+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23520 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of RSV preF bound by Fabs 32.4K and 01.4B | |||||||||
Map data | Full map, sharpened with DeepEMhancer | |||||||||
Sample |
| |||||||||
Function / homology | Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / 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 / Fusion glycoprotein F0 Function and homology information | |||||||||
Biological species | Respiratory syncytial virus / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.21 Å | |||||||||
Authors | Wrapp D / McLellan JS | |||||||||
Citation | Journal: Immunity / Year: 2021 Title: Vaccination with prefusion-stabilized respiratory syncytial virus fusion protein induces genetically and antigenically diverse antibody responses. Authors: Maryam Mukhamedova / Daniel Wrapp / Chen-Hsiang Shen / Morgan S A Gilman / Tracy J Ruckwardt / Chaim A Schramm / Larissa Ault / Lauren Chang / Alexandrine Derrien-Colemyn / Sarah A M Lucas / ...Authors: Maryam Mukhamedova / Daniel Wrapp / Chen-Hsiang Shen / Morgan S A Gilman / Tracy J Ruckwardt / Chaim A Schramm / Larissa Ault / Lauren Chang / Alexandrine Derrien-Colemyn / Sarah A M Lucas / Amy Ransier / Samuel Darko / Emily Phung / Lingshu Wang / Yi Zhang / Scott A Rush / Bharat Madan / Guillaume B E Stewart-Jones / Pamela J Costner / LaSonji A Holman / Somia P Hickman / Nina M Berkowitz / Nicole A Doria-Rose / Kaitlyn M Morabito / Brandon J DeKosky / Martin R Gaudinski / Grace L Chen / Michelle C Crank / John Misasi / Nancy J Sullivan / Daniel C Douek / Peter D Kwong / Barney S Graham / Jason S McLellan / John R Mascola / Abstract: An effective vaccine for respiratory syncytial virus (RSV) is an unrealized public health goal. A single dose of the prefusion-stabilized fusion (F) glycoprotein subunit vaccine (DS-Cav1) ...An effective vaccine for respiratory syncytial virus (RSV) is an unrealized public health goal. A single dose of the prefusion-stabilized fusion (F) glycoprotein subunit vaccine (DS-Cav1) substantially increases serum-neutralizing activity in healthy adults. We sought to determine whether DS-Cav1 vaccination induces a repertoire mirroring the pre-existing diversity from natural infection or whether antibody lineages targeting specific epitopes predominate. We evaluated RSV F-specific B cell responses before and after vaccination in six participants using complementary B cell sequencing methodologies and identified 555 clonal lineages. DS-Cav1-induced lineages recognized the prefusion conformation of F (pre-F) and were genetically diverse. Expressed antibodies recognized all six antigenic sites on the pre-F trimer. We identified 34 public clonotypes, and structural analysis of two antibodies from a predominant clonotype revealed a common mode of recognition. Thus, vaccination with DS-Cav1 generates a diverse polyclonal response targeting the antigenic sites on pre-F, supporting the development and advanced testing of pre-F-based vaccines against RSV. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23520.map.gz | 124.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-23520-v30.xml emd-23520.xml | 23.3 KB 23.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23520_fsc.xml | 12.6 KB | Display | FSC data file |
Images | emd_23520.png | 155.1 KB | ||
Others | emd_23520_additional_1.map.gz emd_23520_half_map_1.map.gz emd_23520_half_map_2.map.gz | 136.6 MB 134.2 MB 134.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23520 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23520 | HTTPS FTP |
-Validation report
Summary document | emd_23520_validation.pdf.gz | 682.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_23520_full_validation.pdf.gz | 682.2 KB | Display | |
Data in XML | emd_23520_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | emd_23520_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23520 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23520 | HTTPS FTP |
-Related structure data
Related structure data | 7lucMC 7ludC 7lueC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_23520.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Full map, sharpened with DeepEMhancer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.073 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: Focused map (C1)
File | emd_23520_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Focused map (C1) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map B
File | emd_23520_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map B | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map A
File | emd_23520_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Prefusion RSV F bound by Fabs 01.4B and 32.4K
Entire | Name: Prefusion RSV F bound by Fabs 01.4B and 32.4K |
---|---|
Components |
|
-Supramolecule #1: Prefusion RSV F bound by Fabs 01.4B and 32.4K
Supramolecule | Name: Prefusion RSV F bound by Fabs 01.4B and 32.4K / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Respiratory syncytial virus |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Experimental: 440 KDa |
-Macromolecule #1: Fusion glycoprotein F0
Macromolecule | Name: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Respiratory syncytial virus |
Molecular weight | Theoretical: 58.615941 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QNITEEFYQS TCSAVSKGYL SALRTGWYTS VITIELSNIK EIKCNGTDAK VKLIKQELDK YKNAVTELQL LMQSTPATNN RARRELPRF MNYTLNNAKK TNVTLSKKRK RRFLGFLLGV GSAIASGVAV SKVLHLEGEV NKIKSALLST NKAVVSLSNG V SVLTSKVL ...String: QNITEEFYQS TCSAVSKGYL SALRTGWYTS VITIELSNIK EIKCNGTDAK VKLIKQELDK YKNAVTELQL LMQSTPATNN RARRELPRF MNYTLNNAKK TNVTLSKKRK RRFLGFLLGV GSAIASGVAV SKVLHLEGEV NKIKSALLST NKAVVSLSNG V SVLTSKVL DLKNYIDKQL LPIVNKQSCS IPNIETVIEF 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 DELLSAIGGY IPEAPRDGQA YVRKDGEWVL LSTFLGSLEV LFQ |
-Macromolecule #2: 01.4B Fab Heavy chain
Macromolecule | Name: 01.4B Fab Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.154789 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: QVQLVQSGAE VKKPGASVKL SCQASGYTFN NYGVSWLRQA PGQGLEWMGW ISAYNGNKKY APKFQGRLTL TTVTSTGTAY MELRSLKSD DTALYFCARD PPAVAAAMFD FWGQGTQVTV SS |
-Macromolecule #3: 01.4B Fab Light chain
Macromolecule | Name: 01.4B Fab Light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 12.499002 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DVVLTQSPLS LPVTLGQPAS ISCRSSQSLV LSDGNTYLSW FHQRPGHSPR RLIYRISHRD SGVPDRFSGS ESGTDFTLKI SRVEAEDVG IYYCMQGTHW PRTFGQGTKV EIK |
-Macromolecule #4: 32.4K Fab Heavy chain
Macromolecule | Name: 32.4K Fab Heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 14.140781 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVQSGAE VKKPGESLKI SCKGSADSFT NHWIGWVRQT PGKGLEWMGM IYPGDSDTRY SPSFQGQVTL SVDKSVTTVY LQWNSLKAS DTAIYYCARQ VGGVVVAEPP PYYYYGMDAW GQGTTVTVSS |
-Macromolecule #5: 32.4K Fab Light chain
Macromolecule | Name: 32.4K Fab Light chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 11.664103 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQLTQSPSS LSASVGDRVT LTCRASQSIA TFLNWFQQRP GKAPKLLMFD ASKLQTGVPS RFSGSGSGTH FTLTISTLQP EDFATYYCQ QSYDLPLTFG PGTKVEIK |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.7 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
| ||||||||||||
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 37.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |