

-
Supramolecule #2: Fusion glycoprotein F1 and F2 fused with Fibritin trimerization d...

SupramoleculeName: Fusion glycoprotein F1 and F2 fused with Fibritin trimerization domain.
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Respiratory syncytial virus A2

-
Supramolecule #3: Fab AM14 heavy and light chain

SupramoleculeName: Fab AM14 heavy and light chain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Fusion glycoprotein F0,Envelope glycoprotein

MacromoleculeName: Fusion glycoprotein F0,Envelope glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.806496 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QNITEEFYQS TCSAVSKGYL SALRTGWYTS VITIELSNIK ENKCNGTDAK VKLIKQELDK YKNAVTELQL LMQSTPATNN RAFLGFLLG VGSAIASGVA VCKVLHLEGE VNKIKSALLS TNKAVVSLSN GVSVLTFKVL DLKNYIDKQL LPILNKQSCS I SNIETVIE ...String:
QNITEEFYQS TCSAVSKGYL SALRTGWYTS VITIELSNIK ENKCNGTDAK VKLIKQELDK YKNAVTELQL LMQSTPATNN RAFLGFLLG VGSAIASGVA VCKVLHLEGE VNKIKSALLS TNKAVVSLSN GVSVLTFKVL DLKNYIDKQL LPILNKQSCS I SNIETVIE FQQKNNRLLE ITREFSVNAG VTTPVSTYML TNSELLSLIN DMPITNDQKK LMSNNVQIVR QQSYSIMCII KE EVLAYVV QLPLYGVIDT PCWKLHTSPL CTTNTKEGSN ICLTRTDRGW YCDNAGSVSF FPQAETCKVQ SNRVFCDTMN SLT LPSEVN LCNVDIFNPK YDCKIMTSKT DVSSSVITSL GAIVSCYGKT KCTASNKNRG IIKTFSNGCD YVSNKGVDTV SVGN TLYYV NKQEGKSLYV KGEPIINFYD PLVFPSDEFD ASISQVNEKI NQSLAFIRKS DELLSAIGGY IPEAPRDGQA YVRKD GEWV LLSTFLGGLV PR

UniProtKB: Fusion glycoprotein F0, Envelope glycoprotein

-
Macromolecule #2: AM14 Fab Heavy Chain

MacromoleculeName: AM14 Fab Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.380352 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: CVQLVESGGG VVQPGRSLRL SCAASGFSFS HYAMHWVRQA PGKGLEWVAV ISYDGENTYY ADSVKGRFSI SRDNSKNTVS LQMNSLRPE DTALYYCARD RIVDDYYYYG MDVWGQGATV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
CVQLVESGGG VVQPGRSLRL SCAASGFSFS HYAMHWVRQA PGKGLEWVAV ISYDGENTYY ADSVKGRFSI SRDNSKNTVS LQMNSLRPE DTALYYCARD RIVDDYYYYG MDVWGQGATV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK GSENLYFQGS HH HHHH

-
Macromolecule #3: AM14 Fab Light Chain

MacromoleculeName: AM14 Fab Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.870906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METPAELLFL LLLWLPDTTG DIQMTQSPSS LSASVGDRVT ITCQASQDIK KYLNWYHQKP GKVPELLMHD ASNLETGVPS RFSGRGSGT DFTLTISSLQ PEDIGTYYCQ QYDNLPPLTF GGGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ ...String:
METPAELLFL LLLWLPDTTG DIQMTQSPSS LSASVGDRVT ITCQASQDIK KYLNWYHQKP GKVPELLMHD ASNLETGVPS RFSGRGSGT DFTLTISSLQ PEDIGTYYCQ QYDNLPPLTF GGGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ WKVDNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

-
Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / 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

Concentration0.5 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
10.0 mMHEPES(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)
150.0 mMNaClSodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsDS-Cav1-FabAM14.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 1078 / Average exposure time: 60.0 sec. / Average electron dose: 26.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE / Details: cisTEM Ab-initio 3D reconstruction.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0.0) / Number images used: 23737
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cisTEM (ver. 1.0.0)
Final angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cisTEM (ver. 1.0.0)
Final 3D classificationNumber classes: 250 / Software - Name: cisTEM (ver. 1.0.0)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7mpg:
Cryo-EM structure of Prefusion-stabilized RSV F (DS-Cav1) in complex with Fab AM14

+
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