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Yorodumi- EMDB-7774: 3.9A Cryo-EM structure of murine antibody bound at a novel epitop... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7774 | |||||||||
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Title | 3.9A Cryo-EM structure of murine antibody bound at a novel epitope of respiratory syncytial virus fusion protein | |||||||||
Map data | 3.9A density map of R4.C6 in complex with RSV F710 | |||||||||
Sample |
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Function / homology | Function and homology information positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane ...positive regulation of syncytium formation by virus / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / 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 / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Human respiratory syncytial virus A2 / Human immunodeficiency virus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Xie Q / Wang Z / Chen X / Ni F / Ma J / Wang Q | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7774.map.gz | 59.9 MB | EMDB map data format | |
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Header (meta data) | emd-7774-v30.xml emd-7774.xml | 16.1 KB 16.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7774_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_7774.png | 47.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7774 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7774 | HTTPS FTP |
-Related structure data
Related structure data | 6cxcMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_7774.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3.9A density map of R4.C6 in complex with RSV F710 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2546 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Complex of R4.C6 Fab with RSV F protein
Entire | Name: Complex of R4.C6 Fab with RSV F protein |
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Components |
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-Supramolecule #1: Complex of R4.C6 Fab with RSV F protein
Supramolecule | Name: 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
Supramolecule | Name: R4.C6 Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Mus musculus (house mouse) |
-Supramolecule #3: RSV F protein
Supramolecule | Name: RSV F protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: Human respiratory syncytial virus A2 |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Macromolecule #1: R4.C6 Fab Heavy Chain
Macromolecule | Name: R4.C6 Fab Heavy Chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 12.831376 KDa |
Recombinant expression | Organism: Mus musculus (house mouse) |
Sequence | String: MAEVQLQQSG PELVKPGASV KISCKASGYA FSNSWMSWVK QRPGKGLEWI GRLFPADGDI TYNGHFKDKA ALTADKSSNT AYIQLSSLT SEDSAVYFCA RMDNSEVFWG QGTLVTVSA |
-Macromolecule #2: R4.C6 Fab Light Chain
Macromolecule | Name: R4.C6 Fab Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 13.457151 KDa |
Recombinant expression | Organism: Mus musculus (house mouse) |
Sequence | String: MADILLTQSQ KFMSTSVGDR VSITCKASQN VRTGVSWYQR KPGQSPKALI YLASNRHTGV PDRFTGRGSG TDFTLTISEV QSEDLADYF CLQHWTVPYT FGGGTKLEIK RTAAAPSRAN SFK |
-Macromolecule #3: Fusion glycoprotein F0, Envelope glycoprotein chimera
Macromolecule | Name: Fusion glycoprotein F0, Envelope glycoprotein chimera / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Molecular weight | Theoretical: 60.728047 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: 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 |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 6 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: GRAPHENE OXIDE |
Vitrification | Cryogen name: NITROGEN / Chamber humidity: 98 % / Chamber temperature: 295 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Image recording | Film 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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.7 mm |
Sample stage | Specimen holder model: JEOL 3200FSC CRYOHOLDER / Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-6cxc: |