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Yorodumi- PDB-7umt: Structure of the VP5*/VP8* assembly from the human rotavirus stra... -
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-Basic information
Entry | Database: PDB / ID: 7umt | ||||||
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Title | Structure of the VP5*/VP8* assembly from the human rotavirus strain CDC-9 - Reversed conformation | ||||||
Components |
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Keywords | VIRUS / Rotavirus / human / CDC-9 / VP4 / VP5* / VP8* / antibody #41 / broadly neutralizing / cryo-EM | ||||||
Function / homology | Function and homology information viral intermediate capsid / host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / host cell rough endoplasmic reticulum / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / membrane => GO:0016020 ...viral intermediate capsid / host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / host cell rough endoplasmic reticulum / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / membrane => GO:0016020 / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Rotavirus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Jenni, S. / Zongli, L. / Wang, Y. / Bessey, T. / Salgado, E.N. / Schmidt, A.G. / Greenberg, H.B. / Jiang, B. / Harrison, S.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: J Virol / Year: 2022 Title: Rotavirus VP4 Epitope of a Broadly Neutralizing Human Antibody Defined by Its Structure Bound with an Attenuated-Strain Virion. Authors: Simon Jenni / Zongli Li / Yuhuan Wang / Theresa Bessey / Eric N Salgado / Aaron G Schmidt / Harry B Greenberg / Baoming Jiang / Stephen C Harrison / Abstract: Rotavirus live-attenuated vaccines, both mono- and pentavalent, generate broadly heterotypic protection. B-cells isolated from adults encode neutralizing antibodies, some with affinity for VP5*, that ...Rotavirus live-attenuated vaccines, both mono- and pentavalent, generate broadly heterotypic protection. B-cells isolated from adults encode neutralizing antibodies, some with affinity for VP5*, that afford broad protection in mice. We have mapped the epitope of one such antibody by determining the high-resolution cryo-EM structure of its antigen-binding fragment (Fab) bound to the virion of a candidate vaccine strain, CDC-9. The Fab contacts both the distal end of a VP5* β-barrel domain and the two VP8* lectin-like domains at the tip of a projecting spike. Its interactions with VP8* do not impinge on the likely receptor-binding site, suggesting that the mechanism of neutralization is at a step subsequent to initial attachment. We also examined structures of CDC-9 virions from two different stages of serial passaging. Nearly all the VP4 (cleaved to VP8*/VP5*) spikes on particles from the earlier passage (wild-type isolate) had transitioned from the "upright" conformation present on fully infectious virions to the "reversed" conformation that is probably the end state of membrane insertion, unable to mediate penetration, consistent with the very low infectivity of the wild-type isolate. About half the VP4 spikes were upright on particles from the later passage, which had recovered substantial infectivity but had acquired an attenuated phenotype in neonatal rats. A mutation in VP4 that occurred during passaging appears to stabilize the interface at the apex of the spike and could account for the greater stability of the upright spikes on the late-passage, attenuated isolate. Rotavirus live-attenuated vaccines generate broadly heterotypic protection, and B-cells isolated from adults encode antibodies that are broadly protective in mice. Determining the structural and mechanistic basis of broad protection can contribute to understanding the current limitations of vaccine efficacy in developing countries. The structure of an attenuated human rotavirus isolate (CDC-9) bound with the Fab fragment of a broadly heterotypic protective antibody shows that protection is probably due to inhibition of the conformational transition in the viral spike protein (VP4) critical for viral penetration, rather than to inhibition of receptor binding. A comparison of structures of CDC-9 virus particles at two stages of serial passaging supports a proposed mechanism for initial steps in rotavirus membrane penetration. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7umt.cif.gz | 4.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7umt.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7umt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/7umt ftp://data.pdbj.org/pub/pdb/validation_reports/um/7umt | HTTPS FTP |
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-Related structure data
Related structure data | 26609MC 7umsC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
-Outer capsid ... , 2 types, 21 molecules 123abcdefghijklmnopqr
#1: Protein | Mass: 59605.254 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rotavirus / Strain: CDC-9 Gene: VP4, W907_45309gpVP4, W907_45314gpVP4, W907_45315gpVP4, W907_45321gpVP4, W907_45328gpVP4, W907_45346gpVP4 Production host: Chlorocebus aethiops (grivet) / References: UniProt: X4YMN0 #3: Protein | Mass: 37435.934 Da / Num. of mol.: 18 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rotavirus / Strain: CDC-9 Gene: VP7, NC78_51708gpVP7, NC78_52349gpVP7, NC78_52352gpVP7, NC78_52353gpVP7, NC78_52354gpVP7, NC78_52356gpVP7, NC78_52357gpVP7b, W907_45360gpVP7, W907_45361gpVP7, W907_45368gpVP7 Production host: Chlorocebus aethiops (grivet) / References: UniProt: B1NP55 |
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-Protein / Non-polymers , 2 types, 90 molecules ABCDEFGHIJKLMNOPQR
#2: Protein | Mass: 44994.965 Da / Num. of mol.: 18 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rotavirus / Strain: CDC-9 / Gene: VP6 / Production host: Chlorocebus aethiops (grivet) / References: UniProt: A0A223GHC7 #6: Chemical | ChemComp-CA / |
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-Sugars , 2 types, 36 molecules
#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Sugar | ChemComp-NAG / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Rotavirus / Type: VIRUS / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: Rotavirus |
Source (recombinant) | Organism: Chlorocebus aethiops (grivet) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 359970 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.47 Å2 | ||||||||||||||||||||||||
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