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- PDB-5vm7: Pseudo-atomic model of the MurA-A2 complex -

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Basic information

Entry
Database: PDB / ID: 5vm7
TitlePseudo-atomic model of the MurA-A2 complex
Components
  • Maturation protein A2
  • UDP-N-acetylglucosamine 1-carboxyvinyltransferase
KeywordsVIRUS/TRANSFERASE / Qbeta / ssRNA / phage / virus / VIRUS-TRANSFERASE complex
Function / homology
Function and homology information


symbiont-mediated suppression of host cell wall biogenesis / symbiont-mediated suppression of host peptidoglycan biosynthetic process / viral release via suppression of host peptidoglycan biosynthetic process / virion attachment to host cell pilus / UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / adhesion receptor-mediated virion attachment to host cell / peptidoglycan biosynthetic process / viral release from host cell by cytolysis ...symbiont-mediated suppression of host cell wall biogenesis / symbiont-mediated suppression of host peptidoglycan biosynthetic process / viral release via suppression of host peptidoglycan biosynthetic process / virion attachment to host cell pilus / UDP-N-acetylglucosamine 1-carboxyvinyltransferase activity / UDP-N-acetylgalactosamine biosynthetic process / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / adhesion receptor-mediated virion attachment to host cell / peptidoglycan biosynthetic process / viral release from host cell by cytolysis / cell wall organization / virion component / regulation of cell shape / cell division / cytoplasm
Similarity search - Function
Assembly protein / Phage maturation protein / UDP-N-acetylglucosamine 1-carboxyvinyltransferase / : / Enolpyruvate transferase domain / Enolpyruvate transferase domain superfamily / EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase) / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta
Similarity search - Domain/homology
UDP-N-acetylglucosamine 1-carboxyvinyltransferase / Maturation protein A2
Similarity search - Component
Biological speciesEscherichia phage Qbeta (virus)
Escherichia coli O139:H28 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.7 Å
AuthorsCui, Z. / Zhang, J.
Funding support United States, 4items
OrganizationGrant numberCountry
Welch FoundationA-1863 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116787 United States
Public Health ServiceGM27099 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Structures of Qβ virions, virus-like particles, and the Qβ-MurA complex reveal internal coat proteins and the mechanism of host lysis.
Authors: Zhicheng Cui / Karl V Gorzelnik / Jeng-Yih Chang / Carrie Langlais / Joanita Jakana / Ry Young / Junjie Zhang /
Abstract: In single-stranded RNA bacteriophages (ssRNA phages) a single copy of the maturation protein binds the genomic RNA (gRNA) and is required for attachment of the phage to the host pilus. For the ...In single-stranded RNA bacteriophages (ssRNA phages) a single copy of the maturation protein binds the genomic RNA (gRNA) and is required for attachment of the phage to the host pilus. For the canonical Qβ the maturation protein, A, has an additional role as the lysis protein, by its ability to bind and inhibit MurA, which is involved in peptidoglycan biosynthesis. Here, we determined structures of Qβ virions, virus-like particles, and the Qβ-MurA complex using single-particle cryoelectron microscopy, at 4.7-Å, 3.3-Å, and 6.1-Å resolutions, respectively. We identified the outer surface of the β-region in A as the MurA-binding interface. Moreover, the pattern of MurA mutations that block Qβ lysis and the conformational changes of MurA that facilitate A binding were found to be due to the intimate fit between A and the region encompassing the closed catalytic cleft of substrate-liganded MurA. Additionally, by comparing the Qβ virion with Qβ virus-like particles that lack a maturation protein, we observed a structural rearrangement in the capsid coat proteins that is required to package the viral gRNA in its dominant conformation. Unexpectedly, we found a coat protein dimer sequestered in the interior of the virion. This coat protein dimer binds to the gRNA and interacts with the buried α-region of A, suggesting that it is sequestered during the early stage of capsid formation to promote the gRNA condensation required for genome packaging. These internalized coat proteins are the most asymmetrically arranged major capsid proteins yet observed in virus structures.
History
DepositionApr 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Author supporting evidence / Data collection / Structure summary
Category: em_entity_assembly / em_virus_entity
Item: _em_entity_assembly.type / _em_virus_entity.entity_assembly_id
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jul 18, 2018Group: Data collection / Experimental preparation / Category: em_sample_support / Item: _em_sample_support.grid_type
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Maturation protein A2
B: UDP-N-acetylglucosamine 1-carboxyvinyltransferase


Theoretical massNumber of molelcules
Total (without water)93,4852
Polymers93,4852
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2890 Å2
ΔGint-14 kcal/mol
Surface area40310 Å2

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Components

#1: Protein Maturation protein A2 / MP / A2 protein


Mass: 48613.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage Qbeta (virus) / References: UniProt: Q8LTE2
#2: Protein UDP-N-acetylglucosamine 1-carboxyvinyltransferase / Enoylpyruvate transferase / UDP-N-acetylglucosamine enolpyruvyl transferase / EPT


Mass: 44871.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli O139:H28 (strain E24377A / ETEC) (bacteria)
Strain: E24377A / ETEC
References: UniProt: A7ZS86, UDP-N-acetylglucosamine 1-carboxyvinyltransferase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Enterobacteria phage Qbeta virion with MurACOMPLEXall0NATURAL
2Enterobacteria phage QbetaVIRUS#11NATURAL
3UDP-N-acetylglucosamine 1-carboxyvinyltransferaseCOMPLEX#21NATURAL
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Enterobacteria phage Qbeta (virus)39803
33Escherichia coli O139:H28 (strain E24377A / ETEC) (bacteria)331111
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K
Details: Blotted for 6s, Plunged into liquid ethane (FEI VITROBOT MARK III)

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
EM imaging

Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Mode: BRIGHT FIELD / Specimen-ID: 1

IDAccelerating voltage (kV)CryogenModelNominal magnification (X)
1300NITROGENJEOL 3200FSC30000
2200FEI TECNAI F2029000
Image recording
IDImaging-IDAverage exposure time (sec.)Electron dose (e/Å2)Detector modeFilm or detector model
110.21SUPER-RESOLUTIONGATAN K2 SUMMIT (4k x 4k)
220.21.1SUPER-RESOLUTIONGATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryImaging-ID
1EMANparticle selection
3SerialEMimage acquisition1
5CTFFIND4CTF correction
8UCSF Chimeramodel fitting
10SerialEMimage acquisition2
15RELION1.43D reconstruction
16MDFFmodel refinement
17NAMDmodel refinement
18PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25597 / Symmetry type: POINT

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