[English] 日本語
Yorodumi- PDB-7mfg: Cryo-EM structure of the VRC310 clinical trial, vaccine-elicited,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mfg | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the VRC310 clinical trial, vaccine-elicited, human antibody 310-030-1D06 Fab in complex with an H1 NC99 HA trimer | |||||||||
Components |
| |||||||||
Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / VRC / IMMUNE SYSTEM / VRC310 / H1 / Fab / Flu / IMMUNE SYSTEM-Viral protein complex / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane Similarity search - Function | |||||||||
Biological species | Influenza A virus Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.87 Å | |||||||||
Authors | Gorman, J. / Kwong, P.D. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Nat Med / Year: 2022 Title: A single residue in influenza virus H2 hemagglutinin enhances the breadth of the B cell response elicited by H2 vaccination. Authors: Sarah F Andrews / Julie E Raab / Jason Gorman / Rebecca A Gillespie / Crystal S F Cheung / Reda Rawi / Lauren Y Cominsky / Jeffrey C Boyington / Adrian Creanga / Chen-Hsiang Shen / Darcy R ...Authors: Sarah F Andrews / Julie E Raab / Jason Gorman / Rebecca A Gillespie / Crystal S F Cheung / Reda Rawi / Lauren Y Cominsky / Jeffrey C Boyington / Adrian Creanga / Chen-Hsiang Shen / Darcy R Harris / Adam S Olia / Alexandra F Nazzari / Tongqing Zhou / Katherine V Houser / Grace L Chen / John R Mascola / Barney S Graham / Masaru Kanekiyo / Julie E Ledgerwood / Peter D Kwong / Adrian B McDermott / Abstract: Conserved epitopes on the influenza hemagglutinin (HA) stem are an attractive target for universal vaccine strategies as they elicit broadly neutralizing antibodies. Such antibody responses to stem- ...Conserved epitopes on the influenza hemagglutinin (HA) stem are an attractive target for universal vaccine strategies as they elicit broadly neutralizing antibodies. Such antibody responses to stem-specific epitopes have been extensively characterized for HA subtypes H1 and H5 in humans. H2N2 influenza virus circulated 50 years ago and represents a pandemic threat due to the lack of widespread immunity, but, unlike H1 and H5, the H2 HA stem contains Phe45 predicted to sterically clash with HA stem-binding antibodies characterized to date. To understand the effect of Phe45, we compared the HA stem-specific B cell response in post hoc analyses of two phase 1 clinical trials, one testing vaccination with an H2 ferritin nanoparticle immunogen ( NCT03186781 ) and one with an inactivated H5N1 vaccine ( NCT01086657 ). In H2-naive individuals, the magnitude of the B cell response was equivalent, but H2-elicited HA stem-binding B cells displayed greater cross-reactivity than those elicited by H5. However, in individuals with childhood H2 exposure, H5-elicited HA stem-binding B cells also displayed high cross-reactivity, suggesting recall of memory B cells formed 50 years ago. Overall, we propose that a one-residue difference on an HA immunogen can alter establishment and expansion of broadly neutralizing memory B cells. These data have implications for stem-based universal influenza vaccination strategies. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7mfg.cif.gz | 381.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7mfg.ent.gz | 313.2 KB | Display | PDB format |
PDBx/mmJSON format | 7mfg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mfg_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7mfg_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7mfg_validation.xml.gz | 64.8 KB | Display | |
Data in CIF | 7mfg_validation.cif.gz | 95.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/7mfg ftp://data.pdbj.org/pub/pdb/validation_reports/mf/7mfg | HTTPS FTP |
-Related structure data
Related structure data | 23816MC 7l0lC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Hemagglutinin ... , 2 types, 6 molecules ACGBDI
#1: Protein | Mass: 36407.852 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Homo sapiens (human) / References: UniProt: Q6WG00 #2: Protein | Mass: 25263.104 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Homo sapiens (human) / References: UniProt: Q289M7 |
---|
-Antibody , 2 types, 6 molecules HEJLFK
#3: Antibody | Mass: 13000.457 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #4: Antibody | Mass: 11658.904 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
---|
-Sugars , 2 types, 24 molecules
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
---|
-Details
Has ligand of interest | N |
---|---|
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 310-030-1D06 Fab in complex with an H1 NC99 HA trimer / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Source (natural) |
| ||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||
Buffer component | Formula: PBS | ||||||||||||
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: 310-030-1D06 Fab in complex with an H1 NC99 HA trimer | ||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 70.13 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36235 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | ||||||||||||||||||||||||
Refine LS restraints |
|