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- EMDB-7774: 3.9A Cryo-EM structure of murine antibody bound at a novel epitop... -

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Basic information

Entry
Database: EMDB / ID: EMD-7774
Title3.9A Cryo-EM structure of murine antibody bound at a novel epitope of respiratory syncytial virus fusion protein
Map data3.9A density map of R4.C6 in complex with RSV F710
Sample
  • Complex: Complex of R4.C6 Fab with RSV F protein
    • Complex: R4.C6 Fab
      • Protein or peptide: R4.C6 Fab Heavy Chain
      • Protein or peptide: R4.C6 Fab Light Chain
    • Complex: RSV F protein
      • Protein or peptide: Fusion glycoprotein F0, Envelope glycoprotein chimera
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


positive regulation of syncytium formation by virus / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
Envelope glycoprotein / Fusion glycoprotein F0
Similarity search - Component
Biological speciesMus musculus (house mouse) / Human respiratory syncytial virus A2 / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsXie Q / Wang Z / Chen X / Ni F / Ma J / Wang Q
CitationJournal: PLoS One / Year: 2019
Title: Structure basis of neutralization by a novel site II/IV antibody against respiratory syncytial virus fusion protein.
Authors: Qingqing Xie / Zhao Wang / Fengyun Ni / Xiaorui Chen / Jianpeng Ma / Nita Patel / Hanxin Lu / Ye Liu / Jing-Hui Tian / David Flyer / Michael J Massare / Larry Ellingsworth / Gregory Glenn / ...Authors: Qingqing Xie / Zhao Wang / Fengyun Ni / Xiaorui Chen / Jianpeng Ma / Nita Patel / Hanxin Lu / Ye Liu / Jing-Hui Tian / David Flyer / Michael J Massare / Larry Ellingsworth / Gregory Glenn / Gale Smith / Qinghua Wang /
Abstract: Globally, human respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infections in newborns, young children, and the elderly for which there is no vaccine. The RSV fusion ...Globally, human respiratory syncytial virus (RSV) is a leading cause of lower respiratory tract infections in newborns, young children, and the elderly for which there is no vaccine. The RSV fusion (F) glycoprotein is a major target for vaccine development. Here, we describe a novel monoclonal antibody (designated as R4.C6) that recognizes both pre-fusion and post-fusion RSV F, and binds with nanomole affinity to a unique neutralizing site comprised of antigenic sites II and IV on the globular head. A 3.9 Å-resolution structure of RSV F-R4.C6 Fab complex was obtained by single particle cryo-electron microscopy and 3D reconstruction. The structure unraveled detailed interactions of R4.C6 with antigenic site II on one protomer and site IV on a neighboring protomer of post-fusion RSV F protein. These findings significantly further our understanding of the antigenic complexity of the F protein and provide new insights into RSV vaccine design.
History
DepositionApr 2, 2018-
Header (metadata) releaseJul 25, 2018-
Map releaseJul 31, 2019-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0232
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0232
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6cxc
  • Surface level: 0.0232
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7774.png

Downloads & links

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Map

FileDownload / File: emd_7774.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3.9A density map of R4.C6 in complex with RSV F710
Voxel sizeX=Y=Z: 1.2546 Å
Density
Contour LevelBy AUTHOR: 0.0232 / Movie #1: 0.0232
Minimum - Maximum-0.03947702 - 0.0792006
Average (Standard dev.)0.00010288416 (±0.0029554246)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 321.1776 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.25460156251.25460156251.2546015625
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z321.178321.178321.178
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0390.0790.000

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Supplemental data

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Sample components

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Entire : Complex of R4.C6 Fab with RSV F protein

EntireName: Complex of R4.C6 Fab with RSV F protein
Components
  • Complex: Complex of R4.C6 Fab with RSV F protein
    • Complex: R4.C6 Fab
      • Protein or peptide: R4.C6 Fab Heavy Chain
      • Protein or peptide: R4.C6 Fab Light Chain
    • Complex: RSV F protein
      • Protein or peptide: Fusion glycoprotein F0, Envelope glycoprotein chimera
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of R4.C6 Fab with RSV F protein

SupramoleculeName: Complex of R4.C6 Fab with RSV F protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: R4.C6 Fab

SupramoleculeName: R4.C6 Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Mus musculus (house mouse)

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Supramolecule #3: RSV F protein

SupramoleculeName: RSV F protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Human respiratory syncytial virus A2
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: R4.C6 Fab Heavy Chain

MacromoleculeName: R4.C6 Fab Heavy Chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.831376 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
MAEVQLQQSG PELVKPGASV KISCKASGYA FSNSWMSWVK QRPGKGLEWI GRLFPADGDI TYNGHFKDKA ALTADKSSNT AYIQLSSLT SEDSAVYFCA RMDNSEVFWG QGTLVTVSA

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Macromolecule #2: R4.C6 Fab Light Chain

MacromoleculeName: R4.C6 Fab Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.457151 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
MADILLTQSQ KFMSTSVGDR VSITCKASQN VRTGVSWYQR KPGQSPKALI YLASNRHTGV PDRFTGRGSG TDFTLTISEV QSEDLADYF CLQHWTVPYT FGGGTKLEIK RTAAAPSRAN SFK

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Macromolecule #3: Fusion glycoprotein F0, Envelope glycoprotein chimera

MacromoleculeName: Fusion glycoprotein F0, Envelope glycoprotein chimera / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 60.728047 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: QNITEEFYQS TCSAVSKGYL SALRTGWYTS VITIELSNIK ENKCNGTDAK VKLIKQELDK YKNAVTELQL LMQSTPATNN RARRELPRF MNYTLNNAKK TNVTLSKKQK QQFLGFLLGV GSAIASGVAV SKVLHLEGEV NKIKSALLST NKAVVSLSNG V SVLTSKVL ...String:
QNITEEFYQS TCSAVSKGYL SALRTGWYTS VITIELSNIK ENKCNGTDAK VKLIKQELDK YKNAVTELQL LMQSTPATNN RARRELPRF MNYTLNNAKK TNVTLSKKQK QQFLGFLLGV GSAIASGVAV SKVLHLEGEV NKIKSALLST NKAVVSLSNG V SVLTSKVL DLKNYIDKQL LPIVNKQSCS ISNIETVIEF QQKNNRLLEI TREFSVNAGV TTPVSTYMLT NSELLSLIND MP ITNDQKK LMSNNVQIVR QQSYSIMSII KEEVLAYVVQ LPLYGVIDTP CWKLHTSPLC TTNTKEGSNI CLTRTDRGWY CDN AGSVSF FPQAETCKVQ SNRVFCDTMN SLTLPSEVNL CNVDIFNPKY DCKIMTSKTD VSSSVITSLG AIVSCYGKTK CTAS NKNRG IIKTFSNGCD YVSNKGVDTV SVGNTLYYVN KQEGKSLYVK GEPIINFYDP LVFPSDEFDA SISQVNEKIN QSLAF IRKS DELLHNVNAG KSTTNIMGAL VPRGSPGSGY IPEAPRDGQA YVRKDGEWVL LSTFLGSSHH HHHH

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: GRAPHENE OXIDE
VitrificationCryogen name: NITROGEN / Chamber humidity: 98 % / Chamber temperature: 295 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeJEOL 3200FSC
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 4.7 mm
Sample stageSpecimen holder model: JEOL 3200FSC CRYOHOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2

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Image processing

CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN2
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 543639
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6cxc:
3.9A Cryo-EM structure of murine antibody bound at a novel epitope of respiratory syncytial virus fusion protein

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