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- PDB-7no2: Structure of the mature RSV CA lattice: hexamer derived from tube... -

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Entry
Database: PDB / ID: 7no2
TitleStructure of the mature RSV CA lattice: hexamer derived from tubes (C2-symmetric)
ComponentsCapsid protein p27, alternate cleaved 1
KeywordsVIRAL PROTEIN / Retrovirus / Rous sarcoma virus / capsid protein / IP6
Function / homology
Function and homology information


host cell nucleoplasm / viral procapsid maturation / host cell nucleolus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / viral capsid / structural constituent of virion / nucleic acid binding / aspartic-type endopeptidase activity / viral translational frameshifting / host cell plasma membrane ...host cell nucleoplasm / viral procapsid maturation / host cell nucleolus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / viral capsid / structural constituent of virion / nucleic acid binding / aspartic-type endopeptidase activity / viral translational frameshifting / host cell plasma membrane / proteolysis / zinc ion binding / membrane
Similarity search - Function
Retroviral Gag polyprotein, M / Retroviral M domain / : / gag protein p24 N-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic ...Retroviral Gag polyprotein, M / Retroviral M domain / : / gag protein p24 N-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Biological speciesRous sarcoma virus
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 4.3 Å
AuthorsObr, M. / Ricana, C.L. / Nikulin, N. / Feathers, J.-P.R. / Klanschnig, M. / Thader, A. / Johnson, M.C. / Vogt, V.M. / Schur, F.K.M. / Dick, R.A.
Funding support Austria, United States, European Union, 5items
OrganizationGrant numberCountry
Austrian Science FundP31445 Austria
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI147890 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI150454 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R35GM136258 United States
European Union (EU)Horizon 2020, iNEXT (PID4246) , Grant number 653706European Union
CitationJournal: Nat Commun / Year: 2021
Title: Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer.
Authors: Martin Obr / Clifton L Ricana / Nadia Nikulin / Jon-Philip R Feathers / Marco Klanschnig / Andreas Thader / Marc C Johnson / Volker M Vogt / Florian K M Schur / Robert A Dick /
Abstract: Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold ...Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles.
History
DepositionFeb 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

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Assembly

Deposited unit
A: Capsid protein p27, alternate cleaved 1
B: Capsid protein p27, alternate cleaved 1
C: Capsid protein p27, alternate cleaved 1


Theoretical massNumber of molelcules
Total (without water)74,3213
Polymers74,3213
Non-polymers00
Water00
1
A: Capsid protein p27, alternate cleaved 1
B: Capsid protein p27, alternate cleaved 1
C: Capsid protein p27, alternate cleaved 1

A: Capsid protein p27, alternate cleaved 1
B: Capsid protein p27, alternate cleaved 1
C: Capsid protein p27, alternate cleaved 1


Theoretical massNumber of molelcules
Total (without water)148,6426
Polymers148,6426
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
MethodUCSF CHIMERA

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Components

#1: Protein Capsid protein p27, alternate cleaved 1


Mass: 24773.594 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus (strain Prague C) / Strain: Prague C / Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03322

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Rous sarcoma virus - Prague C / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rous sarcoma virus - Prague C
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: unidentified
Virus shellName: CANC tubes
Buffer solutionpH: 6.2
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM2-(N-morpholino)ethanesulfonic acidMES1
2100 mMsodium chlorideNaCl1
32 nMtris(2-carboxyethyl)phosphineTCEP1
4100 microMinositol hexakisphosphateIP61
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 2.5 seconds blotting time

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Details: Areas of interest for high-resolution data collection were identified in low magnification montages. Prior to tomogram acquisition, gain references were acquired and the filter was fully ...Details: Areas of interest for high-resolution data collection were identified in low magnification montages. Prior to tomogram acquisition, gain references were acquired and the filter was fully tuned. Microscope tuning was performed using the FEI AutoCTF software. The ilumination mode used during acquisition was nanoprobe.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.4 sec. / Electron dose: 3.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansWidth: 3708 / Height: 3838 / Movie frames/image: 10 / Used frames/image: 1-10

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Processing

EM software
IDNameVersionCategoryDetails
1MATLABR2018bvolume selection
2IMOD4.9volume selection
3Dynamo1.1.333volume selection
4SerialEMimage acquisition
5DigitalMicrographimage acquisition
7CTFFIND4.1.10CTF correction
8IMOD4.9CTF correction
9NOVACTFCTF correction
12UCSF Chimera1.13.1model fitting
13Coot0.8.9.1model fitting
16Dynamo1.1.333final Euler assignment
17MATLABR2018bclassification
18Dynamo1.1.3333D reconstruction
19AV33D reconstructionamplitude reweighting using AV3
20PHENIX1.18model refinement
21Coot0.8.9.1model refinement
CTF correctionDetails: CTF-correction was initially performed using ctfphaseflip in IMOD and NovaCTF in the final steps
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40962 / Algorithm: BACK PROJECTION / Symmetry type: POINT
EM volume selectionNum. of tomograms: 44 / Num. of volumes extracted: 45088
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient
Details: Three copies of CA monomer were rigid body-fitted into the EM density to accommodate the 3 symmetry independent CA copies. The fit was further refined in Coot. The symmetry independent ...Details: Three copies of CA monomer were rigid body-fitted into the EM density to accommodate the 3 symmetry independent CA copies. The fit was further refined in Coot. The symmetry independent copies were expanded according to the C2 symmetry, and an additional ring of CTDs adjacent to the CA hexamer was added to account for the continuous lattice during the refinement. The model was refined by iterating between automatic real space refinement in Phenix and manual model inspection/editing in Coot.
Atomic model buildingPDB-ID: 3TIR

3tir


Pdb chain-ID: A / Accession code: 3TIR / Pdb chain residue range: 10-226 / Source name: PDB / Type: experimental model

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